Author: "Polat Abdubek" / Topic: molecular biology - Searchworks@Jio Institute Digital Library Search Results

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1. SALL4 mediates teratogenicity as a thalidomide-dependent cereblon substrate

Author: Mariko Riley, Katie Stamp, Xinde Zheng, Yan Ren, Kate Blease, Chin-Chun Lu, Julia Hui, Lawrence G Hamann, Philip P Chamberlain, Gang Lu, Polat Abdubek, Mary E Matyskiela, Gondi Kumar, Maria Wang, Wei Fang, Aaron Carpenter, Thomas Clayton, Clifton Drew, Suzana Couto, Chung-Wein Lee, Mark Rolfe, Rupert Vessey, and James Hartke
Subjects: Male, 0301 basic medicine, Ubiquitin-Protein Ligases, Transgene, Induced Pluripotent Stem Cells, Mice, Transgenic, Nerve Tissue Proteins, Phocomelia, Protein degradation, Ligands, medicine.disease_cause, 01 natural sciences, Mice, 03 medical and health sciences, SALL4, Testis, Animals, Humans, Medicine, Molecular Biology, Adaptor Proteins, Signal Transducing, Zinc finger, Mutation, 010405 organic chemistry, business.industry, Cereblon, Homozygote, Zinc Fingers, Cell Biology, medicine.disease, Immunohistochemistry, eye diseases, Thalidomide, 0104 chemical sciences, DNA-Binding Proteins, Teratogens, 030104 developmental biology, Gene Expression Regulation, Proteolysis, Cancer research, Rabbits, business, Peptide Hydrolases, Transcription Factors, medicine.drug
Abstract: Targeted protein degradation via small-molecule modulation of cereblon offers vast potential for the development of new therapeutics. Cereblon-binding therapeutics carry the safety risks of thalidomide, which caused an epidemic of severe birth defects characterized by forelimb shortening or phocomelia. Here we show that thalidomide is not teratogenic in transgenic mice expressing human cereblon, indicating that binding to cereblon is not sufficient to cause birth defects. Instead, we identify SALL4 as a thalidomide-dependent cereblon neosubstrate. Human mutations in SALL4 cause Duane-radial ray, IVIC, and acro-renal-ocular syndromes with overlapping clinical presentations to thalidomide embryopathy, including phocomelia. SALL4 is degraded in rabbits but not in resistant organisms such as mice because of SALL4 sequence variations. This work expands the scope of cereblon neosubstrate activity within the formerly 'undruggable' C2H2 zinc finger family and offers a path toward safer therapeutics through an improved understanding of the molecular basis of thalidomide-induced teratogenicity.
Published: 2018
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2. Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution

Author: Jeff Velasquez, Tanya Biorac, Adam Godzik, Peter Kuhn, Raymond C. Stevens, Guenter Wolf, Jie Ouyang, Heath E. Klock, Ross Floyd, Xiaoping Dai, Andreas Kreusch, Rebecca Page, Bill West, Keith O. Hodgson, Alyssa Robb, Hsiu-Ju Chiu, Jaume M. Canaves, Xianhong Wang, Scott A. Lesley, Linda S. Brinen, Andrew T. Morse, Juli Vincent, John S. Kovarik, Timothy M. McPhillips, Kin Moy, Marc-André Elsliger, Ashley M. Deacon, Mitchell D. Miller, Robert Schwarzenbacher, Ian A. Wilson, Frank von Delft, Eileen Ambing, Glen Spraggon, Mike DiDonato, Said Eshagi, Henry van den Bedem, Eric Hampton, Jamison Cambell, Eric Koesema, Carina Grittini, Kevin Quijano, Cathy Karlak, Polat Abdubek, Daniel McMullan, Inna Levin, John Wooley, Slawomir K. Grzechnik, Lukasz Jaroszewski, and Qingping Xu
Subjects: Models, Molecular, biology, Protein Conformation, Chemistry, Molecular Sequence Data, Resolution (electron density), Imidazoles, Reproducibility of Results, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Lyase, Biochemistry, Crystallography, Mutase, Structural Biology, Thermotoga maritima, Amino Acid Sequence, Crystallization, Intramolecular Transferases, Molecular Biology
Published: 2016

3. Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution

Author: Jeff Velasquez, Mike DiDonato, Kevin Quijano, Xianhong Wang, Scott A. Lesley, Henry van den Bedem, Qingping Xu, Marc-André Elsliger, Polat Abdubek, Eric Hampton, Jie Ouyang, Timothy M. McPhillips, Xiaoping Dai, Jaume M. Canaves, Said Eshagi, Bill West, Guenter Wolf, Frank von Delft, Carina Grittini, Alyssa Robb, Lukasz Jaroszewski, Keith O. Hodgson, John Wooley, Andrew T. Morse, Mitchell D. Miller, Daniel McMullan, Inna Levin, Juli Vincent, H.-J. Chiu, Cathy Karlak, Robert Schwarzenbacher, Kin Moy, Slawomir K. Grzechnik, John S. Kovarik, Jamison Cambell, Eric Koesema, Peter Kuhn, Adam Godzik, Raymond C. Stevens, Tanja Biorac, Ross Floyd, Heath E. Klock, Linda S. Brinen, Andreas Kreusch, Rebecca Page, Glen Spraggon, Ashley M. Deacon, Ian A. Wilson, and Eileen Ambing
Subjects: Physics, Models, Molecular, biology, PII Nitrogen Regulatory Proteins, Resolution (electron density), Molecular Sequence Data, Synchrotron radiation, Reproducibility of Results, Particle accelerator, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, law.invention, Crystallography, Bacterial Proteins, Structural Biology, law, Signaling proteins, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Signal Transduction
Published: 2016
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4. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution

Author: Lukasz Jaroszewski, Eric Hampton, Carina Grittini, Keith O. Hodgson, Tanya Biorac, Said Eshaghi, Adam Godzik, Kin Moy, Kevin Quijano, Marc-André Elsliger, Daniel McMullan, Inna Levin, Fred Rezezadeh, John Wooley, Alyssa Robb, Raymond C. Stevens, Frank von Delft, Guenter Wolf, Heath E. Klock, Timothy M. McPhillips, Qingping Xu, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Xiaoping Dai, Cathy Karlak, Eric Sims, Slawomir K. Grzechnik, Mike DiDonato, Jaume M. Canaves, Polat Abdubek, Henry van den Bedem, Peter Kuhn, Jie Ouyang, Bill West, Xianhong Wang, Scott A. Lesley, Ross Floyd, Jeff Velasquez, Eric Koesema, Ron Reyes, Robert Schwarzenbacher, Mitchell D. Miller, Andreas Kreusch, Rebecca Page, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, and Glen Spraggon
Subjects: chemistry.chemical_classification, Models, Molecular, Binding Sites, Magnetic Resonance Spectroscopy, biology, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Crystallography, Enzyme, chemistry, Bacterial Proteins, Structural Biology, Structural Homology, Protein, Thermotoga maritima, Amino Acid Sequence, Crystallization, Molecular Biology, Conserved Sequence
Published: 2016
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5. Crystal structure of an Udp-n-acetylmuramate-alanine ligase MurC (TM0231) from Thermotoga maritima at 2.3 A resolution

Author: Guenter Wolf, Peter Kuhn, Daniel McMullan, Inna Levin, Ross Floyd, Hsiu-Ju Chiu, Carina Grittini, John S. Kovarik, Ian A. Wilson, Eric Hampton, Kin Moy, Eileen Ambing, Glen Spraggon, Alyssa Robb, Jaume M. Canaves, Heath E. Klock, Kevin Quijano, John Wooley, Marc-André Elsliger, Andrew T. Morse, Timothy M. McPhillips, Bill West, Juli Vincent, Christian C. Lee, Polat Abdubek, Jie Ouyang, Frank von Delft, Xiaoping Dai, Jeff Velasquez, Linda S. Brinen, Slawomir K. Grzechnik, Tanya Biorac, Adam Godzik, Raymond C. Stevens, Jamison Cambell, Eric Koesema, Ashley M. Deacon, Andreas Kreusch, Rebecca Page, Xianhong Wang, Scott A. Lesley, Robert Schwarzenbacher, Mike DiDonato, Cathy Karlak, Henry van den Bedem, Qingping Xu, Keith O. Hodgson, Lukasz Jaroszewski, Said Eshagi, and Mitchell D. Miller
Subjects: Models, Molecular, chemistry.chemical_classification, DNA ligase, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Crystallography, Bacterial Proteins, UDP-N-acetylmuramate-alanine ligase, Structural Biology, Thermotoga maritima, Amino Acid Sequence, Peptide Synthases, Molecular Biology
Published: 2016

6. The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

Author: Gye Won Han, Dana Weekes, Lian Duan, Keith O. Hodgson, Polat Abdubek, Winnie W Lam, Joanna C Grant, Hsiu-Ju Chiu, Herbert L. Axelrod, Mitchell D. Miller, Dennis Carlton, Ashley M. Deacon, Anna Grzechnik, Ian A. Wilson, Christina Puckett, Sanjay Krishna, Kyle Ellrott, Mark W. Knuth, John Wooley, Abhinav Kumar, Ron Reyes, Connie Chen, Thomas Clayton, Qingping Xu, Kevin K. Jin, Henry van den Bedem, Debanu Das, Andrew P. Yeh, Tiffany Wooten, Edward Nigoghossian, Tamara Astakhova, Christine B Trame, Jiadong Zhou, Robert D. Finn, Lukasz Jaroszewski, Julie Feuerhelm, Linda Okach, Scott A. Lesley, Marc C. Deller, Andrew T. Morse, Marc André Elsliger, Constantina Bakolitsa, Xiaohui Cai, Piotr Kozbial, David Marciano, Henry J Tien, Adam Godzik, Heath E. Klock, Carol L. Farr, Amanda Nopakun, and Michelle Chiu
Subjects: 0303 health sciences, Sequence analysis, Repressor, Sequence alignment, Plasma protein binding, Biology, Biochemistry, Hedgehog signaling pathway, Structural genomics, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Molecular Biology, Peptide sequence, Function (biology), 030304 developmental biology
Abstract: Sufu (Suppressor of Fused), a two-domain protein, plays a critical role in regulating Hedgehog signaling and is conserved from flies to humans. A few bacterial Sufu-like proteins have previously been identified based on sequence similarity to the N-terminal domain of eukaryotic Sufu proteins, but none have been structurally or biochemically characterized and their function in bacteria is unknown. We have determined the crystal structure of a more distantly related Sufu-like homolog, NGO1391 from Neisseria gonorrhoeae, at 1.4 A resolution, which provides the first biophysical characterization of a bacterial Sufu-like protein. The structure revealed a striking similarity to the N-terminal domain of human Sufu (r.m.s.d. of 2.6 A over 93% of the NGO1391 protein), despite an extremely low sequence identity of ∼15%. Subsequent sequence analysis revealed that NGO1391 defines a new subset of smaller, Sufu-like proteins that are present in ∼200 bacterial species and has resulted in expansion of the SUFU (PF05076) family in Pfam.
Published: 2010
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7. Crystal Structure of the First Eubacterial Mre11 Nuclease Reveals Novel Features that May Discriminate Substrates During DNA Repair

