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Start Over Author "Johnson, Hope" Journal acta crystallographica section f structural biology and crystallization communications
9 results on '"Johnson, Hope"'

1. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 fromExiguobacterium sibiricum255-15

Author

Han, Gye Won, primary, Elsliger, Marc-André, additional, Yeates, Todd O., additional, Xu, Qingping, additional, Murzin, Alexey G., additional, Krishna, S. Sri, additional, Jaroszewski, Lukasz, additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ernst, Dustin, additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Kumar, Abhinav, additional, Lam, Winnie W., additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Okach, Linda, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Hodgson, Keith O., additional, Wooley, John, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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2. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

Author

Han, Gye Won, primary, Bakolitsa, Constantina, additional, Miller, Mitchell D., additional, Kumar, Abhinav, additional, Carlton, Dennis, additional, Najmanovich, Rafael J., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Ernst, Dustin, additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Marciano, David, additional, McMullan, Daniel, additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Okach, Linda, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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3. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of theBacilluschorismate mutase fold and suggest a role in amino-acid metabolism

Author

Bakolitsa, Constantina, primary, Kumar, Abhinav, additional, Jin, Kevin K., additional, McMullan, Daniel, additional, Krishna, S. Sri, additional, Miller, Mitchell D., additional, Abdubek, Polat, additional, Acosta, Claire, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Burra, Prasad, additional, Carlton, Dennis, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Clayton, Thomas, additional, Das, Debanu, additional, Deller, Marc C., additional, Duan, Lian, additional, Elias, Ylva, additional, Ellrott, Kyle, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grant, Joanna C., additional, Grzechnik, Anna, additional, Grzechnik, Slawomir K., additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Marciano, David, additional, Morse, Andrew T., additional, Murphy, Kevin D., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, Trout, Christina V., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, White, Aprilfawn, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-Andre, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2010
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4. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Author

Das, Debanu, primary, Grishin, Nick V., additional, Kumar, Abhinav, additional, Carlton, Dennis, additional, Bakolitsa, Constantina, additional, Miller, Mitchell D., additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Burra, Prasad, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grzechnik, Anna, additional, Grzechnik, Slawomir K., additional, Grant, Joanna C., additional, Han, Gye Won, additional, Jaroszewski, Lukasz, additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Kozbial, Piotr, additional, Krishna, S. Sri, additional, Marciano, David, additional, McMullan, Daniel, additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Oommachen, Silvya, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Elsliger, Marc-André, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2009
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5. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein fromKlebsiella pneumoniae, reveals an OB-fold

Author

Das, Debanu, primary, Kozbial, Piotr, additional, Han, Gye Won, additional, Carlton, Dennis, additional, Jaroszewski, Lukasz, additional, Abdubek, Polat, additional, Astakhova, Tamara, additional, Axelrod, Herbert L., additional, Bakolitsa, Constantina, additional, Chen, Connie, additional, Chiu, Hsiu-Ju, additional, Chiu, Michelle, additional, Clayton, Thomas, additional, Deller, Marc C., additional, Duan, Lian, additional, Ellrott, Kyle, additional, Elsliger, Marc-André, additional, Ernst, Dustin, additional, Farr, Carol L., additional, Feuerhelm, Julie, additional, Grzechnik, Anna, additional, Grant, Joanna C., additional, Jin, Kevin K., additional, Johnson, Hope A., additional, Klock, Heath E., additional, Knuth, Mark W., additional, Krishna, S. Sri, additional, Kumar, Abhinav, additional, Marciano, David, additional, McMullan, Daniel, additional, Miller, Mitchell D., additional, Morse, Andrew T., additional, Nigoghossian, Edward, additional, Nopakun, Amanda, additional, Okach, Linda, additional, Oommachen, Silvya, additional, Paulsen, Jessica, additional, Puckett, Christina, additional, Reyes, Ron, additional, Rife, Christopher L., additional, Sefcovic, Natasha, additional, Tien, Henry J., additional, Trame, Christine B., additional, van den Bedem, Henry, additional, Weekes, Dana, additional, Wooten, Tiffany, additional, Xu, Qingping, additional, Hodgson, Keith O., additional, Wooley, John, additional, Deacon, Ashley M., additional, Godzik, Adam, additional, Lesley, Scott A., additional, and Wilson, Ian A., additional

Published
2009
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6. Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

Author

Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Bacillales enzymology, Pyrophosphatases chemistry
Abstract

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.

Published
2010
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7. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation.

Author

Das D, Grishin NV, Kumar A, Carlton D, Bakolitsa C, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Burra P, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grzechnik SK, Grant JC, Han GW, Jaroszewski L, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Genome, Bacterial, Models, Molecular, Molecular Sequence Data, Neisseria gonorrhoeae genetics, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Bacterial Proteins chemistry, Gene Expression Regulation, Neisseria gonorrhoeae chemistry, Transcription, Genetic
Abstract

Proteins with the DUF2063 domain constitute a new Pfam family, PF09836. The crystal structure of a member of this family, NGO1945 from Neisseria gonorrhoeae, has been determined and reveals that the N-terminal DUF2063 domain is likely to be a DNA-binding domain. In conjunction with the rest of the protein, NGO1945 is likely to be involved in transcriptional regulation, which is consistent with genomic neighborhood analysis. Of the 216 currently known proteins that contain a DUF2063 domain, the most significant sequence homologs of NGO1945 (∼40-99% sequence identity) are from various Neisseria and Haemophilus species. As these are important human pathogens, NGO1945 represents an interesting candidate for further exploration via biochemical studies and possible therapeutic intervention.

Published
2010
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8. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold.

Author

Das D, Kozbial P, Han GW, Carlton D, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Elsliger MA, Ernst D, Farr CL, Feuerhelm J, Grzechnik A, Grant JC, Jin KK, Johnson HA, Klock HE, Knuth MW, Krishna SS, Kumar A, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Nopakun A, Okach L, Oommachen S, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Tertiary, Bacterial Proteins chemistry, Klebsiella pneumoniae chemistry, Lipoproteins chemistry
Abstract

KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family.

Published
2010
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9. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.

Author

Bakolitsa C, Kumar A, Jin KK, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Burra P, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Elias Y, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Grzechnik SK, Han GW, Jaroszewski L, Johnson HA, Klock HE, Knuth MW, Kozbial P, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Nopakun A, Okach L, Paulsen J, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, Trout CV, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacillus enzymology, Chorismate Mutase metabolism, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Amino Acids metabolism, Bordetella bronchiseptica enzymology, Chorismate Mutase chemistry, Protein Folding, Rhodobacteraceae enzymology
Abstract

The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.

Published
2010
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