276 results on '"Maikun Teng"'
Search Results
52. Crystal Structures and RNA-binding Properties of the RNA Recognition Motifs of Heterogeneous Nuclear Ribonucleoprotein L
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Maikun Teng, Xu Li, Liwen Niu, Fuxing Zeng, Yan Zhao, Hui Lv, Yiwei Liu, and Wenjuan Zhang
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RNA ,Repressor ,RNA-binding protein ,Cell Biology ,Biology ,Heterogeneous ribonucleoprotein particle ,Biochemistry ,Molecular biology ,Cell biology ,RNA-Protein Interaction ,RNA splicing ,Binding site ,Molecular Biology ,Ribonucleoprotein - Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNP L) is an abundant RNA-binding protein implicated in many bioprocesses, including pre-mRNA processing, mRNA export of intronless genes, internal ribosomal entry site-mediated translation, and chromatin modification. It contains four RNA recognition motifs (RRMs) that bind with CA repeats or CA-rich elements. In this study, surface plasmon resonance spectroscopy assays revealed that all four RRM domains contribute to RNA binding. Furthermore, we elucidated the crystal structures of hnRNP L RRM1 and RRM34 at 2.0 and 1.8 Å, respectively. These RRMs all adopt the typical β1α1β2β3α2β4 topology, except for an unusual fifth β-strand in RRM3. RRM3 and RRM4 interact intimately with each other mainly through helical surfaces, leading the two β-sheets to face opposite directions. Structure-based mutations and surface plasmon resonance assay results suggested that the β-sheets of RRM1 and RRM34 are accessible for RNA binding. FRET-based gel shift assays (FRET-EMSA) and steady-state FRET assays, together with cross-linking and dynamic light scattering assays, demonstrated that hnRNP L RRM34 facilitates RNA looping when binding to two appropriately separated binding sites within the same target pre-mRNA. EMSA and isothermal titration calorimetry binding studies with in vivo target RNA suggested that hnRNP L-mediated RNA looping may occur in vivo. Our study provides a mechanistic explanation for the dual functions of hnRNP L in alternative splicing regulation as an activator or repressor.
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- 2013
53. AhV_aPA-induced vasoconstriction involves the IP3Rs-mediated Ca2+ releasing
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Liwen Niu, Maikun Teng, Xu Li, Zhisong Zou, and Fuxing Zeng
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chemistry.chemical_classification ,Phospholipase A ,Contraction (grammar) ,Ryanodine receptor ,Endoplasmic reticulum ,Inositol trisphosphate ,Biology ,Toxicology ,Molecular biology ,chemistry.chemical_compound ,Enzyme ,Biochemistry ,chemistry ,medicine ,medicine.symptom ,Receptor ,Vasoconstriction - Abstract
AhV_aPA, the acidic PLA 2 purified from Agkistrodon halys pallas venom, was previously reported to possess a strong enzymatic activity and can remarkably induce a further contractile response on the 60 mM K + -induced contraction with an EC 50 in 369 nM on mouse thoracic aorta rings. In the present study, we found that the p -bromo-phenacyl-bromide ( p BPB), which can completely inhibit the enzymatic activity of AhV_aPA, did not significantly reduce the contractile response on vessel rings induced by AhV_aPA, indicating that the vasoconstrictor effects of AhV_aPA are independent of the enzymatic activity. The inhibitor experiments showed that the contractile response induced by AhV_aPA is mainly attributed to the Ca 2+ releasing from Ca 2+ store, especially sarcoplasmic reticulum (SR). Detailed studies showed that the Ca 2+ release from SR is related to the activation of inositol trisphosphate receptors (IP 3 Rs) rather than ryanodine receptors (RyRs). Furthermore, the vasoconstrictor effect could be strongly reduced by pre-incubation with heparin, indicating that the basic amino acid residues on the surface of AhV_aPA may be involved in the interaction between AhV_aPA and the molecular receptors. These findings offer new insights into the functions of snake PLA 2 and provide a novel pathogenesis of A. halys pallas venom.
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- 2013
54. Crystal structure of wild-type and mutant human Ap4A hydrolase
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Maikun Teng, Liwen Niu, Xiaofang Chen, Honghua Ge, and Weili Yang
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Stereochemistry ,Molecular Sequence Data ,Mutant ,Biophysics ,Sulfuric Acid Esters ,Crystallography, X-Ray ,Biochemistry ,Article ,Protein Structure, Secondary ,chemistry.chemical_compound ,Nudix ,Hydrolase ,medicine ,Humans ,Moiety ,Amino Acid Sequence ,Molecular Biology ,chemistry.chemical_classification ,Binding Sites ,Crystal structure ,Polyphosphate ,Wild type ,Cell Biology ,Adenosine ,Phosphoric Monoester Hydrolases ,Acid Anhydride Hydrolases ,Diphosphates ,Enzyme ,chemistry ,Mutation ,Ap4A hydrolase ,Mutant Proteins ,Ap4A ,medicine.drug - Abstract
Highlights ► We present the crystal structure of the wild-type enzyme and its E58A mutant. ► Our proposal supports the recognition “trigger” event during substrate-binding step. ► The structure has implications in substrate binding mode in this class of enzymes., Ap4A hydrolase (asymmetrical diadenosine tetraphosphate hydrolase, EC 3.6.1.17), an enzyme involved in a number of biological processes, is characterized as cleaving the polyphosphate chain at the fourth phosphate from the bound adenosine moiety. This paper presents the crystal structure of wild-type and E58A mutant human Ap4A hydrolase. Similar to the canonical Nudix fold, human Ap4A hydrolase shows the common αβα-sandwich architecture. Interestingly, two sulfate ions and one diphosphate coordinated with some conserved residues were observed in the active cleft, which affords a better understanding of a possible mode of substrate binding.
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- 2013
55. The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding
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Zexian Liu, Fuxing Zeng, Liwen Niu, Hong Wang, Qiao Liu, Maikun Teng, Xu Li, and Huihui Liu
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Conformational change ,RNA-induced transcriptional silencing ,Protein Conformation ,HU Protein ,Crystallography, X-Ray ,Mice ,Structural Biology ,Protein Interaction Mapping ,Animals ,RNA, Messenger ,Nucleotide Motifs ,AU Rich Elements ,Chemistry ,RNA-Binding Proteins ,RNA ,General Medicine ,DNA Methylation ,Non-coding RNA ,Molecular biology ,Protein Structure, Tertiary ,ELAV Proteins ,Tandem Repeat Sequences ,Biophysics ,Linker ,Fluorescence anisotropy ,Protein Binding ,Binding domain - Abstract
Human RNA-binding protein (HuR), a ubiquitously expressed member of the Hu protein family, plays an important role in mRNA degradation and has been implicated as a key post-transcriptional regulator. HuR contains three RNA-recognition motif (RRM) domains. The two N-terminal tandem RRM domains can selectively bind AU-rich elements (AREs), while the third RRM domain (RRM3) contributes to interactions with the poly-A tail of target mRNA and other ligands. Here, the X-ray structure of two methylated tandem RRM domains (RRM1/2) of HuR in their RNA-free form was solved at 2.9 Å resolution. The crystal structure of RRM1/2 complexed with target mRNA was also solved at 2.0 Å resolution; comparisons of the two structures show that HuR RRM1/2 undergoes conformational changes upon RNA binding. Fluorescence polarization assays (FPA) were used to study the protein-RNA interactions. Both the structure and the FPA analysis indicated that RRM1 is the primary ARE-binding domain in HuR and that the conformational changes induce subsequent contacts of the RNA substrate with the inter-domain linker and RRM2 which greatly improve the RNA-binding affinity of HuR.
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- 2013
56. Purification, crystallization and preliminary X-ray diffraction analysis of an acidic phospholipase A2with vasoconstrictor activity fromAgkistrodon halys pallasvenom
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Liwen Niu, Maikun Teng, Xu Li, Lu Zhang, Zhisong Zou, and Fuxing Zeng
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Male ,Agkistrodon ,Myotoxin ,Biophysics ,Venom ,In Vitro Techniques ,Phospholipase ,Crystallography, X-Ray ,complex mixtures ,Biochemistry ,law.invention ,Mice ,Phospholipase A2 ,Structural Biology ,law ,Crotalid Venoms ,Genetics ,Animals ,Crystallization ,Aorta ,Phospholipids ,chemistry.chemical_classification ,Mice, Inbred ICR ,Chromatography ,Dose-Response Relationship, Drug ,biology ,Chromatography, Ion Exchange ,Condensed Matter Physics ,biology.organism_classification ,Phospholipases A2 ,Enzyme ,chemistry ,Crystallization Communications ,biological sciences ,X-ray crystallography ,health occupations ,Chromatography, Gel ,biology.protein ,bacteria ,lipids (amino acids, peptides, and proteins) ,Muscle Contraction - Abstract
Phospholipases A2(PLA2s) are the major component of snake venoms and exert a variety of relevant toxic actions such as neurotoxicity and myotoxicity, amongst others. An acidic PLA2, here named AhV_aPA, was purified fromAgkistrodon halys pallasvenom by means of a three-step chromatographic procedure. AhV_aPA migrated as a single band on SDS–PAGE gels, with a molecular weight of about 14 kDa. Like other acidic aPLA2s, AhV_aPA has high enzymatic activity. Tension measurements of mouse thoracic aortic rings remarkably indicated that AhV_aPA could induce a further contractile response on the 60 mMK+-induced contraction, with an EC50of 369 nmol l−1. Rod-shaped crystals were obtained by the hanging-drop vapour-diffusion method and diffracted to a resolution limit of 2.30 Å. The crystals belonged to space groupP222, with unit-cell parametersa= 44.27,b= 68.39,c= 81.54 Å.