Author: Mitchell D. Miller, Anna Grzechnik, Heath E. Klock, Keith O. Hodgson, Linda Okach, Prasad Burra, Polat Abdubek, John Wooley, Debanu Das, Qingping Xu, Sanjay Krishna, Thomas Clayton, Abhinav Kumar, Henry van den Bedem, Ian A. Wilson, Gye Won Han, Dana Weekes, Davide Moiani, Lian Duan, Christopher L. Rife, Jessica Paulsen, Julie Feuerhelm, Tamara Astakhova, Mark W. Knuth, Marc C. Deller, Ashley M. Deacon, Marc André Elsliger, Scott A. Lesley, Slawomir K. Grzechnik, John A. Tainer, Andrew T. Morse, Daniel McMullan, Lukasz Jaroszewski, Dennis Carlton, Edward Nigoghossian, Christine B Trame, David Marciano, Herbert L. Axelrod, Natasha Sefcovic, Hsiu-Ju Chiu, Joanna C Grant, Adam Godzik, Ron Reyes, Piotr Kozbial, Henry J Tien, Kevin K. Jin, and Dustin C. Ernst
Subjects: Exonuclease, DNA Repair, Protein Conformation, DNA repair, Molecular Sequence Data, DNA, Single-Stranded, Crystallography, X-Ray, Article, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Hydrolase, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Nuclease, Endodeoxyribonucleases, Sequence Homology, Amino Acid, biology, DNA, biology.organism_classification, enzymes and coenzymes (carbohydrates), DNA/RNA non-specific endonuclease, Exodeoxyribonucleases, Models, Chemical, chemistry, Biochemistry, biology.protein, Micrococcal nuclease
Abstract: Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.
Published: 2010
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8. Crystal Structure of Histidine Phosphotransfer Protein ShpA, an Essential Regulator of Stalk Biogenesis in Caulobacter crescentus

Author: Marc C. Deller, Adam Godzik, Mark W. Knuth, Kevin K. Jin, Joanna C Grant, Ron Reyes, Ylva Elias, Henry van den Bedem, Andrew T. Morse, Linda Okach, Mitchell D. Miller, Anna Grzechnik, Keith O. Hodgson, Christopher L. Rife, Hsiu-Ju Chiu, Piotr Kozbial, Prasad Burra, Lian Duan, Heath E. Klock, Tamara Astakhova, Julie Feuerhelm, Jessica Paulsen, Abhinav Kumar, Thomas Clayton, Marc André Elsliger, Dana Weekes, Christina V. Trout, Gye Won Han, Edward Nigoghossian, Silvya Oommachen, Daniel McMullan, John Wooley, Polat Abdubek, Sanjay Krishna, Dennis Carlton, Natasha Sefcovic, Lukasz Jaroszewski, Qingping Xu, Christine B Trame, David Marciano, Ian A. Wilson, Scott A. Lesley, Ashley M. Deacon, and Slawomir K. Grzechnik
Subjects: Models, Molecular, Helix bundle, biology, Protein Conformation, Caulobacter crescentus, Molecular Sequence Data, Phosphotransferases, Histidine kinase, Crystallography, X-Ray, biology.organism_classification, Article, Response regulator, Protein structure, Bacterial Proteins, Biochemistry, Structural Biology, Phosphorylation, Histidine, Amino Acid Sequence, Molecular Biology, Biogenesis
Abstract: Cell cycle regulated stalk biogenesis in Caulobacter crescentus is controlled by a multi-step phosphorelay system consisting of the hybrid histidine kinase ShkA, the histidine-phosphotransfer protein ShpA and the response regulator TacA. ShpA shuttles phosphoryl groups between ShkA and TacA. When phosphorylated, TacA triggers a downstream transcription cascade for stalk synthesis in an RpoN-dependent manner. The crystal structure of ShpA was determined to 1.52 Å resolution. ShpA belongs to a family of monomeric histidine phosphotransfer (HPt) proteins, which feature a highly conserved four-helix bundle. The phosphorylatable histidine, His56, is located on the surface of the helix bundle and is fully solvent exposed. One end of the four-helix bundle in ShpA is shorter compared to other characterized histidine phosphotransfer proteins, whereas the face that potentially interacts with the response regulators is structurally conserved. Similarities of the interaction surface around the phosphorylation site suggest that ShpA is likely to share a common mechanism for molecular recognition and phosphotransfer with yeast phosphotransfer protein YPD1 despite low overall sequence similarity.
Published: 2009
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9. Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

Author: Lukasz Jaroszewski, Ashley M. Deacon, Julie Feuerhelm, Hsiu-Ju Chiu, Debanu Das, Dana Weekes, Jessica Paulsen, Qingping Xu, Marc C. Deller, Piotr Kozbial, Ian A. Wilson, Christina Puckett, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Marc André Elsliger, Amanda Nopakun, Natasha Sefcovic, Linda Okach, Edward Nigoghossian, Herbert L. Axelrod, Keith O. Hodgson, Dennis Carlton, Scott A. Lesley, Mark W. Knuth, Heath E. Klock, Henry Tien, Carol L. Farr, Kevin D. Murphy, Hope A. Johnson, Slawomir K. Grzechnik, Kevin K. Jin, Henry van den Bedem, Ylva Elias, Adam Godzik, Dustin C. Ernst, Tamara Astakhova, Andrew T. Morse, Aprilfawn White, Thomas Clayton, John Wooley, Connie Chen, Christine B Trame, Daniel McMullan, Christina V. Trout, Joanna Hale, Ron Reyes, Claire Acosta, David Marciano, Polat Abdubek, Lian Duan, Sanjay Krishna, Christopher L. Rife, Prasad Burra, Sebastian Sudek, Mitchell D. Miller, and Anna Grzechnik
Subjects: Genetics, Viral protein, RNA, Cyanophage, RNA-binding protein, Biology, medicine.disease_cause, Biochemistry, Structural genomics, Protein structure, Structural Biology, Nucleic acid, medicine, Molecular Biology, Peptide sequence
Abstract: ECX21941 represents a very large family (over 600 members) of novel, ocean metagenome-specific proteins identified by clustering of the dataset from the Global Ocean Sampling expedition. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The ECX21941 protein assembles as a homopentamer in solution and in the crystal structure when expressed in Escherichia coli and represents the first pentameric structure for this Sm/LSm family of proteins, although the actual oligomeric form in vivo is currently not known. The genomic neighborhood analysis of ECX21941 and its homologs combined with sequence similarity searches suggest a cyanophage origin for this protein. The specific functions of members of this family are unknown, but our structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing.
Published: 2008
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10. Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 Å resolution

Author: Henry Tien, Keith O. Hodgson, Aprilfawn White, Linda Okach, Tamara Astakhova, Marc-André Elsliger, Qingping Xu, Edward Nigoghossian, Julie Feuerhelm, Kevin K. Jin, Dustin C. Ernst, Andrew T. Morse, Christine B Trame, Henry van den Bedem, Slawomir K. Grzechnik, Prasad Burra, Abhinav Kumar, Hsiu-Ju Chiu, Herbert L. Axelrod, Heath E. Klock, Thomas Clayton, David Marciano, Polat Abdubek, Gye Won Han, Marc C. Deller, Dennis Carlton, Christina V. Trout, Joanna Hale, Silvya Oommachen, Ashley M. Deacon, Natasha Sefcovic, Debanu Das, Scott A. Lesley, Sanjay Krishna, Lukasz Jaroszewski, Ylva Elias, Ian A. Wilson, Mitchell D. Miller, Anna Grzechnik, Christopher L. Rife, Daniel McMullan, John Wooley, Claire Acosta, Piotr Kozbial, Kevin D. Murphy, Mark W. Knuth, Adam Godzik, Dana Weekes, Lian Duan, Ron Reyes, and Jessica Paulsen
Subjects: Shewanella, Protein family, Protein Conformation, Protein subunit, Amino Acid Motifs, Molecular Sequence Data, Protein Data Bank (RCSB PDB), Biology, Crystallography, X-Ray, Biochemistry, DNA-binding protein, Article, Structural genomics, Protein structure, Bacterial Proteins, Structural Biology, Amino Acid Sequence, Molecular Biology, DNA, DNA-binding domain, computer.file_format, Protein Data Bank, Protein Structure, Tertiary, Dimerization, computer, Protein Binding
Abstract: The protein SO4266 (gi|24375750) from the bacterium Shewanella oneidensis MR-1 is annotated as a member of Pfam PF02661. This family consists of Fic (filamentation induced by cAMP) proteins and their relatives, and is characterized by the presence of a well-conserved HPFXXGNG motif 1. The biochemistry of Fic proteins has not been characterized extensively and their exact molecular functions remain unknown. From early studies in Escherichia coli, it is believed that Fic proteins and cAMP may be involved in a regulatory mechanism of cell division, including folate metabolism by the synthesis of p-aminobenzoic acid (PABA) or folate 1. Proteins containing the Fic domain are present in all kingdoms of life and range in size from ~200 to 500 amino acids. The Fic protein family contains 647 members, including two human proteins, according to Pfam (May 2008). Sequence-based clustering 2 of this protein family, at 30% sequence identity, groups these proteins into 18 clusters. Three crystal structures of Fic proteins from bacteria (unpublished) are available in the Protein Data Bank [accession codes 2g03 (194 residues, 2.2 A), 2f6s (201 residues, 2.5 A) and 3cuc (262 residues, 2.7 A)]. The first two of these proteins belong to a single cluster of 16 members and share ~60% sequence identity. The anti-apoptotic bacterial effector protein BepA, which is a type IV secretion (T4S) system substrate, also contains an N-terminal Fic domain 3. In humans, the Fic domain is present in the Huntingtin Interacting Protein E (HYPE; Uniprot entry Q9BVA6_HUMAN), a protein of unknown function that is thought to interact with Huntingtin, one of the major proteins in the Huntington's disease protein interaction network (listed as NAD- or FAD-binding) 4. Bioinformatics analysis of prokaryotic toxin-antitoxin networks 5 suggests that Fic proteins are putative death-on-curing (Doc) toxins that are part of the Phd-Doc system. These proteins likely function as metal-dependent nucleases or RNA-processing enzymes, 5 while more recent studies suggest that Doc toxicity is caused by inhibition of translation elongation 6. SO4266 (Uniprot entry Q8E9K5_SHEON), at 372 amino acids, is one of the largest Fic domain-containing proteins to have its structure determined. Interestingly, both HYPE and SO4266 belong to the largest sequence cluster in this family (n.b. our B. thetaiotaomicron {"type":"entrez-protein","attrs":{"text":"NP_811426.1","term_id":"29347923","term_text":"NP_811426.1"}}NP_811426.1 structure with PDB id 3cuc also belongs to this cluster), which comprises 466 out of 647 proteins, and share ~32% sequence identity in the Fic domain. Here, we report the crystal structure of the SO4266 protein at 1.6 A resolution. The structure reveals a dimeric protein with additional electron density in the vicinity of the highly conserved HPFXXGNG motif in the Fic domain of one subunit that corresponds to the N-terminus of a symmetry-related molecule. In addition, the study also reveals a C-terminal winged-helix DNA-binding domain that sets it apart from the other Fic protein structures. The structure presented here is a representative of the largest sequence cluster and together with the structures of the other Fic proteins paves the way for further structure-based functional characterization.
Published: 2008
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11. Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus