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- 2012
57. Structural basis for the specificity of the GAE domain of yGGA2 for its accessory proteins Ent3 and Ent5
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Pengfei Fang, Xu Li, Jing Wang, Liwen Niu, and Maikun Teng
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Mutagenesis -- Analysis ,Phenylalanine -- Chemical properties ,Protein binding -- Analysis ,Brewer's yeast -- Genetic aspects ,Biological sciences ,Chemistry - Abstract
Crystal structure and mutagenesis analysis of the yGGA2_GAE in the domain of GAE proteins (Ent3 and Ent5) in Saccharomyces cerevisiae are performed to understand the domain binding mechanism of Ent3/5. The results suggested that Ent3 and Ent5 play a distinct role in trafficking by fine tuning the GGA adaptor dependence by adjusting their non-acidic-phenylalanine residues.
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- 2010
58. The crystal structure of the human nascent polypeptide-associated complex domain reveals a nucleic acid-binding region on the NACA subunit
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Yiwei Liu, Yingxia Hu, Xu Li, Liwen Niu, and Maikun Teng
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Archaeabacteria -- Genetic aspects ,Archaeabacteria -- Physiological aspects ,Nucleic acids -- Structure ,Nucleic acids -- Chemical properties ,Polypeptides -- Structure ,Polypeptides -- Chemical properties ,Genetic translation -- Analysis ,Biological sciences ,Chemistry - Abstract
The crystal structure of the human nascent polypeptide-associated complex (NAC) domain was characterized to demonstrate the kinetics of human NAC dimerization. The results identified a region in the NAC domain of the human NAC [alpha]-subunit as a new nucleic acid-binding region which is blocked from binding nucleic acids in the heterodimeric complex by a helix region in the [beta]-subunit.
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- 2010
59. Structural and histone binding ability characterization of the ARB2 domain of a histone deacetylase Hda1 from Saccharomyces cerevisiae
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Hui Shen, Yuwei Zhu, Hui Yan, Maikun Teng, Xu Li, and Chongyuan Wang
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0301 basic medicine ,Histone deacetylase 5 ,Multidisciplinary ,030102 biochemistry & molecular biology ,Histone deacetylase 2 ,Biology ,Article ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,Histone H1 ,Biochemistry ,Histone H2A ,Histone code ,Histone octamer ,Histone binding ,Binding domain - Abstract
Hda1 is the catalytic core component of the H2B- and H3- specific histone deacetylase (HDAC) complex from Saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. Though the N-terminal catalytic HDAC domain of Hda1 is well characterized, the function of the C-terminal ARB2 domain remains unknown. In this study, we determine the crystal structure of the ARB2 domain from S. cerevisiae Hda1 at a resolution of 2.7 Å. The ARB2 domain displays an α/β sandwich architecture with an arm protruding outside. Two ARB2 domain molecules form a compact homo-dimer via the arm elements, and assemble as an inverse “V” shape. The pull-down and ITC results reveal that the ARB2 domain possesses the histone binding ability, recognizing both the H2A-H2B dimer and H3-H4 tetramer. Perturbation of the dimer interface abolishes the histone binding ability of the ARB2 domain, indicating that the unique dimer architecture of the ARB2 domain coincides with the function for anchoring to histone. Collectively, our data report the first structure of the ARB2 domain and disclose its histone binding ability, which is of benefit for understanding the deacetylation reaction catalyzed by the class II Hda1 HDAC complex.
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- 2016
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60. Crystal structure of the two-subunit tRNA m1A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae
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Yuwei Zhu, Zhi Qiao, Liwen Niu, Mingxing Wang, Mohammad Ebrahimi, Maikun Teng, Xu Li, Chongyuan Wang, Xiaojiao Fan, and Xuguang Jiang
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Models, Molecular ,Protein Conformation, alpha-Helical ,0301 basic medicine ,S-Adenosylmethionine ,RNA, Transfer, Met ,Saccharomyces cerevisiae Proteins ,Stereochemistry ,Protein subunit ,Amino Acid Motifs ,Saccharomyces cerevisiae ,Gene Expression ,Crystallography, X-Ray ,Methylation ,Article ,Substrate Specificity ,03 medical and health sciences ,0302 clinical medicine ,Protein structure ,Catalytic Domain ,Transferase ,Protein Interaction Domains and Motifs ,Cloning, Molecular ,RNA Processing, Post-Transcriptional ,tRNA Methyltransferases ,Binding Sites ,Multidisciplinary ,biology ,Chemistry ,biology.organism_classification ,Heterotetramer ,TRNA binding ,Recombinant Proteins ,030104 developmental biology ,Transfer RNA ,Protein Conformation, beta-Strand ,Protein Multimerization ,Holoenzymes ,030217 neurology & neurosurgery ,Protein Binding - Abstract
The N1 methylation of adenine at position 58 (m1A58) of tRNA is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine tRNAiMet. In eukaryotes, this modification is performed by the TRM6-TRM61 holoenzyme. To understand the molecular mechanism that underlies the cooperation of TRM6 and TRM61 in the methyl transfer reaction, we determined the crystal structure of TRM6-TRM61 holoenzyme from Saccharomyces cerevisiae in the presence and absence of its methyl donor S-Adenosyl-L-methionine (SAM). In the structures, two TRM6-TRM61 heterodimers assemble as a heterotetramer. Both TRM6 and TRM61 subunits comprise an N-terminal β-barrel domain linked to a C-terminal Rossmann-fold domain. TRM61 functions as the catalytic subunit, containing a methyl donor (SAM) binding pocket. TRM6 diverges from TRM61, lacking the conserved motifs used for binding SAM. However, TRM6 cooperates with TRM61 forming an L-shaped tRNA binding regions. Collectively, our results provide a structural basis for better understanding the m1A58 modification of tRNA occurred in Saccharomyces cerevisiae.
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- 2016
61. Structural and functional insight into the N-terminal domain of the clathrin adaptor Ent5 from Saccharomyces cerevisiae
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Yang Song, Liwen Niu, Maikun Teng, Xu Li, Mohammad Ebrahimi, and Fan Zhang
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0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Endosome ,Protein Conformation ,Saccharomyces cerevisiae ,Biophysics ,Biochemistry ,Clathrin ,Evolution, Molecular ,03 medical and health sciences ,Structure-Activity Relationship ,Protein Domains ,Lysosome ,medicine ,Molecular Biology ,biology ,Vesicle ,Vesicle coat ,Cell Biology ,biology.organism_classification ,Transport protein ,Cell biology ,Adaptor Proteins, Vesicular Transport ,030104 developmental biology ,medicine.anatomical_structure ,biology.protein ,Biogenesis - Abstract
Clathrin-coated vesicles (CCVs) play critical roles in multiple cellular processes, including nutrient uptake, endosome/lysosome biogenesis, pathogen invasion, regulation of signalling receptors, etc. Saccharomyces cerevisiae Ent5 (ScEnt5) is one of the two major adaptors supporting the CCV-mediated TGN/endosome traffic in yeast cells. However, the classification and phosphoinositide binding characteristic of ScEnt5 remain elusive. Here we report the crystal structures of the ScEnt5 N-terminal domain, and find that ScEnt5 contains an insertion α' helix that does not exist in other ENTH or ANTH domains. Furthermore, we investigate the classification of ScEnt5-N(31-191) by evolutionary history analyses and structure comparisons, and find that the ScEnt5 N-terminal domain shows different phosphoinositide binding property from rEpsin1 and rCALM. Above results facilitate the understanding of the ScEnt5-mediated vesicle coat formation process.
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- 2016
62. Differentially expressed mitochondrial genes in breast cancer cells: Potential new targets for anti-cancer therapies
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Liwen Niu, Qinglin Zhang, Maikun Teng, Yongxiang Gao, and Zhi Liang
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0301 basic medicine ,Stromal cell ,Glutamine ,Breast Neoplasms ,Biology ,Mitochondrion ,Bioinformatics ,Metastasis ,03 medical and health sciences ,0302 clinical medicine ,Breast cancer ,Genetics ,medicine ,Humans ,Inner mitochondrial membrane ,Cancer ,Reproducibility of Results ,Epithelial Cells ,General Medicine ,medicine.disease ,Up-Regulation ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Genes, Mitochondrial ,Tumor progression ,030220 oncology & carcinogenesis ,Cancer cell ,Genome, Mitochondrial ,Cancer research ,Female ,Stromal Cells ,Algorithms - Abstract
It has been reported that tumor growth and proliferation correspond to mitochondrial dysfunction and that the tumor cellular microenvironment plays a key role in tumor progression, representing an area that might be manipulated to confer therapeutic anti-tumor benefits. In this article, we have identified mitochondrial genes, largely nuclear-encoded genes, which are differentially expressed in breast cancer epithelial and stromal cells compared to cells from normal breast tissues. We determined that gene expression of the mitochondrial membrane respiratory chain complex I and IV and ATP synthesis were reduced in both in epithelial and stromal cancer cells compared to normal breast cells. We also found transport-related genes were significantly more highly expressed in breast cancer epithelial cells. Our data also suggest that mitochondria are likely to proliferate in breast cancer stromal cells, which is supported by the observation that MRPL12, POLG, and RNASEH1 are all up-regulated in cancerous stromal cells. In addition, we present an improved simulated annealing algorithm, SANetWalker, which can be used to detect the functional module. At the same time, this method has a minimal effect on network topology and can be used to identify the highest confidence functional module. Using SANetWalker, we obtained the highest confidence (90%) functional module with a fumarate hydratase (FH)-centered network with 40 nodes and 107 edges. Functional analysis revealed that glutamine metabolism genes were significantly up-regulated in both epithelial and stromal cells from breast cancer tissues, which implicates glutamine metabolism in breast cancer growth and metastasis.
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- 2016
63. Structural insights into the methyl donor recognition model of a novel membrane-binding protein UbiG
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Yang Liu, Liwen Niu, Chongyuan Wang, Maikun Teng, Xu Li, Yuwei Zhu, Linjuan Zhang, Xiaojiao Fan, and Xuguang Jiang
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0301 basic medicine ,Methyltransferase ,Protein Conformation ,Stereochemistry ,Mutant ,Plasma protein binding ,Biology ,medicine.disease_cause ,Article ,03 medical and health sciences ,Protein structure ,medicine ,Escherichia coli ,Mutation ,Crystallography ,Multidisciplinary ,030102 biochemistry & molecular biology ,Escherichia coli Proteins ,Methyltransferases ,Protein engineering ,S-Adenosylhomocysteine ,030104 developmental biology ,Membrane ,Biochemistry ,Crystallization ,Protein Binding - Abstract
UbiG is a SAM-dependent O-methyltransferase, catalyzing two O-methyl transfer steps for ubiquinone biosynthesis in Escherichia coli. UbiG possesses a unique sequence insertion between β4 and α10, which is used for membrane lipid interaction. Interestingly, this sequence insertion also covers the methyl donor binding pocket. Thus, the relationship between membrane binding and entrance of the methyl donor of UbiG during the O-methyl transfer process is a question that deserves further exploration. In this study, we reveal that the membrane-binding region of UbiG gates the entrance of methyl donor. When bound with liposome, UbiG displays an enhanced binding ability toward the methyl donor product S-adenosylhomocysteine. We further employ protein engineering strategies to design UbiG mutants by truncating the membrane interacting region or making it more flexible. The ITC results show that the binding affinity of these mutants to SAH increases significantly compared with that of the wild-type UbiG. Moreover, we determine the structure of UbiG∆165–187 in complex with SAH. Collectively, our results provide a new angle to cognize the relationship between membrane binding and entrance of the methyl donor of UbiG, which is of benefit for better understanding the O-methyl transfer process for ubiquinone biosynthesis.
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- 2016
64. Structural Analysis of Shu Proteins Reveals a DNA Binding Role Essential for Resisting Damage
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Liwen Niu, Shali Qi, Yiwei Liu, Maikun Teng, Xu Li, Jianbin Ruan, and Yuyong Tao
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Saccharomyces cerevisiae Proteins ,HMG-box ,DNA damage ,RAD51 ,Saccharomyces cerevisiae ,Biology ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,Structure-Activity Relationship ,chemistry.chemical_compound ,Protein structure ,Shu complex ,Humans ,Protein–DNA interaction ,DNA, Fungal ,Protein Structure, Quaternary ,Molecular Biology ,Cell Biology ,Protein Structure, Tertiary ,Cell biology ,DNA-Binding Proteins ,chemistry ,Multiprotein Complexes ,Protein Structure and Folding ,Homologous recombination ,DNA - Abstract
The yeast Shu complex, consisting of the proteins Shu1, Shu2, Psy3, and Csm2, maintains genomic stability by coupling post-replication repair to homologous recombination. However, a lack of biochemical and structural information on the Shu proteins precludes revealing their precise roles within the pathway. Here, we report on the 1.9-Å crystal structure of the Psy3-Csm2 complex. The crystal structure shows that Psy3 forms a heterodimer with Csm2 mainly through a hydrophobic core. Unexpectedly, Psy3 and Csm2 share a similar architecture that closely resembles the ATPase core domain of Rad51. The L2 loop present in Psy3 and Csm2 is similar to that of Rad51 and confers the DNA binding activity of the Shu complex. As with Rad51, the Shu complex appears to form a nucleoprotein filament by binding nonspecifically to DNA. Structure-based mutagenesis studies have demonstrated that the DNA binding activity of the Shu complex is essential for repair of the methyl methanesulfonate-induced DNA damage. Our findings provide good foundations for the understanding of the Srs2 regulation by the Shu complex.
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- 2012
65. Crystal structure of agkisacucetin, a Gpib-binding snake C-type lectin that inhibits platelet adhesion and aggregation
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Hong-Kai Chen, Liwen Niu, Yongxiang Gao, Xiaoyi Li, Honghua Ge, Heng Li, Jing Liu, Maikun Teng, Lan Chen, and Yiwei Liu
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Models, Molecular ,Protein Conformation ,Molecular Sequence Data ,Venom ,Crystal structure ,Crystallography, X-Ray ,medicine.disease_cause ,Platelet membrane glycoprotein ,Biochemistry ,Von Willebrand factor ,Structural Biology ,C-type lectin ,Crotalid Venoms ,von Willebrand Factor ,medicine ,Lectins, C-Type ,Amino Acid Sequence ,Molecular Biology ,Membrane Glycoproteins ,biology ,Toxin ,Chemistry ,Lectin ,Blood Proteins ,Molecular biology ,Protein Subunits ,biology.protein ,Sequence Alignment ,Platelet Aggregation Inhibitors ,Cysteine - Abstract
Agkisacucetin is a snake C-type lectin isolated from the venom of Agkistrodon acutus (A. acutus). It binds specifically to the platelet glycoprotein (GP) Ib and prevents the von Willebrand factor (VWF) accessing it. We determined the crystal structure of agkisacucetin to 1.9A resolution. The structure of agkisacucetin has an (αβ) fold similar to another GPIb-binding protein, flavocetin-A, but lacks the C-terminal cysteine in the β-subunit, does not form (βα)4 tetramers, and does not cluster GPIbs, like flavocetin-A. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
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- 2012
66. Crystal Structure of Human SSRP1 Middle Domain Reveals a Role in DNA Binding
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Hui Lv, Sai Li, Wenjuan Zhang, Yiwei Liu, Liwen Niu, Yunyu Shi, Fuxing Zeng, Maikun Teng, Xu Li, and Chen Shao
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0301 basic medicine ,HMG-box ,Protein Conformation ,Protein domain ,Cell Cycle Proteins ,Biology ,Crystallography, X-Ray ,Article ,Histones ,03 medical and health sciences ,Protein Domains ,SeqA protein domain ,EVH1 domain ,Humans ,B3 domain ,Genetics ,Multidisciplinary ,High Mobility Group Proteins ,DNA ,DNA-binding domain ,Cell biology ,DNA-Binding Proteins ,030104 developmental biology ,Cyclic nucleotide-binding domain ,Transcriptional Elongation Factors ,Transcription Factors ,Binding domain - Abstract
SSRP1 is a subunit of the FACT complex, an important histone chaperone required for transcriptional regulation, DNA replication and damage repair. SSRP1 also plays important roles in transcriptional regulation independent of Spt16 and interacts with other proteins. Here, we report the crystal structure of the middle domain of SSRP1. It consists of tandem pleckstrin homology (PH) domains. These domains differ from the typical PH domain in that PH1 domain has an extra conserved βαβ topology. SSRP1 contains the well-characterized DNA-binding HMG-1 domain. Our studies revealed that SSRP1-M can also participate in DNA binding and that this binding involves one positively charged patch on the surface of the structure. In addition, SSRP1-M did not bind to histones, which was assessed through pull-down assays. This aspect makes the protein different from other related proteins adopting the double PH domain structure. Our studies facilitate the understanding of SSRP1 and provide insights into the molecular mechanisms of interaction with DNA and histones of the FACT complex.
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- 2015
67. Structural Insights into the Down-regulation of Overexpressed p185 Protein of Transformed Cells by the Antibody chA21
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Jing Liu, Siyi Hu, Huihao Zhou, Liansheng Cheng, Hongtao Zhang, Juanjuan Zhu, Yang Liu, Guodong Shen, Maikun Teng, Liwen Niu, Mark I. Greene, and Zhao Zha
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animal structures ,Kinase ,medicine.drug_class ,media_common.quotation_subject ,Cell Biology ,Biology ,Monoclonal antibody ,Biochemistry ,Molecular biology ,In vitro ,ErbB ,Cancer cell ,medicine ,Homomeric ,Kinase activity ,skin and connective tissue diseases ,Internalization ,Molecular Biology ,media_common - Abstract
p185(her2/neu) belongs to the ErbB receptor tyrosine kinase family, which has been associated with human breast, ovarian, and lung cancers. Targeted therapies employing ectodomain-specific p185(her2/neu) monoclonal antibodies (mAbs) have demonstrated clinical efficacy for breast cancer. Our previous studies have shown that p185(her2/neu) mAbs are able to disable the kinase activity of homomeric and heteromeric kinase complexes and induce the conversion of the malignant to normal phenotype. We previously developed a chimeric antibody chA21 that specifically inhibits the growth of p185(her2/neu)-overexpressing cancer cells in vitro and in vivo. Herein, we report the crystal structure of the single-chain Fv of chA21 in complex with an N-terminal fragment of p185(her2/neu), which reveals that chA21 binds a region opposite to the dimerization interface, indicating that chA21 does not directly disrupt the dimerization. In contrast, the bivalent chA21 leads to internalization and down-regulation of p185(her2/neu). We propose a structure-based model in which chA21 cross-links two p185(her2/neu) molecules on separate homo- or heterodimers to form a large oligomer in the cell membrane. This model reveals a mechanism for mAbs to drive the receptors into the internalization/degradation path from the inactive hypophosphorylated tetramers formed dynamically by active dimers during a "physiologic process."