Author: John Wooley, Mark W. Knuth, Ashley M. Deacon, Lukasz Jaroszewski, Ian A. Wilson, Thomas Clayton, Hsiu-Ju Chiu, Lian Duan, Abhinav Kumar, Adam Godzik, Scott A. Lesley, Gye Won Han, Kevin K. Jin, Marc-André Elsliger, Joanna Hale, Silvya Oommachen, Edward Nigoghossian, Keith O. Hodgson, Heath E. Klock, Slawomir K. Grzechnik, Qingping Xu, Julie Feuerhelm, Mitchell D. Miller, Henry van den Bedem, Dennis Carlton, Christopher L. Rife, Ron Reyes, Andrew T. Morse, Jessica Paulsen, Linda Okach, Tamara Astakhova, Daniel McMullan, Polat Abdubek, and Sanjay Krishna
Subjects: ved/biology, Sulfolobus solfataricus, ved/biology.organism_classification_rank.species, Biology, Biochemistry, AAA proteins, Structural genomics, Protein structure, Structural Biology, NAIP, Sequence motif, Molecular Biology, Peptide sequence, Protein Structure Initiative
Abstract: Signal transduction ATPases with numerous domains (STAND), a large class of P-loop NTPases, belong to AAA+ ATPases. They include AP(apoptotic)-ATPases (e.g., animal apoptosis regulators CED4/Apaf-1, plant disease resistance proteins, and bacterial AfsR-like transcription regulators), NACHT NTPases (e.g. CARD4, NAIP, Het-E-1, TLP1), and several other less well-characterized families. STAND differ from other P-loop NTPases by their unique sequence motifs, which include an hhGRExE (h, hydrophobic; x, any residue) motif at the N-terminal region, a GxP/GxxP motif at the C-terminal region of the NTPase domain, in addition to a C-terminal helical domain and additional domains such as WD40, TPR, LRR or catalytic modules. Despite significant biological interests, structural coverage of STAND proteins is very limited and only two other structures are currently known: the cell death regulators Apaf-1 and CED-4. Here, we report the crystal structure of SSO1545 from Sulfolobus solfataricus, which was determined using the semi-automated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG; http://www.jcsg.org), as part of the National Institute of General Medical Sciences' Protein Structure Initiative (PSI). SSO1545 (NP-342973.1), a representative of the archaeal STANDs, is a member of Pfam PF01637 and encodes a protein of 356 residues with calculated molecular weight and isoelectric point of 41.7more » kD and 8.2, respectively.« less
Published: 2008
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12. Crystal structures of MW1337R and lin2004: Representatives of a novel protein family that adopt a four-helical bundle fold

Author: Abhinav Kumar, Ron Reyes, Henry van den Bedem, Marc André Elsliger, Aprilfawn White, Scott A. Lesley, Ian A. Wilson, Keith O. Hodgson, Guenter Wolf, Linda Okach, David Marciano, Edward Nigoghossian, Piotr Kozbial, Christopher L. Rife, Chloe Zubieta, Ylva Elias, Eric Koesema, Ashley M. Deacon, Glen Spraggon, Kevin K. Jin, Kevin D. Murphy, Herbert L. Axelrod, Hsiu-Ju Chiu, Andrew T. Morse, Mitchell D. Miller, Dennis Carlton, Mark W. Knuth, Adam Godzik, Gye Won Han, Silvya Oommachen, John Wooley, Thomas Clayton, Christina V. Trout, Dana Weekes, Lian Duan, Daniel McMullan, Joanna Hale, Tamara Astakhova, Polat Abdubek, Sanjay Krishna, Claire Acosta, Slawomir K. Grzechnik, Lukasz Jaroszewski, Julie Feuerhelm, Marc C. Deller, Qingping Xu, and Heath E. Klock
Subjects: Genetics, Protein Folding, Accession number (library science), Operon, Molecular Sequence Data, Bacillus subtilis, Biology, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Structural genomics, chemistry.chemical_compound, Protein structure, Bacterial Proteins, chemistry, Structural Biology, Complementary DNA, Amino Acid Sequence, Molecular Biology, Gene, DNA
Abstract: To extend the structural coverage of proteins with unknown functions, we targeted a novel protein family (Pfam accession number PF08807, DUF1798) for which we proposed and determined the structures of two representative members. The MW1337R gene of Staphylococcus aureus subsp. aureus Rosenbach (Wood 46) encodes a protein with a molecular weight of 13.8 kDa (residues 1-116) and a calculated isoelectric point of 5.15. The lin2004 gene of the nonspore-forming bacterium Listeria innocua Clip11262 encodes a protein with a molecular weight of 14.6 kDa (residues 1-121) and a calculated isoelectric point of 5.45. MW1337R and lin2004, as well as their homologs, which, so far, have been found only in Bacillus, Staphylococcus, Listeria, and related genera (Geobacillus, Exiguobacterium, and Oceanobacillus), have unknown functions and are annotated as hypothetical proteins. The genomic contexts of MW1337R and lin2004 are similar and conserved in related species. In prokaryotic genomes, most often, functionally interacting proteins are coded by genes, which are colocated in conserved operons. Proteins from the same operon as MW1337R and lin2004 either have unknown functions (i.e., belong to DUF1273, Pfam accession number PF06908) or are similar to ypsB from Bacillus subtilis. The function of ypsB is unclear, although it has a strong similaritymore » to the N-terminal region of DivIVA, which was characterized as a bifunctional protein with distinct roles during vegetative growth and sporulation. In addition, members of the DUF1273 family display distant sequence similarity with the DprA/Smf protein, which acts downstream of the DNA uptake machinery, possibly in conjunction with RecA. The RecA activities in Bacillus subtilis are modulated by RecU Holliday-junction resolvase. In all analyzed cases, the gene coding for RecU is in the vicinity of MW1337R, lin2004, or their orthologs, but on a different operon located in the complementary DNA strand. Here, we report the crystal structures of MW1337R and lin2004, which were determined using the semiautomated, high-throughput pipeline of the Joint Center for Structural Genomics (JCSG), part of the National Institute of General Medical Sciences Protein Structure Initiative.« less
Published: 2008
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13. Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 Å resolution

Author: Aprilfawn White, Jessica Paulsen, Polat Abdubek, Michael DiDonato, Sanjay Krishna, John Wooley, Daniel McMullan, Lian Duan, Andrew T. Morse, Henry van den Bedem, Christopher L. Rife, Slawomir K. Grzechnik, Mitchell D. Miller, Hsiu-Ju Chiu, Julie Feuerhelm, Keith O. Hodgson, Heath E. Klock, Marc-André Elsliger, Edward Nigoghossian, Thomas Clayton, Herbert L. Axelrod, Joanna Hale, Lukasz Jaroszewski, Qingping Xu, Scott A. Lesley, Piotr Kozbial, Ron Reyes, Scott M. Brittain, Ashley M. Deacon, Ian A. Wilson, Scott B. Ficarro, Adam Godzik, and Gye Won Han
Subjects: Biochemistry, Structural Biology, Thermophile, Thermotoga maritima, Posttranslational modification, Cytidine deaminase, Crystal structure, Biology, biology.organism_classification, Molecular Biology, Structural genomics
Published: 2008
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14. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) fromThermotoga maritima at 1.88 Å resolution

Author: Lukasz Jaroszewski, Keith O. Hodgson, Marc-André Elsliger, John Wooley, Edward Nigoghossian, Andrew T. Morse, Scott A. Lesley, Tamara Astakhova, Jessica Paulsen, Guenter Wolf, Ron Reyes, Henry van den Bedem, Polat Abdubek, Aprilfawn White, Gye Won Han, Sanjay Krishna, Adam Godzik, Hsiu-Ju Chiu, Mitchell D. Miller, Silvya Oommachen, Qingping Xu, Daniel McMullan, Christopher L. Rife, Slawomir K. Grzechnik, Herbert L. Axelrod, Thomas Clayton, Joanna Hale, Eric Koesema, Heath E. Klock, Lian Duan, Julie Feuerhelm, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, Dennis Carlton, Mark W. Knuth, Kevin Quijano, Dana Weekes, Kevin K. Jin, Justin Haugen, and Linda Okach
Subjects: Hydroxymethyl and Formyl Transferases, Models, Molecular, Binding Sites, Materials science, AICAR TRANSFORMYLASE/IMP CYCLOHYDROLASE, biology, Stereochemistry, Molecular Sequence Data, Resolution (electron density), Crystal structure, Crystallography, X-Ray, Multienzyme complexes, biology.organism_classification, Biochemistry, Multienzyme Complexes, Nucleotide Deaminases, Structural Biology, Thermotoga maritima, Phosphofructokinase 2, Amino Acid Sequence, Crystallization, Purine metabolism, Molecular Biology
Published: 2008
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15. Crystal structure of MtnX phosphatase fromBacillus subtilisat 2.0 Å resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate

Author: Slawomir K. Grzechnik, Qingping Xu, Herbert L. Axelrod, Heath E. Klock, Aprilfawn White, Henry van den Bedem, John Wooley, Robert Schwarzenbacher, Guenter Wolf, Ian A. Wilson, Eric Koesema, Keith O. Hodgson, Justin Haugen, Polat Abdubek, Hsiu-Ju Chiu, Linda Okach, Sanjay Agarwalla, Christopher L. Rife, Ron Reyes, Andrew T. Morse, Eileen Ambing, Dennis Carlton, Sanjay Krishna, Mark W. Knuth, Mitchell D. Miller, Gye Won Han, Silvya Oommachen, Michael DiDonato, Marc-André Elsliger, Edward Nigoghossian, Eric Hampton, Lukasz Jaroszewski, Kumar Singh Saikatendu, Julie Feuerhelm, Jessica Paulsen, Thomas Clayton, Joanna Hale, Ashley M. Deacon, Adam Godzik, Daniel McMullan, Tamara Astakhova, Kevin K. Jin, Scott A. Lesley, and Lian Duan
Subjects: biology, Resolution (mass spectrometry), Chemistry, Stereochemistry, Hydrolysis, Molecular Sequence Data, Phosphatase, Crystal structure, Bacillus subtilis, Crystallography, X-Ray, biology.organism_classification, Phosphate, Biochemistry, Organophosphates, Phosphoric Monoester Hydrolases, chemistry.chemical_compound, Crystallography, Bacterial Proteins, Thioglycosides, Structural Biology, Hydrolase, Amino Acid Sequence, Molecular Biology
Published: 2007
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16. Identification and structural characterization of heme binding in a novel dye-decolorizing peroxidase, TyrA