- Published
- 2011
68. MicroRNA Cluster 302–367 Enhances Somatic Cell Reprogramming by Accelerating a Mesenchymal-to-Epithelial Transition
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Duanqing Pei, Wenbo Liu, Liwen Niu, Ruosi Zhang, Shipeng Feng, Liangxue Lai, Jie Cai, Maikun Teng, Xichen Bao, Jiayan Wu, Miguel A. Esteban, Baoming Qin, Longqi Liu, Athanasios Zovoilis, Baojian Liao, Yanting Xue, Xiangpeng Guo, and Biliang Zhang
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Male ,Somatic cell ,Induced Pluripotent Stem Cells ,Biology ,Biochemistry ,Mesoderm ,Kruppel-Like Factor 4 ,Mice ,SOX2 ,Transforming Growth Factor beta ,Cell Adhesion ,Animals ,Induced pluripotent stem cell ,Molecular Biology ,Cell potency ,Induced stem cells ,Stem Cells ,Epithelial Cells ,Cell Biology ,Fibroblasts ,Cell biology ,MicroRNAs ,Phenotype ,KLF4 ,Female ,Stem cell ,Reprogramming - Abstract
MicroRNAs (miRNAs) are emerging critical regulators of cell function that frequently reside in clusters throughout the genome. They influence a myriad of cell functions, including the generation of induced pluripotent stem cells, also termed reprogramming. Here, we have successfully delivered entire miRNA clusters into reprogramming fibroblasts using retroviral vectors. This strategy avoids caveats associated with transient transfection of chemically synthesized miRNA mimics. Overexpression of 2 miRNA clusters, 106a-363 and in particular 302-367, allowed potent increases in induced pluripotent stem cell generation efficiency in mouse fibroblasts using 3 exogenous factors (Sox2, Klf4, and Oct4). Pathway analysis highlighted potential relevant effectors, including mesenchymal-to-epithelial transition, cell cycle, and epigenetic regulators. Further study showed that miRNA cluster 302-367 targeted TGFβ receptor 2, promoted increased E-cadherin expression, and accelerated mesenchymal-to-epithelial changes necessary for colony formation. Our work thus provides an interesting alternative for improving reprogramming using miRNAs and adds new evidence for the emerging relationship between pluripotency and the epithelial phenotype.
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- 2011
69. Preliminary crystallographic analysis of the RNA-binding domain of HuR and its poly(U)-binding properties
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Liwen Niu, Hui Shi, Hong Wang, Heng Li, Maikun Teng, Yang Liu, Hui Zhao, Xu Li, and Huihui Liu
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Poly U ,Molecular Sequence Data ,HU Protein ,Biophysics ,Regulator ,Biology ,Crystallography, X-Ray ,Biochemistry ,ELAV-Like Protein 1 ,law.invention ,Antigen ,Structural Biology ,law ,Genetics ,Humans ,Post-transcriptional regulation ,Base Sequence ,Binding properties ,RNA-Binding Proteins ,RNA ,Condensed Matter Physics ,Crystallography ,ELAV Proteins ,Crystallization Communications ,Antigens, Surface ,Recombinant DNA ,Sequence Alignment ,Protein Binding ,Binding domain - Abstract
Human antigen R (HuR), a ubiquitously expressed member of the Hu protein family, is an important post-transcriptional regulator which has three RNA-recognition motif (RRM) domains. The two tandem N-terminal RRM domains can selectively bind to the AU-rich element (ARE), while the third one interacts with the poly(A) tail and other proteins. Here, the recombinant ARE-binding region of HuR (residues 18-186) was crystallized in space group P2(1)2(1)2, with unit-cell parameters a = 41.2, b = 133.1, c = 31.4 Å. X-ray diffraction data were collected to a resolution of 2.8 Å. Mutagenesis analysis and SPR assays revealed its poly(U)-binding properties.
- Published
- 2011
70. Carnitine palmitoyltransferase 1A prevents fatty acid-induced adipocyte dysfunction through suppression of c-Jun N-terminal kinase
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Donghai Wu, Kuai Li, Pentao Liu, Maikun Teng, Aimin Xu, Gary Sweeney, Xiaoyan Hui, Xiangping Kong, Yu Wang, and Xuefei Gao
- Subjects
medicine.medical_specialty ,Cellular differentiation ,Biochemistry ,Gene Expression Regulation, Enzymologic ,Mice ,chemistry.chemical_compound ,Insulin resistance ,3T3-L1 Cells ,Internal medicine ,Adipocyte ,Adipocytes ,medicine ,Animals ,Humans ,Carnitine ,adipocyte protein 2 ,Molecular Biology ,chemistry.chemical_classification ,Carnitine O-Palmitoyltransferase ,biology ,Fatty Acids ,c-jun ,JNK Mitogen-Activated Protein Kinases ,Fatty acid ,Cell Differentiation ,Cell Biology ,Lipid Metabolism ,medicine.disease ,Endocrinology ,chemistry ,biology.protein ,Epoxy Compounds ,Etomoxir ,medicine.drug - Abstract
The adipocyte is the principal cell type for fat storage. CPT1 (carnitine palmitoyltransferase-1) is the rate-limiting enzyme for fatty acid β-oxidation, but the physiological role of CPT1 in adipocytes remains unclear. In the present study, we focused on the specific role of CPT1A in the normal functioning of adipocytes. Three 3T3-L1 adipocyte cell lines stably expressing hCPT1A (human CPT1A) cDNA, mouse CPT1A shRNA (short-hairpin RNA) or GFP (green fluorescent protein) were generated and the biological functions of these cell lines were characterized. Alteration in CPT1 activity, either by ectopic overexpression or pharmacological inhibition using etomoxir, did not affect adipocyte differentiation. However, overexpression of hCPT1A significantly reduced the content of intracellular NEFAs (non-esterified fatty acids) compared with the control cells when adipocytes were challenged with fatty acids. The changes were accompanied by an increase in fatty acid uptake and a decrease in fatty acid release. Interestingly, CPT1A protected against fatty acid-induced insulin resistance and expression of pro-inflammatory adipokines such as TNF-α (tumour necrosis factor-α) and IL-6 (interleukin-6) in adipocytes. Further studies demonstrated that JNK (c-Jun N terminal kinase) activity was substantially suppressed upon CPT1A overexpression, whereas knockdown or pharmacological inhibition of CPT1 caused a significant enhancement of JNK activity. The specific inhibitor of JNK SP600125 largely abolished the changes caused by the shRNA- and etomoxir-mediated decrease in CPT1 activity. Moreover, C2C12 myocytes co-cultured with adipocytes pre-treated with fatty acids displayed altered insulin sensitivity. Taken together, our findings have identified a favourable role for CPT1A in adipocytes to attenuate fatty acid-evoked insulin resistance and inflammation via suppression of JNK.
- Published
- 2011
71. Crystal structure of the pyrimidine 5′-nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5′-monophosphate provides further insight into ligand binding
- Author
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Yujie Zhang, Liwen Niu, Nuo Shi, Hong-Kai Chen, Maikun Teng, and Yongxiang Gao
- Subjects
Models, Molecular ,Binding Sites ,Saccharomyces cerevisiae Proteins ,Amino Acid Motifs ,biology ,Chemistry ,Stereochemistry ,Saccharomyces cerevisiae ,Crystal structure ,Plasma protein binding ,Crystallography, X-Ray ,Ligands ,biology.organism_classification ,Biochemistry ,Sequence Analysis, Protein ,Structural Biology ,Binding site ,Uridine Monophosphate ,5'-Nucleotidase ,Molecular Biology ,PYRIMIDINE 5 NUCLEOTIDASE ,Protein Binding ,Uridine 5' Monophosphate - Published
- 2011
72. Crystal structure of isoamyl acetate-hydrolyzing esterase from Saccharomyces cerevisiae reveals a novel active site architecture and the basis of substrate specificity
- Author
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Liwen Niu, Ye Yuan, Kuai Li, Jinming Ma, Yongxiang Gao, Wei Zhao, Maikun Teng, Honghua Ge, and Qianda Lu
- Subjects
Saccharomyces cerevisiae Proteins ,Stereochemistry ,Recombinant Fusion Proteins ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Isoamyl acetate ,Crystal structure ,Crystallography, X-Ray ,Biochemistry ,Esterase ,chemistry.chemical_compound ,Structural Biology ,Catalytic Domain ,Hydrolase ,Amino Acid Sequence ,Molecular Biology ,Enzyme Assays ,biology ,Active site ,biology.organism_classification ,chemistry ,Structural Homology, Protein ,biology.protein ,Substrate specificity ,Protein Multimerization ,Carboxylic Ester Hydrolases ,Sequence Alignment - Published
- 2010
73. Crystal structure of Glutamate1-semialdehyde aminotransferase from Bacillus subtilis with bound pyridoxamine-5′-phosphate
- Author
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Liwen Niu, Jun Fan, Honghua Ge, Maikun Teng, Yongxiang Gao, and Xinhuai Lv
- Subjects
Protein Conformation ,Transamination ,Stereochemistry ,Molecular Sequence Data ,Biophysics ,Isomerase ,Bacillus subtilis ,Crystal structure ,Crystallography, X-Ray ,Biochemistry ,Substrate Specificity ,chemistry.chemical_compound ,Molecular replacement ,Amino Acid Sequence ,Intramolecular Transferases ,Molecular Biology ,Synechococcus ,chemistry.chemical_classification ,biology ,Substrate (chemistry) ,Cooperative binding ,Cell Biology ,biology.organism_classification ,Crystallography ,chemistry ,Pyridoxamine ,Protein Binding - Abstract
Glutamate-1-semialdehyde aminotransferase (GSA-AT), also named glutamate-1-semialdehyde aminomutase (GSAM), a pyridoxamine-5′-phosphate (PMP)/pyridoxal-5′-phosphate (PLP) dependent enzyme, catalyses the transamination of the substrate glutamate-1-semialdehyde (GSA) to the product 5-Aminolevulinic acid (ALA) by an unusual intramolecular exchange of amino and oxo groups within the catalytic intermediate 4,5-diaminovalerate (DAVA). This paper presents the crystal structure of GSA-AT from Bacillus subtilis (GSA-ATBsu) in its PMP-bound form at 2.3 A resolution. The structure was determined by molecular replacement using the Synechococcus GSAM (GSAMSyn) structure as a search model. Unlike the previous reported GSAM/GSA-AT structures, GSA-ATBsu is a symmetric homodimer in the PMP-bound form, which shows the structural symmetry at the gating loop region with open state, as well as identical cofactor (PMP) binding in each monomer. This observation of PMP in combination with an “open” lid supports one characteristic feature for this enzyme, as the catalyzed reaction is believed to be initiated by PMP. Furthermore, the symmetry of GSA-ATBsu structure challenges the previously proposed negative cooperativity between monomers of this enzyme.
- Published
- 2010
74. Coevolution is a short-distance force at the protein interaction level and correlates with the modular organization of protein networks
- Author
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Liwen Niu, Maikun Teng, Jiarui Wu, Zhi Liang, and Meng Xu
- Subjects
Saccharomyces cerevisiae Proteins ,Modularity (biology) ,Biophysics ,Modularity ,Biology ,Biochemistry ,Protein–protein interaction ,Evolution, Molecular ,Fungal Proteins ,Structural Biology ,Interaction network ,Protein Interaction Mapping ,Genetics ,Protein Interaction Domains and Motifs ,Databases, Protein ,Molecular Biology ,Coevolution ,business.industry ,Computational Biology ,Cell Biology ,Modular design ,Protein interaction network ,Short distance ,Close relationship ,Evolutionary biology ,business ,Protein network - Abstract
We investigated what roles coevolution plays in shaping yeast protein interaction network (PIN). We found that the extent of coevolution between two proteins decreases rapidly as their interacting distance on the PIN increases, suggesting coevolutionary constraint is a short-distance force at the molecular level. We also found that protein–protein interactions (PPIs) with strong coevolution tend to be enriched in interconnected clusters, whereas PPIs with weak coevolution are more frequently present at inter-cluster region. The findings indicate the close relationship between coevolution and modular organization of PINs, and may provide insights into evolution and modularity of cellular networks.
- Published
- 2010
75. Structure of native laccase B fromTrametessp. AH28-2
- Author
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Honghua Ge, Yuzhi Hong, Maikun Teng, Liwen Niu, Yongxiang Gao, Yazhong Xiao, and Min Zhang
- Subjects
Stereochemistry ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Crystallography, X-Ray ,Biochemistry ,Substrate Specificity ,Conserved sequence ,Trametes ,Structural Biology ,Oxidoreductase ,Genetics ,Structural Communications ,Amino Acid Sequence ,Binding site ,Peptide sequence ,Conserved Sequence ,Laccase ,chemistry.chemical_classification ,Binding Sites ,biology ,Protein Stability ,Condensed Matter Physics ,biology.organism_classification ,Enzyme ,chemistry ,Structural Homology, Protein ,Sequence Alignment - Abstract
Fungal laccases are oxidoreductases that belong to the multinuclear copper-containing oxidases. They are able to oxidize a wide range of substrates, preferably phenolic compounds, which makes them suitable for employment in the bioremediation of soil and water as well as in other biotechnological applications. Here, the structural analysis of natural laccase B (LacB) from Trametes sp. AH28-2 is presented. This structure provides the opportunity to study the natural post-translational modifications of the enzyme. The overall fold shows a high homology to those of previously analyzed laccases with known three-dimensional structure. However, LacB contains a new structural element, a protruding loop near the substrate-binding site, compared with the previously reported laccase structures. This unique structural feature may be involved in modulation of the substrate recognition of LacB.
- Published
- 2010
76. Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing
- Author
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Jihui Wu, Yingxia Hu, Maikun Teng, Xu Li, Liwen Niu, Jianping Liu, Hongda Huang, Bo O. Zhou, Yunyu Shi, Jin-Qiu Zhou, Shanshan Wang, Jianye Zang, and Yiwei Liu
- Subjects
Models, Molecular ,Saccharomyces cerevisiae Proteins ,Blotting, Western ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Biology ,Crystallography, X-Ray ,Models, Biological ,Biochemistry ,Histones ,Histone H1 ,Gene Expression Regulation, Fungal ,Heterochromatin ,Histone methylation ,Histone H2A ,Histone code ,Nucleosome ,Amino Acid Sequence ,Histone octamer ,DNA, Fungal ,Molecular Biology ,Silent Information Regulator Proteins, Saccharomyces cerevisiae ,Genetics ,Binding Sites ,Sequence Homology, Amino Acid ,Cell Biology ,Nucleosomes ,Protein Structure, Tertiary ,Cell biology ,DNA-Binding Proteins ,Histone methyltransferase ,Protein Structure and Folding ,Mutation ,Heterochromatin protein 1 ,Molecular Chaperones ,Protein Binding - Abstract
Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 A crystal structure of the core domain of Rtt106p, which adopts an unusual "double pleckstrin homology" domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.
- Published
- 2010
77. Loss-of-Function Mutations in the PRPS1 Gene Cause a Type of Nonsyndromic X-linked Sensorineural Deafness, DFN2
- Author
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Zhanguo Jin, Li L. Du, Jianzhong Li, Jonathan G. Seidman, Albena Kantardzhieva, Denise Yan, Maria Bitner-Glindzicz, Zheng-Yi Chen, Dongyi Han, Xiaomei Ouyang, Christine E. Seidman, Jing Cheng, Maikun Teng, Xu Li, Youqin Wang, Roland D. Eavey, Huijun Yuan, Xuezhong Liu, Bing Han, Pu Dai, Heng Xu, and Xiangyin Kong
- Subjects
Adult ,Male ,Models, Molecular ,Heterozygote ,Candidate gene ,Hearing loss ,Hearing Loss, Sensorineural ,Locus (genetics) ,Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Report ,Ribose-Phosphate Pyrophosphokinase ,otorhinolaryngologic diseases ,Genetics ,medicine ,Animals ,Humans ,Missense mutation ,Genetics(clinical) ,Nonsyndromic deafness ,Gene ,Genetics (clinical) ,Loss function ,Spiral ganglion ,Aged ,030304 developmental biology ,Chromosomes, Human, X ,0303 health sciences ,Genetic Diseases, X-Linked ,Middle Aged ,medicine.disease ,Pedigree ,Phenotype ,medicine.anatomical_structure ,Mutation ,Female ,medicine.symptom ,030217 neurology & neurosurgery - Abstract
We report a large Chinese family with X-linked postlingual nonsyndromic hearing impairment in which the critical linkage interval spans a genetic distance of 5.41 cM and a physical distance of 15.1 Mb that overlaps the DFN2 locus. Mutation screening of the PRPS1 gene in this family and in the three previously reported DFN2 families identified four different missense mutations in PRPS1. These mutations result in a loss of phosphoribosyl pyrophosphate (PRPP) synthetase 1 activity, as was shown in silico by structural analysis and was shown in vitro by enzymatic activity assays in erythrocytes and fibroblasts from patients. By in situ hybridization, we demonstrate expression of Prps1 in murine vestibular and cochlea hair cells, with continuous expression in hair cells and postnatal expression in the spiral ganglion. Being the second identified gene associated with X-linked nonsyndromic deafness, PRPS1 will be a good candidate gene for genetic testing for X-linked nonsyndromic hearing loss.
- Published
- 2010
78. Structural basis of the autolysis of AaHIV suggests a novel target recognizing model for ADAM/reprolysin family proteins
- Author
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Maikun Teng, Yongxiang Gao, Jianye Zang, Liwen Niu, Xiao Zhang, Zhiqiang Zhu, Yang Yu, and Zhongliang Zhu
- Subjects
Autolysis (biology) ,Proteolysis ,Molecular Sequence Data ,Biophysics ,Biology ,Biochemistry ,Catalytic Domain ,Crotalid Venoms ,Hydrolase ,medicine ,Disintegrin ,Animals ,Amino Acid Sequence ,Molecular Biology ,Metalloproteinase ,medicine.diagnostic_test ,Hydrolysis ,Cell Biology ,Protein Structure, Tertiary ,Cell biology ,carbohydrates (lipids) ,ADAM Proteins ,Models, Chemical ,Docking (molecular) ,Snake venom ,Jararhagin ,biology.protein ,Agkistrodon - Abstract
AaHIV, a P-III-type snake venom metalloproteinase (SVMP), consists of metalloproteinase/disintegrin/cysteine-rich (MDC) domains and is homologous to a disintegrin and metalloproteinase (ADAM) family proteins. Similar to brevilysin H6 and jararhagin, AaHIV can easily autolyse to release a stable protein named acucetin, which contains disintegrin-like and cysteine-rich domains. In this study, we determined the crystal structure of AaHIV and investigated the autolysis mechanism. Based on the structure of AaHIV and the results from docking experiments, we present a new model for target recognition in which two protein molecules form a functional unit, and the DC domain of one molecule is used for target recognition while the M-domain of the other is used for target proteolysis. Our results shed new light on the mechanism of target recognition and processing in ADAM/reprolysin family proteins.