Author: Chloe Zubieta, Abhinav Kumar, Keith O. Hodgson, Aprilfawn White, Mark W. Knuth, Polat Abdubek, Rosanne Joseph, Marc C. Deller, David Marciano, Heath E. Klock, Sanjay Krishna, Lian Duan, Hsiu-Ju Chiu, Slawomir K. Grzechnik, Scott A. Lesley, Henry van den Bedem, Paul Schimmel, Linda Okach, Gye Won Han, Silvya Oommachen, John Wooley, Christopher L. Rife, Mitchell D. Miller, Claire Acosta, Marc-André Elsliger, Edward Nigoghossian, Daniel McMullan, Mili Kapoor, Dana Weekes, Herbert L. Axelrod, Ylva Elias, Dennis Carlton, Lukasz Jaroszewski, Thomas Clayton, Tamara Astakhova, Julie Feuerhelm, Christina V. Trout, Kevin K. Jin, Joanna Hale, Qingping Xu, Ashley M. Deacon, Ian A. Wilson, Andrew T. Morse, Kevin D. Murphy, Adam Godzik, Piotr Kozbial, and Ron Reyes
Subjects: Shewanella, Heme binding, Stereochemistry, Molecular Sequence Data, Heme, Crystallography, X-Ray, Biochemistry, Structural genomics, chemistry.chemical_compound, Bacterial Proteins, Multienzyme Complexes, Structural Biology, Amino Acid Sequence, Binding site, Coloring Agents, Molecular Biology, Peptide sequence, Dye decolorizing peroxidase, Binding Sites, biology, Active site, Peroxidases, chemistry, biology.protein, Protein Binding, Peroxidase
Abstract: TyrA is a member of the dye-decolorizing peroxidase (DyP) family, a new family of heme-dependent peroxidase recently identified in fungi and bacteria. Here, we report the crystal structure of TyrA in complex with iron protoporphyrin (IX) at 2.3 A. TyrA is a dimer, with each monomer exhibiting a two-domain, alpha/beta ferredoxin-like fold. Both domains contribute to the heme-binding site. Co-crystallization in the presence of an excess of iron protoporphyrin (IX) chloride allowed for the unambiguous location of the active site and the specific residues involved in heme binding. The structure reveals a Fe-His-Asp triad essential for heme positioning, as well as a novel conformation of one of the heme propionate moieties compared to plant peroxidases. Structural comparison to the canonical DyP family member, DyP from Thanatephorus cucumeris (Dec 1), demonstrates conservation of this novel heme conformation, as well as residues important for heme binding. Structural comparisons with representative members from all classes of the plant, bacterial, and fungal peroxidase superfamily demonstrate that TyrA, and by extension the DyP family, adopts a fold different from all other structurally characterized heme peroxidases. We propose that a new superfamily be added to the peroxidase classification scheme to encompass the DyP family of heme peroxidases.
Published: 2007
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17. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 Å resolution

Author: Lukasz Jaroszewski, Abhinav Kumar, John Wooley, Herbert L. Axelrod, Sanjay Agarwalla, Dennis Carlton, Adam Godzik, Marc-André Elsliger, Hsiu-Ju Chiu, Edward Nigoghossian, Dana Weekes, Daniel McMullan, Keith O. Hodgson, Justin Haugen, Ashley M. Deacon, Mitchell D. Miller, Henry van den Bedem, Mark W. Knuth, Polat Abdubek, Thomas Clayton, Christopher L. Rife, Heath E. Klock, Sanjay Krishna, Qingping Xu, Marc C. Deller, Joanna Hale, Slawomir K. Grzechnik, Scott A. Lesley, Ian A. Wilson, Tamara Astakhova, Lian Duan, Eileen Ambing, Ron Reyes, Kevin K. Jin, Aprilfawn White, Eric Koesema, Andrew T. Morse, Gye Won Han, Silvya Oommachen, Michael DiDonato, David Marciano, Eric Hampton, and Chloe Zubieta
Subjects: Models, Molecular, biology, Protein Conformation, Chemistry, Stereochemistry, Extramural, Molecular Sequence Data, Resolution (electron density), Bacillus cereus, Homoserine O-Succinyltransferase, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Haemophilus influenzae, Biochemistry, Microbiology, Bacterial Proteins, Structural Biology, Homoserine Transsuccinylase, Amino Acid Sequence, Dimerization, Molecular Biology
Published: 2007
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18. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 Å resolution

Author: Peter Kuhn, Raymond C. Stevens, Keith O. Hodgson, Sanjay Agarwalla, Jaume M. Canaves, Marc-André Elsliger, Edward Nigoghossian, Henry van den Bedem, Jie Ouyang, Michael DiDonato, Heath E. Klock, Mitchell D. Miller, Mark W. Knuth, Kevin Quijano, Robert Schwarzenbacher, Guenter Wolf, Eric Koesema, Kin Moy, Aprilfawn White, Gye Won Han, Polat Abdubek, Kevin K. Jin, Eric Hampton, Scott M. Brittain, Slawomir K. Grzechnik, Sanjay Krishna, Xianhong Wang, Bill West, Scott A. Lesley, Hsiu-Ju Chiu, Herbert L. Axelrod, Justin Haugen, Jeff Velasquez, Andrew T. Morse, Daniel McMullan, Adam Godzik, Christopher L. Rife, Lukasz Jaroszewski, Joanna Hale, Tamara Astakhova, Ron Reyes, Sylvia Oommachen, John Wooley, Qingping Xu, Andreas Kreusch, Glen Spraggon, Jessica Paulsen, Ashley M. Deacon, Krzysztof Ginalski, Ian A. Wilson, and Eileen Ambing
Subjects: Materials science, biology, Lipoproteins, Molecular Sequence Data, Resolution (electron density), Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Amino Acid Sequence, Crystallization, Sequence Alignment, Molecular Biology
Published: 2006
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19. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 Å resolution

Author: Glen Spraggon, John Wooley, Jeff Velasquez, Kevin Quijano, Daniel McMullan, Inna Levin, Marc-André Elsliger, Slawomir K. Grzechnik, Edward Nigoghossian, Robert Schwarzenbacher, Ian A. Wilson, Guenter Wolf, Gye Won Han, Adam Godzik, Eileen Ambing, Keith O. Hodgson, Jaume M. Canaves, Ron Reyes, Carina Grittini, Mitchell D. Miller, Peter Kuhn, Henry van den Bedem, Ashley M. Deacon, Eric Hampton, Polat Abdubek, Lukasz Jaroszewski, Aprilfawn White, Justin Haugen, Jessica Paulsen, Eric Koesema, Qingping Xu, Hsiu-Ju Chiu, Andreas Kreusch, Joanna Hale, S. Sri Krishna, Scott A. Lesley, Irimpan I. Mathews, Raymond C. Stevens, Heath E. Klock, Kin Moy, and Michael DiDonato
Subjects: Models, Molecular, chemistry.chemical_classification, DNA ligase, Binding Sites, Molecular Sequence Data, Resolution (electron density), Crystal structure, Biology, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Phosphoribosylformylglycinamidine synthase, Protein Structure, Tertiary, Crystallography, chemistry, Structural Homology, Protein, Structural Biology, Thermotoga maritima, biology.protein, Amino Acid Sequence, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor, Protein Structure, Quaternary, Molecular Biology, Image resolution
Published: 2006
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20. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 Å resolution

Author: Glen Spraggon, Ian A. Wilson, Eileen Ambing, Ashley M. Deacon, Guenter Wolf, Jessica Paulsen, Peter Kuhn, Michael Hornsby, Edward Nigoghossian, Henry van den Bedem, Linda Okach, John Wooley, Joanna Hale, Raymond C. Stevens, Daniel McMullan, Tanya Biorac, Adam Godzik, Mark W. Knuth, Kevin Quijano, Scott A. Lesley, Kin Moy, Julie Feuerhelm, Heath E. Klock, Ron Reyes, Polat Abdubek, Eric Hampton, Eric Koesema, Hsiu-Ju Chiu, Slawomir K. Grzechnik, Keith O. Hodgson, Aprilfawn White, Jeff Velasquez, Christopher L. Rife, S. Sri Krishna, M.A. Elsliger, Carina Grittini, Mitchell D. Miller, Herbert L. Axelrod, Justin Haugen, Michael DiDonato, Andreas Kreusch, Robert Schwarzenbacher, Sanjay Agarwalla, Qingping Xu, and Lukasz Jaroszewski
Subjects: Models, Molecular, HMG-box, Molecular Sequence Data, DNA, Single-Stranded, Crystal structure, Crystallography, X-Ray, Biochemistry, DNA-binding protein, Protein Structure, Secondary, chemistry.chemical_compound, Plasmid, Protein structure, X-Ray Diffraction, Structural Biology, Escherichia coli, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Peptide sequence, biology, biology.organism_classification, Mitochondria, DNA-Binding Proteins, Crystallography, chemistry, Anisotropy, DNA, Plasmids, Transcription Factors
Published: 2006
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21. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 Å resolution

Author: Slawomir K. Grzechnik, Gye Won Han, Michael DiDonato, Heath E. Klock, Sanjay Agarwalla, John Wooley, Robert Schwarzenbacher, Daniel McMullan, Hsiu-Ju Chiu, Guenter Wolf, Ron Reyes, Marc-André Elsliger, Lukasz Jaroszewski, Polat Abdubek, Edward Nigoghossian, Raymond C. Stevens, Eric Hampton, Ashley M. Deacon, Tanya Biorac, Adam Godzik, Jaume M. Canaves, Qingping Xu, Ian A. Wilson, Jeff Velasquez, Mitchell D. Miller, Justin Haugen, Aprilfawn White, Eric Koesema, Kin Moy, Jessica Paulsen, Peter Kuhn, Eileen Ambing, Glen Spraggon, Juli Vincent, Kevin Quijano, Joanna Hale, Carina Grittini, Christopher L. Rife, Andreas Kreusch, Scott A. Lesley, Michael Hornsby, Henry van den Bedem, Herbert L. Axelrod, and Keith O. Hodgson
Subjects: biology, Chemistry, Molecular Sequence Data, Zinc Fingers, Crystal structure, biology.organism_classification, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Chaperone (protein), Hsp33, biology.protein, Amino Acid Sequence, Crystallization, Molecular Biology, Heat-Shock Proteins, Molecular Chaperones
Published: 2005
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22. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 Å resolution reveals a new fold

Author: Keith O. Hodgson, Marc-André Elsliger, Edward Nigoghossian, Aprilfawn White, Lukasz Jaroszewski, Michael Hornsby, Henry van den Bedem, Guenter Wolf, Slawomir K. Grzechnik, Gye Won Han, Qingping Xu, Tanya Biorac, Adam Godzik, Kevin Quijano, Raymond C. Stevens, Joanna Hale, Hsiu-Ju Chiu, Herbert L. Axelrod, Heath E. Klock, Jessica Paulsen, Mitchell D. Miller, Scott A. Lesley, Carina Grittini, John Wooley, Christopher L. Rife, Robert Schwarzenbacher, Daniel McMullan, Michael DiDonato, Justin Haugen, Ron Reyes, Polat Abdubek, Jeff Velasquez, Eric Koesema, Juli Vincent, Eric Hampton, Peter Kuhn, Andreas Kreusch, Ian A. Wilson, Eileen Ambing, Kin Moy, Jaume M. Canaves, Ashley M. Deacon, Glen Spraggon, and Eric Sims
Subjects: Models, Molecular, Regulation of gene expression, Protein Folding, biology, Pseudomonas putida, Chemistry, Molecular Sequence Data, RNA-Binding Proteins, RNA-binding protein, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Microbiology, Bacterial Proteins, Structural Biology, Amino Acid Sequence, Dimerization, Molecular Biology
Published: 2005
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23. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 Å resolution reveals a new fold

Author: Polat Abdubek, Slawomir K. Grzechnik, Scott A. Lesley, Raymond C. Stevens, Kevin Quijano, Michael Hornsby, Henry van den Bedem, Guenter Wolf, Marc-André Elsliger, Heath E. Klock, Edward Nigoghossian, Lukasz Jaroszewski, Keith O. Hodgson, Jie Ouyang, John Wooley, Justin Haugen, Jaume M. Canaves, Jessica Paulsen, Aprilfawn White, Daniel McMullan, Inna Levin, Eric Koesema, Peter Kuhn, Ashley M. Deacon, Mitchell D. Miller, Gye Won Han, Qingping Xu, Ian A. Wilson, Herbert L. Axelrod, Hsiu-Ju Chiu, Eileen Ambing, Glen Spraggon, Tanya Biorac, Adam Godzik, Ron Reyes, Joanna Hale, Juli Vincent, Carina Grittini, Irimpan I. Mathews, Kin Moy, Andreas Kreusch, Michael DiDonato, Robert Schwarzenbacher, Eric Hampton, and Jeff Velasquez
Subjects: Models, Molecular, Protein Folding, biology, Protein Conformation, Chemistry, Stereochemistry, Crystal structure, Isomerase, Crystallography, X-Ray, Ligands, biology.organism_classification, Biochemistry, Protein structure, Structural Biology, Thermotoga maritima, Transfer RNA, Solvents, Protein folding, Isomerases, Molecular Biology
Published: 2005
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24. Structural Basis of Murein Peptide Specificity of a γ-D-glutamyl-L-diamino Acid Endopeptidase