- Published
- 2009
79. Monomeric tRNA (m7G46) methyltransferase fromEscherichia colipresents a novel structure at the function-essential insertion
- Author
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Yongxiang Gao, Qi Liu, Liwen Niu, Maikun Teng, Weili Yang, and Huihao Zhou
- Subjects
Models, Molecular ,tRNA Methyltransferases ,Methyltransferase ,Protein Conformation ,Escherichia coli Proteins ,medicine.disease_cause ,Biochemistry ,Structure-Activity Relationship ,chemistry.chemical_compound ,Monomer ,chemistry ,Structural Biology ,Transfer RNA ,Escherichia coli ,medicine ,Transferase ,Molecular Biology ,Function (biology) - Published
- 2009
80. Crystal structure of NusG N-terminal (NGN) domain fromMethanocaldococcus jannaschiiand its interaction with rpoE″
- Author
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Liwen Niu, Huihao Zhou, Qi Liu, Yongxiang Gao, and Maikun Teng
- Subjects
biology ,Methanocaldococcus jannaschii ,Computational biology ,Crystal structure ,biology.organism_classification ,Biochemistry ,Crystallography ,chemistry.chemical_compound ,chemistry ,Structural Biology ,Transcription (biology) ,Docking (molecular) ,RNA polymerase ,Molecular Biology ,Transcription factor ,Bacteria ,Archaea - Abstract
Transcription in archaea employs a eukaryotic-type transcription apparatus but uses bacterial-type transcription factors. NusG is one of the few archaeal transcription factors whose orthologs are essential in both bacteria and eukaryotes. Archaeal NusG is composed of only an NusG N-terminal (NGN) domain and a KOW domain, which is similar to bacterial NusG but not to the eukaryotic ortholog, Spt5. However, archaeal NusG was confirmed recently to form a complex with rpoE″ that was similar to the Spt5-Spt4 complex. Thus, archaeal NusG presents hybrid features of Spt5 and bacterial NusG. Here we report the crystal structure of NGN from the archaea Methanocaldococcus jannaschii (MjNGN). MjNGN folds to an α-β-α sandwich without the appendant domain of bacterial NGNs, and forms a unique homodimer in crystal and solution. MjNGN alone was found to be sufficient for rpoE″ binding and an MjNGN-rpoE″ model has been constructed by rigid docking. Proteins 2009. © 2009 Wiley-Liss, Inc.
- Published
- 2009
81. Crystallization and Preliminary X-Ray Diffraction Analysis of ARO9, an Aromatic Aminotransferase from Saccharomyces cerevisiae
- Author
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Shuilong Tong, Liwen Niu, Maikun Teng, Xu Li, Hui Chen, and Hua Huang
- Subjects
Saccharomyces cerevisiae Proteins ,Transamination ,Stereochemistry ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Biology ,Crystallography, X-Ray ,Biochemistry ,law.invention ,chemistry.chemical_compound ,Structural Biology ,law ,Aromatic amino acids ,Amino Acid Sequence ,Crystallization ,Transaminases ,chemistry.chemical_classification ,Resolution (electron density) ,Tryptophan ,General Medicine ,biology.organism_classification ,Crystallography ,chemistry ,X-ray crystallography ,Orthorhombic crystal system - Abstract
Saccharomyces cerevisae ARO9 protein, an aromatic aminotransferase II, catalyzes the transamination step of the catabolism of aromatic amino acids, mainly tryptophan. ARO9 also belongs to a novel subfamily of enzymes within the aminotransferase subgroup I. Crystals of ARO9 protein have been grown using the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 75.6 A, b = 117.5 A, c = 134.9 A. Diffraction data were collected to a resolution of 2.6 A using a rotating-anode X-ray source. Analysis indicates the presence of two molecules in an asymmetric unit.
- Published
- 2009
82. Structure of the second PDZ domain from human zonula occludens 2
- Author
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Liwen Niu, Jiawen Wu, Shuilong Tong, Zhiqiang Zhu, Hui Chen, Maikun Teng, and Xu Li
- Subjects
Dimer ,Protein subunit ,PDZ domain ,Biophysics ,Membrane Proteins ,PDZ Domains ,Biology ,Crystallography, X-Ray ,Zonula Occludens-2 Protein ,Condensed Matter Physics ,Biochemistry ,Protein Structure, Secondary ,SH3 domain ,Cell biology ,chemistry.chemical_compound ,Membrane protein ,chemistry ,Structural Biology ,Domain (ring theory) ,Genetics ,Humans ,Structural Communications ,Molecular replacement ,Protein Multimerization - Abstract
Human zonula occludens 2 (ZO-2) protein is a multi-domain protein that consists of an SH3 domain, a GK domain and three copies of a PDZ domain with slight divergence. The three PDZ domains act as protein-recognition modules that may mediate protein assembly and subunit localization. The crystal structure of the second PDZ domain of ZO-2 (ZO-2 PDZ2) was determined by molecular replacement at 1.75 A resolution, revealing a dimer in the asymmetric unit. The dimer is stabilized by extensive symmetrical domain-swapping of the beta1 and beta2 strands. Structural comparison shows that the ZO-2 PDZ2 homodimer may have a similar ligand-binding pattern to the ZO-1 PDZ2-connexin 43 complex.
- Published
- 2009
83. Blocking effect and crystal structure of natrin toxin, a cysteine-rich secretory protein from Naja atra venom that targets the BK(sub Ca) channel
- Author
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Jing Wang, Qingqiu Huang, Quan Hao, Bing Shen, Qun Liu, Min Guo, Liwen Niu, Xiaohua Lou, Maikun Teng, Yuanyuan Duan, and Xin Ping Cheng
- Subjects
Potassium in the body -- Research ,Cysteine proteinases -- Structure ,Cysteine proteinases -- Research ,Crystals -- Structure ,Crystals -- Research ,Biological sciences ,Chemistry - Abstract
Natrin purified from Naja atra venom, a member of the cysteine-rich secretory proteins (CRISP) family, can induce a contractile response in the endothelium-denuded thoracic aorta of mouse which are contracted by a high-K(super +) solution. The experiments show that it could block the high-conductance calcium-activated potassium (BK(sub Ca)) channel that suggest that only a single natrin molecule is required to bind an ion channel to block BK(sub a) current.
- Published
- 2005
84. Crystal structure of human osteoclast stimulating factor
- Author
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Liwen Niu, Shuilong Tong, Maikun Teng, Zhiqiang Zhu, Xiao Zhang, Yongxiang Gao, and Huihao Zhou
- Subjects
Chemistry ,Plasma protein binding ,Crystal structure ,Biochemistry ,SH3 domain ,medicine.anatomical_structure ,Protein structure ,Structural Biology ,Osteoclast ,X-ray crystallography ,medicine ,Ankyrin repeat ,Osteoclast stimulating factor ,Molecular Biology - Published
- 2008
85. Core Structure of the Yeast Spt4-Spt5 Complex: A Conserved Module for Regulation of Transcription Elongation
- Author
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Fei Xu, Jena Yamada, Maikun Teng, Liwen Niu, Thea A. Egelhofer, Grant A. Hartzog, Min Guo, and Yongxiang Gao
- Subjects
Models, Molecular ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Chromosomal Proteins, Non-Histone ,Protein Conformation ,Archaeal Proteins ,Molecular Sequence Data ,Saccharomyces cerevisiae ,Sequence alignment ,RNA polymerase II ,Crystallography, X-Ray ,Article ,Conserved sequence ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Structural Biology ,Amino Acid Sequence ,Molecular Biology ,Conserved Sequence ,030304 developmental biology ,Genetics ,Regulation of gene expression ,0303 health sciences ,biology ,030302 biochemistry & molecular biology ,Nuclear Proteins ,DNA ,biology.organism_classification ,Archaea ,Elongation factor ,chemistry ,biology.protein ,Transcriptional Elongation Factors ,Sequence Alignment ,Protein Binding - Abstract
Spt4-Spt5 complex is an essential RNA Polymerase II elongation factor found in all eukaryotes and important for gene regulation. We report here the crystal structure of Saccharomyces cerevisiae Spt4 bound to the NGN domain of Spt5. This structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4. Mutations that disrupt this interaction disrupt the complex. Residues forming this pivotal interaction are conserved in the archaeal homologues of Spt4 and Spt5, which we demonstrate to also form a complex. Even though bacteria lack an Spt4 homologue, the NGN domains of Spt5 and its bacterial homologues are structurally similar. Spt4 is located at a position that may help to maintain the functional conformation of the following KOW domain in Spt5. This structural and evolutionary perspective of the Spt4-Spt5 complex and its homologues suggest that it is an ancient, core component of the transcription elongation machinery.