Author: Keith O. Hodgson, Jessica Paulsen, Sanjay Krishna, Chloe Zubieta, Marc C. Deller, Polat Abdubek, Ian A. Wilson, Jonathan M. Caruthers, Scott A. Lesley, Lian Duan, Tamara Astakhova, M.A. Elsliger, John Wooley, Claire Acosta, Aprilfawn White, Gye Won Han, Silvya Oommachen, Badry Bursalay, Eileen Ambing, Piotr Kozbial, Christopher L. Rife, Guenter Wolf, Slawomir K. Grzechnik, Kevin K. Jin, Justin Haugen, David H. Jones, Mark W. Knuth, Thomas Clayton, Julie Feuerhelm, Hsiu-Ju Chiu, Heath E. Klock, Adam Godzik, Bernhard H. Geierstanger, David Marciano, Abhinav Kumar, Edward Nigoghossian, Daniel McMullan, Ashley M. Deacon, Dana Weekes, Glen Spraggon, Andrew T. Morse, Ron Reyes, Lukasz Jaroszewski, Linda Okach, Herbert L. Axelrod, Henry van den Bedem, Qingping Xu, Dennis Carlton, Ylva Elias, Christina V. Trout, Joanna Hale, Sebastian Sudek, and Mitchell D. Miller
Subjects: Models, Molecular, PROTEINS, Molecular Sequence Data, Diamino acid, Peptidoglycan, Models, Biological, Article, Substrate Specificity, src Homology Domains, 03 medical and health sciences, chemistry.chemical_compound, Structural Biology, Catalytic Domain, Catalytic triad, Hydrolase, Endopeptidases, Anabaena variabilis, Amino Acid Sequence, Nostoc, Peptide sequence, Molecular Biology, 030304 developmental biology, 0303 health sciences, biology, Sequence Homology, Amino Acid, 030306 microbiology, Nostoc punctiforme, Active site, biology.organism_classification, Endopeptidase, Peptide Fragments, Protein Structure, Tertiary, Cysteine Endopeptidases, Biochemistry, chemistry, biology.protein, Cysteine
Abstract: Crystal structures of two homologous peptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme at 1.05 A and 1.60 A resolution represent the first structures of a large class of cell-wall, cysteine peptidases that contain an N-terminal bacterial SH3-like domain (SH3b) and a C-terminal NlpC/P60 cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases with a Cys126/His176/His188 catalytic triad and a conserved catalytic core. We deduced from structure and sequence analysis, and then experimentally, that that these two proteins act as γ-D-glutamyl-L-diamino acid endopeptidases (EC 3.4.22.-). The active site is located near the interface between the SH3b and NlpC/P60 domains, where the SH3b domain may help define substrate specificity, instead of functioning as a targeting domain, so that only muropeptides with an N-terminal L-alanine can bind to the active site.
Published: 2009

25. Structural and Functional Characterizations of SsgB, a Conserved Activator of Developmental Cell Division in Morphologically Complex Actinomycetes

Author: Julie Feuerhelm, Marc C. Deller, Constantina Bakolitsa, Lukasz Jaroszewski, Bjørn A. Traag, Edward Nigoghossian, Mark W. Knuth, Jessica Paulsen, Mitchell D. Miller, Slawomir K. Grzechnik, Anna Grzechnik, John Wooley, Ian A. Wilson, Andrew T. Morse, Kevin K. Jin, Polat Abdubek, Scott A. Lesley, Connie Chen, Gye Won Han, Sanjay Krishna, Marc André Elsliger, Adam Godzik, Ron Reyes, Dustin C. Ernst, Silvya Oommachen, Christina Puckett, Abhinav Kumar, Linda Okach, Hsiu-Ju Chiu, Lian Duan, Herbert L. Axelrod, Dana Weekes, Amanda Nopakun, Thomas Clayton, Maksymilian Chruszcz, Natasha Sefcovic, Daniel McMullan, Keith O. Hodgson, Piotr Kozbial, Dennis Carlton, Wladek Minor, Qingping Xu, Shuren Wang, A. Mieke Mommaas, Henry J Tien, Henry van den Bedem, Tamara Astakhova, Heath E. Klock, Gilles P. van Wezel, Carol L. Farr, Ashley M. Deacon, Debanu Das, Joost Willemse, Christopher L. Rife, Christine B Trame, David Marciano, Kyle Ellrott, and Joanna C Grant
Subjects: Subfamily, Cell division, Mutant, Molecular Sequence Data, Crystallography, X-Ray, Biochemistry, Streptomyces, DNA-binding protein, chemistry.chemical_compound, Molecular Basis of Cell and Developmental Biology, Bacterial Proteins, Escherichia coli, Microscopy, Phase-Contrast, Amino Acid Sequence, Molecular Biology, Peptide sequence, Genetics, Spores, Bacterial, Binding Sites, biology, Sequence Homology, Amino Acid, Streptomyces coelicolor, Cryoelectron Microscopy, Genetic Complementation Test, Cell Biology, biology.organism_classification, Actinobacteria, chemistry, Microscopy, Fluorescence, Mutation, DNA, Cell Division
Abstract: SsgA-like proteins (SALPs) are a family of homologous cell division-related proteins that occur exclusively in morphologically complex actinomycetes. We show that SsgB, a subfamily of SALPs, is the archetypal SALP that is functionally conserved in all sporulating actinomycetes. Sporulation-specific cell division of Streptomyces coelicolor ssgB mutants is restored by introduction of distant ssgB orthologues from other actinomycetes. Interestingly, the number of septa (and spores) of the complemented null mutants is dictated by the specific ssgB orthologue that is expressed. The crystal structure of the SsgB from Thermobifida fusca was determined at 2.6 Å resolution and represents the first structure for this family. The structure revealed similarities to a class of eukaryotic “whirly” single-stranded DNA/RNA-binding proteins. However, the electro-negative surface of the SALPs suggests that neither SsgB nor any of the other SALPs are likely to interact with nucleotide substrates. Instead, we show that a conserved hydrophobic surface is likely to be important for SALP function and suggest that proteins are the likely binding partners.
Published: 2009

26. A structural basis for the regulatory inactivation of DnaA

Author: Polat Abdubek, Sanjay Krishna, Daniel McMullan, Tamara Astakhova, Ron Reyes, Amanda Nopakun, Lian Duan, Scott A. Lesley, Debanu Das, Dana Weekes, Henry van den Bedem, Adam Godzik, Piotr Kozbial, Edward Nigoghossian, Marc André Elsliger, Keith O. Hodgson, Linda Okach, Christine B Trame, Mark W. Knuth, John Wooley, David Marciano, Mitchell D. Miller, Dennis Carlton, Hope A. Johnson, Christopher L. Rife, Jessica Paulsen, Thomas Clayton, Hsiu-Ju Chiu, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Ashley M. Deacon, Joanna Hale, Ian A. Wilson, Christina Puckett, Andrew T. Morse, Marc C. Deller, Heath E. Klock, Natasha Sefcovic, Qingping Xu, Lukasz Jaroszewski, Julie Feuerhelm, Kevin K. Jin, and Connie Chen
Subjects: Models, Molecular, Shewanella, ATPase, Dimer, Molecular Sequence Data, Antiparallel (biochemistry), Crystallography, X-Ray, DNA-binding protein, Article, chemistry.chemical_compound, Adenosine Triphosphate, Bacterial Proteins, Structural Biology, ATP hydrolysis, Amino Acid Sequence, Protein Structure, Quaternary, Molecular Biology, Adenosine Triphosphatases, DNA clamp, biology, DnaA, AAA proteins, DNA-Binding Proteins, chemistry, Biochemistry, biology.protein, Biophysics, bacteria, Dimerization, Sequence Alignment
Abstract: Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.
Published: 2008

27. Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif

Author: Ron Reyes, Slawomir K. Grzechnik, Andrew T. Morse, Gye Won Han, Silvya Oommachen, Abhinav Kumar, Mark W. Knuth, Marc-André Elsliger, Edward Nigoghossian, Dennis Carlton, Ian A. Wilson, Qingping Xu, Piotr Kozbial, Eric Hampton, Paul Schimmel, Mitchell D. Miller, Adam Godzik, Herbert L. Axelrod, Chloe Zubieta, John Wooley, Daniel McMullan, Thomas Clayton, Eileen Ambing, Christopher L. Rife, Aprilfawn White, Keith O. Hodgson, Dana Weekes, Scott A. Lesley, Hsiu-Ju Chiu, Kevin K. Jin, Joanna Hale, Henry van den Bedem, Tamara Astakhova, Ashley M. Deacon, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Mili Kapoor, Heath E. Klock, Linda Okach, Julie Feuerhelm, Marc C. Deller, David Marciano, and Lian Duan
Subjects: Protein Folding, Shewanella, Heme binding, Amino Acid Motifs, Molecular Sequence Data, Heme, Random hexamer, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, chemistry.chemical_compound, Bacterial Proteins, Structural Biology, Multienzyme Complexes, Catalytic Domain, Bacteroides, Amino Acid Sequence, Shewanella oneidensis, Coloring Agents, Molecular Biology, Conserved Sequence, Dye decolorizing peroxidase, biology, Chemistry, Active site, Isothermal titration calorimetry, biology.organism_classification, A-site, Crystallography, Peroxidases, biology.protein, Protein Binding
Abstract: BtDyP from Bacteroides thetaiotaomicron (strain VPI-5482) and TyrA from Shewanella oneidensis are dye-decolorizing peroxidases (DyPs), members of a new family of heme-dependent peroxidases recently identified in fungi and bacteria. Here, we report the crystal structures of BtDyP and TyrA at 1.6 and 2.7 Angstroms, respectively. BtDyP assembles into a hexamer, while TyrA assembles into a dimer; the dimerization interface is conserved between the two proteins. Each monomer exhibits a two-domain, {alpha}+{beta} ferredoxin-like fold. A site for heme binding was identified computationally, and modeling of a heme into the proposed active site allowed for identification of residues likely to be functionally important. Structural and sequence comparisons with other DyPs demonstrate a conservation of putative heme-binding residues, including an absolutely conserved histidine. Isothermal titration calorimetry experiments confirm heme binding, but with a stoichiometry of 0.3:1 (heme:protein).
Published: 2007

28. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases

Author: Ashley M. Deacon, Ian A. Wilson, Lutz Tautz, Eileen Ambing, Andrew T. Morse, Michael DiDonato, Justin Haugen, Dennis Carlton, Polat Abdubek, Slawomir K. Grzechnik, Thomas Clayton, Tomas Mustelin, Ron Reyes, Eric Koesema, Gye Won Han, Sanjay Krishna, Silvya Oommachen, Joanna Hale, Mark W. Knuth, John Wooley, Mitchell D. Miller, Aprilfawn White, Tamara Astakhova, Christopher L. Rife, Heath E. Klock, Kevin K. Jin, Lukasz Jaroszewski, Daniel McMullan, Scott A. Lesley, Qingping Xu, Dana Weekes, Eric Hampton, Lian Duan, Marc-André Elsliger, Edward Nigoghossian, Hsiu-Ju Chiu, Henry van den Bedem, Adam Godzik, Herbert L. Axelrod, and Keith O. Hodgson
Subjects: Scaffold, Binding Sites, Chemistry, Neisseria meningitidis, Phosphatase, Resolution (electron density), Amino Acid Motifs, Molecular Sequence Data, Crystal structure, medicine.disease_cause, Crystallography, X-Ray, Biochemistry, Phosphoric Monoester Hydrolases, Protein Structure, Secondary, Bacterial Proteins, Structural Biology, Hydrolase, medicine, Amino Acid Sequence, Molecular Biology
Published: 2007

29. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution

Author: Daniel McMullan, Inna Levin, Hope A. Johnson, Ian A. Wilson, Scott A. Lesley, Herbert L. Axelrod, Eileen Ambing, Gye Won Han, Marc Fasnacht, Eric Sims, Silvya Oommachen, Tamara Astakhova, Glen Spraggon, Andreas Kreusch, Keith O. Hodgson, Ron Reyes, Rebecca Page, Justin Haugen, Mitchell D. Miller, Thomas Clayton, Sanjay Agarwalla, Mickey Kosloff, Vandana Sridhar, Jaume M. Canaves, Dennis Carlton, Polat Abdubek, Sanjay Krishna, Henry van den Bedem, Heath E. Klock, Raymond C. Stevens, Hsiu-Ju Chiu, Peter Kuhn, Eric Hampton, Slawomir K. Grzechnik, Robert Schwarzenbacher, Guenter Wolf, Christopher L. Rife, Joanna Hale, Carina Grittini, Ashley M. Deacon, Marc-André Elsliger, Edward Nigoghossian, Mark W. Knuth, Kevin Quijano, John Wooley, Eric Koesema, Aprilfawn White, Julie Feuerhelm, Adam Godzik, Qingping Xu, Andrew T. Morse, Lian Duan, Kin Moy, Kevin K. Jin, Michael DiDonato, Jeff Velasquez, Lukasz Jaroszewski, Linda Okach, and Jessica Paulsen
Subjects: Models, Molecular, Molecular Sequence Data, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural genomics, Bacterial Proteins, Structural Biology, Phylogenetics, Consensus sequence, Transferase, Amino Acid Sequence, Molecular Biology, Peptide sequence, Phylogeny, Glutathione Transferase, chemistry.chemical_classification, biology, Agrobacterium tumefaciens, Protein engineering, biology.organism_classification, Enzyme, chemistry, Dimerization
Abstract: Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies.
Published: 2006

30. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p

Author: Andreas Kreusch, Heath E. Klock, Marc-André Elsliger, Jaume M. Canaves, Edward Nigoghossian, Slawomir K. Grzechnik, Henry van den Bedem, Lukasz Jaroszewski, Justin Haugen, Guenter Wolf, Ron Reyes, Andrew T. Morse, Ashley M. Deacon, Hsiu-Ju Chiu, Thomas Clayton, Ian A. Wilson, Mark W. Knuth, Michael DiDonato, Kevin Quijano, John Wooley, Joanna Hale, Peter Kuhn, Kevin K. Jin, Eileen Ambing, Qingping Xu, Lian Duan, Glen Spraggon, Adam Godzik, Christopher L. Rife, Herbert L. Axelrod, Eric Koesema, Tamara Astakhova, Sanjay Agarwalla, Eric Hampton, Julie Feuerhelm, Gye Won Han, Silvya Oommachen, Dennis Carlton, Keith O. Hodgson, Scott A. Lesley, Robert Schwarzenbacher, Polat Abdubek, Sanjay Krishna, Linda Okach, Mitchell D. Miller, Daniel McMullan, Raymond C. Stevens, Aprilfawn White, and Jessica Paulsen
Subjects: Physics, Models, Molecular, Protein Folding, Saccharomyces cerevisiae Proteins, biology, Molecular Sequence Data, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein tertiary structure, Protein Structure, Secondary, ran GTP-Binding Protein, Ran-binding protein, Bacterial Proteins, Structural Biology, Signaling proteins, Thermotoga maritima, Amino Acid Sequence, Molecular Biology
Published: 2006

31. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site

Author: Lian Duan, Guenter Wolf, Polat Abdubek, Sanjay Krishna, Daniel McMullan, Inna Levin, Keith O. Hodgson, Jessica Paulsen, Jaume M. Canaves, Mark W. Knuth, Kevin Quijano, Joanna Hale, Linda Okach, Michael DiDonato, Andreas Kreusch, Hsiu-Ju Chiu, Sanjay Agarwalla, Marc-André Elsliger, Mitchell D. Miller, Edward Nigoghossian, Scott A. Lesley, Q. Xu, Heath E. Klock, Eric Hampton, Glen Spraggon, Herbert L. Axelrod, Henry van den Bedem, Adam Godzik, Lukasz Jaroszewski, Peter Kuhn, John Wooley, Justin Haugen, Ron Reyes, Robert Schwarzenbacher, Raymond C. Stevens, Eric Koesema, Aprilfawn White, Slawomir K. Grzechnik, Ian A. Wilson, Eileen Ambing, Silvya Oommachen, Scott M. Brittain, Christopher L. Rife, Andrew T. Morse, Ashley M. Deacon, and Kevin K. Jin
Subjects: Models, Molecular, Protein Folding, Binding Sites, Protein Conformation, media_common.quotation_subject, Acid Phosphatase, Molecular Sequence Data, Art, Crystallography, X-Ray, Biochemistry, Structural Biology, 2-phosphosulfolactate phosphatase, Clostridium acetobutylicum, Amino Acid Sequence, Molecular Biology, Humanities, media_common
Abstract: Michael DiDonato, S. Sri Krishna, Robert Schwarzenbacher, Daniel McMullan, Sanjay Agarwalla, Scott M. Brittain, Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Herbert L. Axelrod, JaumeM. Canaves, Hsiu-Ju Chiu, Ashley M. Deacon, Lian Duan, Marc-Andre Elsliger, Adam Godzik, Slawomir K. Grzechnik, Joanna Hale, Eric Hampton, Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, Andreas Kreusch, Peter Kuhn, Scott A. Lesley, Inna Levin, Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvya Oommachen, Jessica Paulsen, Kevin Quijano, Ron Reyes, Christopher L. Rife, Glen Spraggon, Raymond C. Stevens, Henry van den Bedem, AprilfawnWhite, Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, and Ian A. Wilson* The Joint Center for Structural Genomics Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California The University of California, San Diego, La Jolla, California The Genomics Institute of the Novartis Research Foundation, San Diego, California The Scripps Research Institute, La Jolla, California
Published: 2006

32. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution

Author: Glen Spraggon, Aprilfawn White, Lian Duan, Edward Nigoghossian, Sanjay Agarwalla, Andrew T. Morse, Dennis Carlton, Slawomir K. Grzechnik, Guenter Wolf, Adam Godzik, Marc-André Elsliger, Raymond C. Stevens, Sanjay Krishna, Keith O. Hodgson, Silvya Oommachen, John S. Kovarik, Polat Abdubek, Ian A. Wilson, Ron Reyes, Jaume M. Canaves, Christopher L. Rife, Eileen Ambing, Peter Kuhn, Hsiu-Ju Chiu, John Wooley, Jessica Paulsen, Kevin Quijano, Justin Haugen, Eric Hampton, Linda Okach, Inna Levin, Herbert L. Axelrod, Ashley M. Deacon, Michael Didonato, Henry van den Bedem, Eric Koesema, Scott A. Lesley, Kevin K. Jin, Daniel McMullan, Irimpan I. Mathews, Lukasz Jaroszewski, Robert Schwarzenbacher, Qingping Xu, Heath E. Klock, Andreas Kreusch, Mitchell D. Miller, Thomas Clayton, and Joanna Hale
Subjects: chemistry.chemical_classification, DNA ligase, biology, ATP synthase, Stereochemistry, Chemistry, Protein subunit, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Protein structure, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Amino Acid Sequence, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor, Crystallization, Protein Structure, Quaternary, Molecular Biology, Peptide sequence
Published: 2006

33. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution

Author: Justin Haugen, Joanna Hale, John Wooley, Aprilfawn White, Daniel McMullan, Sanjay Agarwalla, Peter Kuhn, Robert Schwarzenbacher, Guenter Wolf, Jessica Paulsen, Ron Reyes, Andreas Kreusch, Mark W. Knuth, Kevin Quijano, Raymond C. Stevens, Kin Moy, Scott A. Lesley, Jaume M. Canaves, Qingping Xu, Slawomir K. Grzechnik, Mitchell D. Miller, Gye Won Han, Lukasz Jaroszewski, Polat Abdubek, Sanjay Krishna, Carina Grittini, Christopher L. Rife, Michael DiDonato, Heath E. Klock, Eric Koesema, Eric Hampton, Michael Hornsby, Henry van den Bedem, Hsiu-Ju Chiu, Keith O. Hodgson, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Jeff Velasquez, Glen Spraggon, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Ian A. Wilson, and Eileen Ambing
Subjects: chemistry.chemical_classification, Models, Molecular, Binding Sites, Molecular Structure, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Biochemistry, Protein Structure, Secondary, Dioxygenases, Protein Structure, Tertiary, Mice, Acireductone dioxygenase, chemistry, Structural Biology, Oxidoreductase, Metals, Animals, Amino Acid Sequence, Crystallization, Databases, Protein, Molecular Biology, Protein Binding
Published: 2006

34. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold

Author: Raymond C. Stevens, Lukasz Jaroszewski, John Wooley, Carina Grittini, Scott A. Lesley, Qingping Xu, Aprilfawn White, Ron Reyes, Adam Godzik, Ashley M. Deacon, Hsiu-Ju Chiu, Marc-André Elsliger, Edward Nigoghossian, Justin Haugen, Daniel McMullan, Joanna Hale, Eric Hampton, Michael Hornsby, Henry van den Bedem, Peter Kuhn, Polat Abdubek, Christopher L. Rife, Julie Feuerhelm, Sanjay Krishna, Slawomir K. Grzechnik, Heath E. Klock, Jaume M. Canaves, Keith O. Hodgson, Kevin K. Jin, Herbert L. Axelrod, Ian A. Wilson, Robert Schwarzenbacher, Gye Won Han, Silvya Oommachen, Guenter Wolf, Eileen Ambing, Glen Spraggon, Eric Koesema, Mitchell D. Miller, Kin Moy, Jeff Velasquez, Mark W. Knuth, Kevin Quijano, Andreas Kreusch, Michael DiDonato, Sanjay Agarwalla, Jessica Paulsen, and Linda Okach
Subjects: Models, Molecular, Protein Folding, Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Polyethylene Glycols, Cyclophilins, Bacterial Proteins, Structural Biology, Humans, Thermotoga maritima, Amino Acid Sequence, Protein Structure, Quaternary, Molecular Biology, Cyclophilin, Peptidylprolyl isomerase, Binding Sites, biology, Chemistry, Fold (geology), Peptidylprolyl Isomerase, biology.organism_classification, Protein Structure, Tertiary, Crystallography
Published: 2006

35. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold

Author: Glen Spraggon, Lukasz Jaroszewski, Robert Schwarzenbacher, Michael DiDonato, Guenter Wolf, Raymond C. Stevens, Christopher L. Rife, Hsiu-Ju Chiu, Carina Grittini, Kin Moy, Marc-André Elsliger, Ashley M. Deacon, Edward Nigoghossian, Andreas Kreusch, Jessica Paulsen, Kevin Quijano, Jaume M. Canaves, Aprilfawn White, Sanjay Agarwalla, Ian A. Wilson, Herbert L. Axelrod, Tanya Biorac, Adam Godzik, Gye Won Han, Scott A. Lesley, Eileen Ambing, Ron Reyes, Keith O. Hodgson, Eric Hampton, Slawomir K. Grzechnik, Jeff Velasquez, John Wooley, Michael Hornsby, Henry van den Bedem, Eric Koesema, Daniel McMullan, Polat Abdubek, Joanna Hale, Mitchell D. Miller, Heath E. Klock, Peter Kuhn, Justin Haugen, and Qingping Xu
Subjects: Physics, Models, Molecular, Protein Folding, biology, Virulence Factors, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Campylobacter jejuni, Virulence factor, Protein Structure, Secondary, Bacterial protein, Bacterial Proteins, Structural Biology, Protein folding, Molecular Biology
Published: 2005

36. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold

Author: Ian A. Wilson, Eileen Ambing, Ashley M. Deacon, Andreas Kreusch, Jeff Velasquez, Jessica Paulsen, Juli Vincent, Hsiu-Ju Chiu, Herbert L. Axelrod, Polat Abdubek, Michael DiDonato, Gye Won Han, Carina Grittini, Jaume M. Canaves, Raymond C. Stevens, Guenter Wolf, Qingping Xu, Heath E. Klock, Slawomir K. Grzechnik, Michael Hornsby, Christopher L. Rife, Henry van den Bedem, Scott A. Lesley, Kevin Quijano, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Keith O. Hodgson, Aprilfawn White, Joanna Hale, Tanya Biorac, Adam Godzik, Eric Hampton, Mitchell D. Miller, Eric Koesema, Justin Haugen, Eric Sims, John Wooley, Ron Reyes, Daniel McMullan, Robert Schwarzenbacher, Kin Moy, Lukasz Jaroszewski, and Glen Spraggon
Subjects: Models, Molecular, Protein Folding, Chemistry, Hypothetical protein, Proteins, Fold (geology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Molecular Weight, Crystallography, Mice, Open Reading Frames, Structural Biology, Transferase, Animals, Databases, Protein, Molecular Biology, Conserved Sequence
Published: 2005

37. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold

Author: Peter Kuhn, Kevin Quijano, Slawomir K. Grzechnik, Marc-André Elsliger, Ian A. Wilson, Justin Haugen, Polat Abdubek, Edward Nigoghossian, Aprilfawn White, Eileen Ambing, John Wooley, Glen Spraggon, Kin Moy, Carina Grittini, Robert Schwarzenbacher, Daniel McMullan, Heath E. Klock, Hsiu-Ju Chiu, Raymond C. Stevens, Ashley M. Deacon, Guenter Wolf, Mitchell D. Miller, Ron Reyes, Joanna Hale, Jessica Paulsen, Eric Koesema, Gye Won Han, Scott A. Lesley, Andreas Kreusch, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Juli Vincent, Qingping Xu, Keith O. Hodgson, Michael Hornsby, Henry van den Bedem, Eric Sims, Herbert L. Axelrod, Michael DiDonato, Jeff Velasquez, Christopher L. Rife, Eric Hampton, and Jaume M. Canaves
Subjects: Regulation of gene expression, Models, Molecular, Protein Folding, biology, Chemistry, Stereochemistry, Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, DNA gyrase, Bacterial Proteins, Structural Biology, DNA Gyrase, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Dimerization
Published: 2005

38. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution

Author: John Wooley, Justin Haugen, Peter Kuhn, Heath E. Klock, Scott A. Lesley, Joanna Hale, Hsiu-Ju Chiu, Guenter Wolf, Tanya Biorac, Adam Godzik, Qingping Xu, Xiaoping Dai, Polat Abdubek, Slawomir K. Grzechnik, Ron Reyes, Glen Spraggon, Michael DiDonato, Eric Koesema, Carina Grittini, Gye Won Han, Raymond C. Stevens, Marc-André Elsliger, Jeff Velasquez, Edward Nigoghossian, Daniel McMullan, Mitchell D. Miller, Kevin Quijano, Keith O. Hodgson, Aprilfawn White, Robert Schwarzenbacher, Eric Hampton, Juli Vincent, Kin Moy, Lukasz Jaroszewski, Ian A. Wilson, Herbert L. Axelrod, Michael Hornsby, Henry van den Bedem, Eileen Ambing, Ashley M. Deacon, Jessica Paulsen, Jaume M. Canaves, Andreas Kreusch, and Timothy M. McPhillips
Subjects: Models, Molecular, Messenger RNA, Chemistry, Resolution (electron density), DCPS, Molecular Sequence Data, RNA-binding protein, Crystal structure, Crystallography, X-Ray, Biochemistry, Sensitivity and Specificity, Protein Structure, Secondary, Mice, Apoenzymes, Structural Biology, Endoribonucleases, Animals, Amino Acid Sequence, RNA, Messenger, Molecular Biology, Decapping enzyme
Published: 2005

39. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold

Author: Jaume M. Canaves, Slawomir K. Grzechnik, Peter Kuhn, Heath E. Klock, Lukasz Jaroszewski, Jie Ouyang, Ron Reyes, Raymond C. Stevens, John Wooley, Keith O. Hodgson, Olga Zagnitko, Kin Moy, Polat Abdubek, Guenter Wolf, Andreas Kreusch, Rebecca Page, Jeff Velasquez, Glen Spraggon, Michael DiDonato, Joanna Hale, Xianhong Wang, Scott A. Lesley, Qingping Xu, Mitchell D. Miller, Cathy Karlak, Michael Hornsby, Henry van den Bedem, Daniel McMullan, Inna Levin, Alyssa Robb, Kevin Quijano, Bill West, Eric Sims, Eric Hampton, Andrew T. Morse, Juli Vincent, Jamison Cambell, Eric Koesema, Justin Haugen, Robert Schwarzenbacher, Ashley M. Deacon, Carina Grittini, Ian A. Wilson, Hsiu-Ju Chiu, Eileen Ambing, Marc-André Elsliger, Edward Nigoghossian, Tanya Biorac, Adam Godzik, and Gye Won Han
Subjects: Models, Molecular, Protein Folding, biology, ATP synthase, Chemistry, Stereochemistry, Protein Conformation, Fold (geology), Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Molecular Biology, Indigoidine, Piperidones
Published: 2005

40. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

Author: Guenter Wolf, Gye Won Han, Kin Moy, Kevin Quijano, Slawomir K. Grzechnik, Michael Hornsby, Henry van den Bedem, Andreas Kreusch, Jessica Paulsen, Heath E. Klock, Polat Abdubek, Hsiu-Ju Chiu, Rebecca Page, Qingping Xu, Ron Reyes, Marc-André Elsliger, Peter Kuhn, Edward Nigoghossian, Eric Hampton, Andrew T. Morse, Jeff Velasquez, Frank von Delft, Juli Vincent, Lukasz Jaroszewski, Tanya Biorac, Adam Godzik, Olga Zagnitko, Michael DiDonato, Daniel McMullan, Inna Levin, Carina Grittini, Bill West, Keith O. Hodgson, Joanna Hale, Xiaoping Dai, Eric Koesema, Mitchell D. Miller, Justin Haugen, John Wooley, Xianhong Wang, Scott A. Lesley, Timothy M. McPhillips, Ashley M. Deacon, Glen Spraggon, Eric Sims, Robert Schwarzenbacher, Ian A. Wilson, Eileen Ambing, Jie Ouyang, Raymond C. Stevens, Jaume M. Canaves, and Aprilfawn White
Subjects: Models, Molecular, Protein Conformation, Stereochemistry, Molecular Sequence Data, Anabaena sp, Alanine glyoxylate aminotransferase, Electrons, Crystal structure, Crystallography, X-Ray, Biochemistry, Cofactor, Structural Biology, Humans, Transferase, Amino Acid Sequence, Molecular Biology, Transaminases, Sequence Homology, Amino Acid, biology, Chemistry, Resolution (electron density), Proteins, Stereoisomerism, Anabaena, Protein Structure, Tertiary, biology.protein
Published: 2005

41. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

Author: Timothy M. McPhillips, Eric Sims, Eric Hampton, Xiaoping Dai, Jaume M. Canaves, John Wooley, Aprilfawn White, Carina Grittini, Slawomir K. Grzechnik, Daniel McMullan, Inna Levin, Joanna Hale, Heath E. Klock, Lukasz Jaroszewski, Peter Kuhn, Keith O. Hodgson, Justin Haugen, Olga Zagnitko, Guenter Wolf, Kevin Quijano, Kin Moy, Hsiu-Ju Chiu, W. Peti, Joseph W. Arndt, Qingping Xu, Polat Abdubek, Mitchell D. Miller, Andrew T. Morse, Jeff Velasquez, Juli Vincent, Bill West, Jie Ouyang, Marc-André Elsliger, Gye Won Han, Edward Nigoghossian, Andreas Kreusch, Michael Hornsby, Henry van den Bedem, Rebecca Page, Robert Schwarzenbacher, Michael Didonato, Eric Koesema, Frank von Delft, Xianhong Wang, Scott A. Lesley, Ashley M. Deacon, Glen Spraggon, Raymond C. Stevens, Ian A. Wilson, Eileen Ambing, Ron Reyes, Tanya Biorac, and Adam Godzik
Subjects: Models, Molecular, Saccharomyces cerevisiae Proteins, Hydrolases, Protein Conformation, Molecular Sequence Data, Saccharomyces cerevisiae, Molecular Conformation, Alpha (ethology), Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Structural Biology, Hydrolase, Serine, Amino Acid Sequence, Beta (finance), Molecular Biology, Binding Sites, biology, Chemistry, Resolution (electron density), Computational Biology, Serine hydrolase, biology.organism_classification, Protein Structure, Tertiary, Software
Published: 2005

42. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold

Author: Keith O. Hodgson, Kin Moy, Jie Ouyang, Polat Abdubek, Guenter Wolf, Heath E. Klock, Hsiu-Ju Chiu, Xiaoping Dai, Mitchell D. Miller, Marc-André Elsliger, Frank von Delft, Robert Schwarzenbacher, Michael Hornsby, Henry van den Bedem, Carina Grittini, Jeff Velasquez, Tanya Biorac, Adam Godzik, Lukasz Jaroszewski, Olga Zagnitko, Eric Sims, Raymond C. Stevens, Qingping Xu, Eric Koesema, Andreas Kreusch, Michael DiDonato, Rebecca Page, Bill West, Jaume M. Canaves, Peter Kuhn, Aprilfawn White, Daniel McMullan, Inna Levin, Alyssa Robb, Andrew T. Morse, Juli Vincent, Eric Hampton, Ian A. Wilson, Slawomir K. Grzechnik, Xianhong Wang, Scott A. Lesley, Eileen Ambing, Ashley M. Deacon, Glen Spraggon, John Wooley, Kevin Quijano, and Ron Reyes
Subjects: Models, Molecular, Ammonia-Lyases, Stereochemistry, Protein Conformation, Molecular Sequence Data, Molecular Conformation, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Formiminotetrahydrofolate cyclodeaminase, Structural Biology, Enzyme Stability, Thermotoga maritima, Amino Acid Sequence, Molecular Biology, Binding Sites, biology, Chemistry, Fold (geology), Lyase, biology.organism_classification, Protein Structure, Tertiary, Models, Chemical, Crystallization
Published: 2005

43. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution

Author: Jaume M. Canaves, Timothy M. McPhillips, Kevin Quijano, Linda S. Brinen, Mitchell D. Miller, Peter Kuhn, Polat Abdubek, Ross Floyd, Mike DiDonato, John Wooley, Guenter Wolf, Jamison Cambell, Eric Koesema, Marc-André Elsliger, Raymond C. Stevens, Carina Grittini, Daniel McMullan, Inna Levin, Xiaoping Dai, Henry van den Bedem, Said Eshagi, Cathy Karlak, Alyssa Robb, Andrew T. Morse, Juli Vincent, Kin Moy, Jie Ouyang, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Bill West, Frank von Delft, Keith O. Hodgson, Heath E. Klock, Hsiu-Ju Chiu, Robert Schwarzenbacher, Xianhong Wang, Scott A. Lesley, John S. Kovarik, Jeff Velasquez, Lukasz Jaroszewski, Qingping Xu, Eric Hampton, Tanya Biorac, Adam Godzik, Ashley M. Deacon, Ian A. Wilson, Eileen Ambing, and Glen Spraggon
Subjects: Models, Molecular, Crystallography, biology, Tandem, Resolution (electron density), Molecular Sequence Data, CBS domain, Cystathionine beta-Synthase, Crystal structure, biology.organism_classification, Biochemistry, Cystathionine beta synthase, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins, Structural Biology, Thermotoga maritima, biology.protein, Transferase, Amino Acid Sequence, Molecular Biology
Published: 2004

44. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution

Author: Lukasz Jaroszewski, Alyssa Robb, Glen Spraggon, John Wooley, Andrew T. Morse, Jie Ouyang, Juli Vincent, Qingping Xu, Jaume M. Canaves, John S. Kovarik, Slawomir K. Grzechnik, Jamison Cambell, Eric Koesema, Mitchell D. Miller, Guenter Wolf, Linda S. Brinen, Daniel McMullan, Bill West, Xianhong Wang, Scott A. Lesley, Eric Hampton, Fred Rezezadeh, Raymond C. Stevens, Inna Levin, Timothy M. McPhillips, Heath E. Klock, Ian A. Wilson, Eric Sims, Mike DiDonato, Jeff Velasquez, Carina Grittini, Peter Kuhn, Eileen Ambing, Henry van den Bedem, Andreas Kreusch, Rebecca Page, Cathy Karlak, Ross Floyd, Robert Schwarzenbacher, Keith O. Hodgson, Ashley M. Deacon, Xiaoping Dai, Kevin Quijano, Kin Moy, Polat Abdubek, Ron Reyes, Tanya Biorac, Adam Godzik, Marc-André Elsliger, Frank von Delft, and Hsiu-Ju Chiu
Subjects: Models, Molecular, biology, Chemistry, Molecular Sequence Data, Resolution (electron density), Saccharomyces cerevisiae, Crystal structure, Crystallography, X-Ray, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Ureohydrolases, Protein Structure, Tertiary, Multienzyme Complexes, Structural Homology, Protein, Structural Biology, Hydrolase, Allantoicase, Amino Acid Sequence, Molecular Biology, Conserved Sequence
Published: 2004

45. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution

Author: Andreas Kreusch, Rebecca Page, Qingping Xu, Henry van den Bedem, Carina Grittini, Xiaoping Dai, Raymond C. Stevens, Slawomir K. Grzechnik, Hsiu-Ju Chiu, Jie Ouyang, Guenter Wolf, Bill West, Kevin Quijano, Heath E. Klock, Xianhong Wang, Scott A. Lesley, Michael Didonato, Jamison Cambell, Polat Abdubek, Marc-André Elsliger, Jaume M. Canaves, Eric Koesema, Kin Moy, Lukasz Jaroszewski, Frank von Delft, Alyssa Robb, Keith O. Hodgson, Andrew T. Morse, Juli Vincent, Inna Levin, Jeff Velasquez, John Wooley, Cathy Karlak, Mitchell D. Miller, Glen Spraggon, Peter Kuhn, Eric Hampton, Robert Schwarzenbacher, Tanya Biorac, Adam Godzik, Daniel McMullan, Ron Reyes, Timothy M. McPhillips, Eric Sims, Ian A. Wilson, Eileen Ambing, and Ashley M. Deacon
Subjects: chemistry.chemical_classification, Models, Molecular, Binding Sites, Chemistry, Stereochemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Crystallography, Mice, Structural Biology, Oxidoreductase, Structural Homology, Protein, Animals, Amino Acid Sequence, Quinone Reductases, Oxidoreductases, Molecular Biology, NADP
Published: 2004

46. Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution

Author: Jie Ouyang, Andreas Kreusch, Rebecca Page, John Wooley, Heath E. Klock, Ashley M. Deacon, Mitchell D. Miller, Hsiu-Ju Chiu, Jaume M. Canaves, Glen Spraggon, Mike DiDonato, Jamison Campbell, Henry van den Bedem, Linda S. Brinen, Guenter Wolf, Kin Moy, Eric Hampton, Marc-André Elsliger, Keith O. Hodgson, Tanya Biorac, Adam Godzik, Ian A. Wilson, Peter Kuhn, Jeff Velasquez, Fred Rezezadeh, Ross Floyd, Bill West, Eileen Ambing, Ron Reyes, Raymond C. Stevens, Timothy M. McPhillips, Frank von Delft, Xiaoping Dai, Eric Sims, John S. Kovarik, Eric Koesema, Robert Schwarzenbacher, Alyssa Robb, Andrew T. Morse, Juli Vincent, Xianhong Wang, Scott A. Lesley, Kevin Quijano, Carina Grittini, Slawomir K. Grzechnik, Polat Abdubek, Daniel McMullan, Inna Levin, Cathy Karlak, Qingping Xu, and Lukasz Jaroszewski
Subjects: Exonucleases, Models, Molecular, Protein Folding, Protein Conformation, Archaeal Proteins, Molecular Sequence Data, Crystal structure, Siphoviridae, Crystallography, X-Ray, Biochemistry, Protein Structure, Secondary, Viral Proteins, Protein structure, Structural Biology, Amino Acid Sequence, Molecular Biology, Peptide sequence, Binding Sites, Sequence Homology, Amino Acid, Resolution (electron density), Archaeoglobus fulgidus, Protein Structure, Tertiary, N-terminus, Crystallography, Protein folding, PIN domain
Published: 2004

47. Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution

Author: Glen Spraggon, Slawomir K. Grzechnik, Andreas Kreusch, Rebecca Page, Kevin Quijano, Polat Abdubek, Jie Ouyang, Marc-André Elsliger, H.-J. Chiu, Cathy Karlak, Adam Godzik, Raymond C. Stevens, Alyssa Robb, Said Eshagi, Frank von Delft, Kin Moy, Tanja Biorac, Guenter Wolf, Andrew T. Morse, Juli Vincent, Linda S. Brinen, Heath E. Klock, Jaume M. Canaves, Carina Grittini, Robert Schwarzenbacher, John Wooley, Ashley M. Deacon, Daniel McMullan, Inna Levin, Peter Kuhn, Xiaoping Dai, Jamison Cambell, Ian A. Wilson, Ross Floyd, Eric Koesema, Mitchell D. Miller, Jeff Velasquez, Eileen Ambing, Xianhong Wang, Scott A. Lesley, Keith O. Hodgson, John S. Kovarik, Lukasz Jaroszewski, Mike DiDonato, Henry van den Bedem, Qingping Xu, Eric Hampton, Bill West, and Timothy M. McPhillips
Subjects: Models, Molecular, biology, Chemistry, Resolution (electron density), Molecular Sequence Data, Crystal structure, biology.organism_classification, Crystallography, X-Ray, Biochemistry, Crystallography, Bacterial Proteins, Structural Biology, Thermotoga maritima, Transferase, Amino Acid Sequence, Aspartate Aminotransferases, Molecular Biology, Peptide sequence
Published: 2004

48. Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Author: Lukasz Jaroszewski, Dustin C. Ernst, Keith O. Hodgson, Lian Duan, Tamara Astakhova, Abhinav Kumar, Tiffany Wooten, Michelle Chiu, Julie Feuerhelm, Edward Nigoghossian, Daniel McMullan, Gye Won Han, Qingping Xu, Christine B Trame, Linda Okach, Debanu Das, Herbert L. Axelrod, Polat Abdubek, Heath E. Klock, Carol L. Farr, Mitchell D. Miller, Sanjay Krishna, Alex Bateman, Henry van den Bedem, Anna Grzechnik, David Marciano, Thomas Clayton, Marc C. Deller, Connie Chen, Christopher L. Rife, Natasha Sefcovic, John Wooley, Constantina Bakolitsa, Kevin K. Jin, Hsiu-Ju Chiu, Amanda Nopakun, Marc André Elsliger, Andrew T. Morse, Dennis Carlton, Ian A. Wilson, Christina Puckett, Adam Godzik, Ashley M. Deacon, Kyle Ellrott, Joanna C Grant, Robert D. Finn, Dana Weekes, Piotr Kozbial, Henry J Tien, Mark W. Knuth, Ron Reyes, and Scott A. Lesley
Subjects: Models, Molecular, asu, asymmetric unit, Protein Data Bank (RCSB PDB), SSRL, Stanford Synchrotron Radiation Lightsource, Crystallography, X-Ray, Protein Structure, Secondary, chemistry.chemical_compound, PH, Pleckstrin homology, Structural Biology, Pleckstrin homology (PH) domain, Conserved Sequence, 0303 health sciences, 030302 biochemistry & molecular biology, bacterial PH domain (PHb), Pleckstrin homology domain, Eukaryotic Cells, Biochemistry, Domain (ring theory), TCEP, higher-order symmetry, DUF1696, domain of unknown function family 1696, lipids (amino acids, peptides, and proteins), VPS36, vacuolar protein sorting protein 36, Protein Binding, Protein family, Surface Properties, Stereochemistry, Molecular Sequence Data, PTB, phosphotyrosine binding, protein assembly, Biology, Ring (chemistry), Article, TEV, tobacco etch virus, Structural genomics, Evolution, Molecular, 03 medical and health sciences, TCEP, tris(2-carboxyethyl)phosphine–HCl, Bacterial Proteins, PDB, Protein Data Bank, MAD, multiwavelength anomalous diffraction, ALS, Advanced Light Source, Amino Acid Sequence, Protein Structure, Quaternary, PIPE, Polymerase Incomplete Primer Extension, protein evolution, Molecular Biology, PEG, polyethylene glycol, 030304 developmental biology, Binding Sites, Bacteria, Sequence Homology, Amino Acid, biology.organism_classification, Protein Structure, Tertiary, JCSG, Joint Center for Structural Genomics, Prokaryotic Cells, chemistry, PHb, bacterial PH domain, Sequence Alignment
Abstract: Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C5 symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C12 symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the β-strands of adjacent protomers that likely mediates protein–protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.
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