- Published
- 2008
86. Crystal structure of the C-terminal conserved domain of human GRP, a galectin-related protein, reveals a function mode different from those of galectins
- Author
-
Dongwen Zhou, Liwen Niu, Honghua Ge, Jianping Sun, Maikun Teng, and Yongxiang Gao
- Subjects
chemistry.chemical_classification ,Galectins ,Molecular Sequence Data ,Protein domain ,Lectin ,Crystal structure ,Biology ,Crystallography, X-Ray ,Biochemistry ,Protein Structure, Secondary ,Protein Structure, Tertiary ,Cell biology ,chemistry ,Terminal (electronics) ,Structural Biology ,C-type lectin ,Lectins ,biology.protein ,Humans ,Amino Acid Sequence ,Glycoprotein ,Molecular Biology ,Conserved Sequence ,Function (biology) ,Galectin - Published
- 2008
87. Crystal structure and possible dimerization of the single RRM of human PABPN1
- Author
-
Shuilong Tong, Liwen Niu, Honghua Ge, Yongxiang Gao, Maikun Teng, and Dongwen Zhou
- Subjects
RNA recognition motif ,biology ,Stereochemistry ,Chemistry ,Binding protein ,RNA-binding protein ,Crystal structure ,Biochemistry ,Poly(A)-Binding Protein II ,Protein structure ,Structural Biology ,Poly(A)-binding protein ,biology.protein ,Molecular Biology ,Peptide sequence - Published
- 2008
88. Crystal structure of Natratoxin, a novel snake secreted phospholipaseA2 neurotoxin from Naja atra venom inhibiting A-type K+ currents
- Author
-
Liwen Niu, Hui-Li Wang, Xiaowei Hou, Pu Hu, Maikun Teng, Lei Sun, Shan-Shan Yu, Ping Zhang, Di-Yun Ruan, Shu Wang, Zhiqiang Zhu, and Ming Wang
- Subjects
Patch-Clamp Techniques ,Potassium Channels ,Protein Conformation ,Guinea Pigs ,Venom ,Gating ,Biology ,Crystallography, X-Ray ,Biochemistry ,Protein structure ,Structural Biology ,Potassium Channel Blockers ,Animals ,Neurotoxin ,Elapidae ,Patch clamp ,Rats, Wistar ,Molecular Biology ,Ion channel ,Elapid Venoms ,Hyperpolarization (biology) ,Rats ,Phospholipases A2 ,Snake venom ,Biophysics - Abstract
Snake secreted phospholipasesA2 (sPLA2s) are widely used as pharmacological tools to investigate their role in diverse pathophysiological processes. Some members of snake venom sPLA2s have been found to block voltage-activated K(+) channels (K(v) channels). However, most studies involved in their effects on ion channels were indirectly performed on motor nerve terminals while few studies were directly done on native neurons. Here, a novel snake sPLA2 peptide neurotoxin, Natratoxin, composed of 119 amino acid residues and purified from Naja atra venom was reported. It was characterized using whole-cell patch-clamp in acutely dissociated rat dorsal root ganglion (DRG) neurons. It was found to effectively inhibit A-type K(+) currents and cause alterations of channel gating characters, such as the shifts of steady-state activation and inactivation curves to hyperpolarization direction and changes of V(1/2) and slope factor. Therefore, Natratoxin was suggested to be a gating modifier of K(v) channel. In addition, this inhibitory effect was found to be independent of its enzymatic activity. These results suggested that the toxin enacted its inhibitory effect by binding to K(v) channel. To further elucidate the structural basis for this electrophysiological phenomenon, we determined the crystal structure of Natratoxin at 2.2 A resolution by molecular replacement method and refined to an R-factor of 0.190. The observed overall fold has a different structural organization from other K(+) channel inhibitors in animal toxins. Compared with other K(v) channel inhibitors, a similar putative functional surface in its C-terminal was revealed to contribute to protein-protein interaction in such a blocking effect. Our results demonstrated that the spatial distribution of key amino acid residues matters most in the recognition of this toxin towards its channel target rather than its type of fold.
- Published
- 2008
89. X-ray absorption near edge structure study on Acutolysin-C, a zinc-metalloproteinase from Agkistrodon acutus venom: Insight into the acid-inactive mechanism
- Author
-
Wangsheng Chu, Maurizio Benfatto, Shujun Li, Maikun Teng, Tiandou Hu, Bin Gao, Ziyu Wu, Wei Zhao, Yiwei Liu, and Liwen Niu
- Subjects
Metalloproteinase ,chemistry.chemical_element ,Venom ,Zinc ,Atomic and Molecular Physics, and Optics ,XANES ,Analytical Chemistry ,Catalysis ,Residue (chemistry) ,Crystallography ,chemistry ,Structural change ,Molecule ,Instrumentation ,Spectroscopy - Abstract
Acutolysin-C, a snake-venom zinc metalloproteinase, displays a distinct pH-dependent proteolytic activity, which has been tentatively assigned to a structural change of the zinc-containing catalytic center. In this work we compare X-ray absorption near-edge structure (XANES) experimental spectra at the Zn K -edge and theoretical calculations of solutions at different pH values. The experimental data show clear differences confirmed by a best fit using the MXAN procedure. The results show that, when pH decreases from pH 8.0 to pH 3.0, the zinc-coordinating catalytic water molecule moves far from the Glu143 residue that is considered to play an essential role in the proteolytic process. Data suggests that this is the possible mechanism that deactivates the metalloproteinase.
- Published
- 2007
90. Quantitative investigation of two metallohydrolases by X-ray absorption spectroscopy near-edge spectroscopy
- Author
-
Liwen Niu, Maikun Teng, Wangsheng Chu, Maurizio Benfatto, Ziyu Wu, N. Shi, Meijuan Yu, Deng-Yi Chen, Weimin Gong, Weichang Zhao, D.W. Zhou, Feifei Yang, Augusto Marcelli, and Guo Xiaoling
- Subjects
Physics ,Nuclear and High Energy Physics ,Crystallography ,X-ray absorption spectroscopy ,Molecular geometry ,Extended X-ray absorption fine structure ,Absorption spectroscopy ,Synchrotron radiation ,Spectroscopy ,Absorption (electromagnetic radiation) ,Instrumentation ,XANES - Abstract
The last several years have witnessed a tremendous increase in biological applications using X-ray absorption spectroscopy (BioXAS), thanks to continuous advancements in synchrotron radiation (SR) sources and detector technology. However, XAS applications in many biological systems have been limited by the intrinsic limitations of the Extended X-ray Absorption Fine Structure (EXAFS) technique e.g., the lack of sensitivity to bond angles. As a consequence, the application of the X-ray absorption near-edge structure (XANES) spectroscopy changed this scenario that is now continuously changing with the introduction of the first quantitative XANES packages such as Minut XANES (MXAN). Here we present and discuss the XANES code MXAN, a novel XANES-fitting package that allows a quantitative analysis of experimental data applied to Zn K-edge spectra of two metalloproteins: Leptospira interrogans Peptide deformylase (LiPDF) and acutolysin-C, a representative of snake venom metalloproteinases (SVMPs) from Agkistrodon acutus venom. The analysis on these two metallohydrolases reveals that proteolytic activities are correlated to subtle conformation changes around the zinc ion. In particular, this quantitative study clarifies the occurrence of the LiPDF catalytic mechanism via a two-water-molecules model, whereas in the acutolysin-C we have observed a different proteolytic activity correlated to structural changes around the zinc ion induced by pH variations.
- Published
- 2007
91. Crystal Structure of Uroporphyrinogen Decarboxylase from Bacillus subtilis
- Author
-
Liwen Niu, Quan Hao, Jun Fan, Qun Liu, and Maikun Teng
- Subjects
Models, Molecular ,Uroporphyrinogen III synthase ,Uroporphyrinogen III decarboxylase ,Molecular Sequence Data ,Bacillus subtilis ,Crystallography, X-Ray ,Microbiology ,Coproporphyrinogen III ,Cofactor ,chemistry.chemical_compound ,Structural Biology ,Catalytic Domain ,Uroporphyrinogen Decarboxylase ,Amino Acid Sequence ,Protein Structure, Quaternary ,Molecular Biology ,Heme ,Conserved Sequence ,biology ,biology.organism_classification ,Lyase ,Biochemistry ,chemistry ,Uroporphyrinogen III ,biology.protein ,Dimerization ,Sequence Alignment - Abstract
Uroporphyrinogen decarboxylase (UROD) is a branch point enzyme in the biosynthesis of the tetrapyrroles. It catalyzes the decarboxylation of four acetate groups of uroporphyrinogen III to yield coproporphyrinogen III, leading to heme and chlorophyll biosynthesis. UROD is a special type of nonoxidative decarboxylase, since no cofactor is essential for catalysis. In this work, the first crystal structure of a bacterial UROD, Bacillus subtilis UROD (UROD Bs), has been determined at a 2.3 Å resolution. The biological unit of UROD Bs was determined by dynamic light scattering measurements to be a homodimer in solution. There are four molecules in the crystallographic asymmetric unit, corresponding to two homodimers. Structural comparison of UROD Bs with eukaryotic URODs reveals a variation of two loops, which possibly affect the binding of substrates and release of products. Structural comparison with the human UROD-coproporphyrinogen III complex discloses a similar active cleft, with five invariant polar residues (Arg29, Arg33, Asp78, Tyr154, and His322) and three invariant hydrophobic residues (Ile79, Phe144, and Phe207), in UROD Bs. Among them, Asp78 may interact with the pyrrole NH groups of the substrate, and Arg29 is a candidate for positioning the acetate groups of the substrate. Both residues may also play catalytic roles. Copyright © 2007, American Society for Microbiology. All Rights Reserved., link_to_subscribed_fulltext
- Published
- 2007
92. Structural analysis of Ca
- Author
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Xiaoting, Qiu, Junyi, Ge, Yongxiang, Gao, Maikun, Teng, and Liwen, Niu
- Subjects
Models, Molecular ,Mice ,Synaptotagmins ,Binding Sites ,Protein Domains ,Animals ,Humans ,Calcium ,Amino Acid Sequence ,Membrane Fusion ,Phospholipids ,Protein Binding ,Rats - Abstract
Synaptotagmins constitute a family of multifunctional integral membrane proteins found predominantly on vesicles in neural and endocrine tissues. 17 isoforms of synaptotagmin family in mammals have been identified, 7 isoforms among them are known to be able to bind Ca
- Published
- 2015
93. Crystallographic analysis of RsmA, a ribosomal RNA small subunit methyltransferase A from Staphylococcus aureus
- Author
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Yang Liu, Yuwei Zhu, Maikun Teng, and Xu Li
- Subjects
Staphylococcus aureus ,Recombinant Fusion Proteins ,Molecular Sequence Data ,Biophysics ,Gene Expression ,macromolecular substances ,Addenda and Errata ,Crystallography, X-Ray ,Biochemistry ,Methylation ,Research Communications ,Structural Biology ,Genetics ,Escherichia coli ,Amino Acid Sequence ,Cloning, Molecular ,RsmA ,Methyltransferases ,methyltransferase A ,Condensed Matter Physics ,enzymes and coenzymes (carbohydrates) ,RNA, Bacterial ,corrigendum ,RNA, Ribosomal ,biological sciences ,health occupations ,bacteria ,Crystallization ,ribosomal RNA ,Sequence Alignment - Abstract
A correction is made to the article by Liu et al. [(2015), Acta Cryst. F71, 1063–1066]., The paper by Liu et al. [(2015), Acta Cryst. F71, 1063–1066] is corrected.
- Published
- 2015
94. Maize uroporphyrinogen III methyltransferase: Overexpression of the functional gene fragments in Escherichia coli and one-step purification
- Author
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Deqiang Wang, Liwen Niu, Min Guo, Jun Fan, Maikun Teng, and Zhi Liang
- Subjects
Signal peptide ,Recombinant Fusion Proteins ,Restriction Mapping ,Mutant ,Biology ,medicine.disease_cause ,Zea mays ,chemistry.chemical_compound ,Biosynthesis ,Complementary DNA ,Escherichia coli ,medicine ,Cloning, Molecular ,Plant Proteins ,Sequence Deletion ,chemistry.chemical_classification ,Circular Dichroism ,Escherichia coli Proteins ,Methyltransferases ,Molecular biology ,Amino acid ,Molecular Weight ,Open reading frame ,chemistry ,Biochemistry ,Mutagenesis ,Uroporphyrinogen III ,Chromatography, Gel ,Electrophoresis, Polyacrylamide Gel ,Biotechnology - Abstract
S-Adenosyl-L-methionine: uroporphyrinogen III methyltransferase (SUMT), a key regulatory enzyme, converts uroporphyrinogen III to precorrin-2 in the porphinoids biosynthesis. In this study, the mature SUMT was signified that the maize SUMT precursor encoded by the open reading frame of maize SUMT cDNA was deleted the first 91 amino acids constituting the postulated signal peptide. Several mature SUMT fusion and deletion mutants were conducted. It actively expressed in Escherichia coli that the mature SUMT, or the truncated one deleting the C-terminal extra 52 amino acids based on SUMT sequence comparisons. On the contrary, it expressed as an inclusion body in E. coli that the mature SUMT fusion mutant, the SUMT precursor, or the mature SUMT deleting the N-terminal 36 amino acids including glycine-rich region involved directly in SAM binding. The purified His6-tagged mature SUMT was homodimer with a molecular weight of 34 kDa, as shown by SDS-PAGE, 52 kDa using gel-filtration chromatography, and 79 kDa by dynamic light scattering assay. Red fluorescent compounds were associated with the recombinant mature SUMT which were identified as sirohydrochlorin and trimethylpyrrocorphin by spectroscopic analysis. This association slightly altered the protein secondary structure confirmed by circular dichroism assay.
- Published
- 2006
95. Structure of the DNA-binding domain of the response regulator SaeR from Staphylococcus aureus
- Author
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Baolin Sun, Xu Zhang, Maikun Teng, Yuwei Zhu, Xiaojiao Fan, Xu Li, and Liwen Niu
- Subjects
Staphylococcus aureus ,Virulence ,Plasma protein binding ,Biology ,medicine.disease_cause ,Crystallography, X-Ray ,DNA-binding protein ,Protein Structure, Secondary ,Bacterial Proteins ,Structural Biology ,medicine ,Humans ,Promoter Regions, Genetic ,Gene ,Genetics ,Physiological function ,General Medicine ,DNA-binding domain ,Gene Expression Regulation, Bacterial ,Staphylococcal Infections ,Protein Structure, Tertiary ,DNA-Binding Proteins ,Response regulator ,Protein Binding ,Transcription Factors - Abstract
The SaeR/S two-component regulatory system is essential for controlling the expression of many virulence factors inStaphylococcus aureus. SaeR, a member of the OmpR/PhoB family, is a response regulator with an N-terminal regulatory domain and a C-terminal DNA-binding domain. In order to elucidate how SaeR binds to the promoter regions of target genes, the crystal structure of the DNA-binding domain of SaeR (SaeRDBD) was solved at 2.5 Å resolution. The structure reveals that SaeRDBDexists as a monomer and has the canonical winged helix–turn–helix module. EMSA experiments suggested that full-length SaeR can bind to the P1 promoter and that the binding affinity is higher than that of its C-terminal DNA-binding domain. Five key residues on the winged helix–turn–helix module were verified to be important for binding to the P1 promoterin vitroand for the physiological function of SaeRin vivo.
- Published
- 2014
96. mFASD: a structure-based algorithm for discriminating different types of metal-binding sites
- Author
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Wei He, Zhi Liang, Liwen Niu, and Maikun Teng
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Statistics and Probability ,Models, Molecular ,Source code ,Computer science ,Protein Conformation ,media_common.quotation_subject ,Metal ions in aqueous solution ,Stability (learning theory) ,Biochemistry ,Measure (mathematics) ,Set (abstract data type) ,Protein structure ,Humans ,Computer Simulation ,Sensitivity (control systems) ,Binding site ,Molecular Biology ,media_common ,Binding Sites ,Metal binding ,Discriminant Analysis ,Proteins ,Biological activity ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,Metals ,Structure based ,Algorithm ,Algorithms - Abstract
Motivation: A large number of proteins contain metal ions that are essential for their stability and biological activity. Identifying and characterizing metal-binding sites through computational methods is necessary when experimental clues are lacking. Almost all published computational methods are designed to distinguish metal-binding sites from non-metal-binding sites. However, discrimination between different types of metal-binding sites is also needed to make more accurate predictions. Results: In this work, we proposed a novel algorithm called mFASD, which could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction. mFASD captures the characteristics of a metal-binding site by investigating the local chemical environment of a set of functional atoms that are considered to be in contact with the bound metal. Then a distance measure defined on functional atom sets enables the comparison between different metal-binding sites. The algorithm could discriminate most types of metal-binding sites from each other with high sensitivity and accuracy. We showed that cascading our method with existing ones could achieve a substantial improvement of the accuracy for metal-binding site prediction. Availability and implementation: Source code and data used are freely available from http://staff.ustc.edu.cn/∼liangzhi/mfasd/ Contact: liangzhi@ustc.edu.cn or hwkobe@mail.ustc.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
- Published
- 2014
97. Blocking Effect and Crystal Structure of Natrin Toxin, a Cysteine-Rich Secretory Protein from Naja atra Venom that Targets the BKCa Channel
- Author
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Bing Shen, Yuanyuan Duan, Maikun Teng, Jing Wang, Qun Liu, Quan Hao, Liwen Niu, Min Guo, Xin Ping Cheng, Qingqiu Huang, and Xiaohua Lou
- Subjects
Male ,Models, Molecular ,Molecular Sequence Data ,Clostridium difficile toxin A ,Aorta, Thoracic ,Venom ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,Muscle, Smooth, Vascular ,Mice ,Potassium Channels, Calcium-Activated ,Cysteine-rich secretory protein ,Crotalid Venoms ,Potassium Channel Blockers ,medicine ,Animals ,Amino Acid Sequence ,Cysteine ,IC50 ,Ion channel ,Elapid Venoms ,Membrane Glycoproteins ,Dose-Response Relationship, Drug ,biology ,Chemistry ,Toxin ,Blocking effect ,Solutions ,Secretory protein ,Models, Chemical ,biology.protein ,Biophysics ,Ion Channel Gating ,Muscle Contraction - Abstract
Cysteine-rich secretory proteins (CRISPs) are widespread in snake venoms. Some members of these CRISPs recently have been found to block L-type Ca(2+) channels or cyclic nucleotide-gated ion (CNG) channels. Here, natrin purified from Naja atra venom, a member of the CRISP family, can induce a further contractile response in the endothelium-denuded thoracic aorta of mouse which has been contracted by a high-K(+) solution. Further experiments show it can block the high-conductance calcium-activated potassium (BK(Ca)) channel in a concentration-dependent manner with an IC(50) of 34.4 nM and a Hill coefficient of 1.02, which suggests that only a single natrin molecule is required to bind an ion channel to block BK(Ca) current. The crystal structure of natrin displaying two domains in tandem shows its cysteine-rich domain (CRD) has relatively independent flexibility, especially for the C-terminal long loop (loop I) of CRD to participate in the interface of two domains. On the basis of previous studies of CNG channel and L-Ca(2+) channel blockers, and the sequence and structural comparison of natrin and stecrisp, the deviation of the vital loop I of CRD is suggested to contribute to different effects of some CRISPs in protein-protein interaction.
- Published
- 2005
98. PALS1 Specifies the Localization of Ezrin to the Apical Membrane of Gastric Parietal Cells
- Author
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Fang Wu, Xia Ding, Qichen Wang, Xinwang Cao, Fei Long, Zhen Guo, Xuebiao Yao, Feng Bi, John G. Forte, Maikun Teng, Fengsong Wang, Rihong Zhou, and Daiming Fan
- Subjects
Recombinant Fusion Proteins ,Moesin ,PDZ domain ,macromolecular substances ,environment and public health ,Biochemistry ,Ezrin ,Parietal Cells, Gastric ,Radixin ,medicine ,Animals ,Humans ,Secretion ,RNA, Small Interfering ,Molecular Biology ,Cells, Cultured ,Cytoskeleton ,Parietal cell ,Chemistry ,Cell Membrane ,Cell Polarity ,Membrane Proteins ,Cell Biology ,Apical membrane ,Phosphoproteins ,Protein Structure, Tertiary ,Cell biology ,Cytoskeletal Proteins ,medicine.anatomical_structure ,Membrane protein ,Rabbits ,Nucleoside-Phosphate Kinase - Abstract
The ERM (ezrin/radixin/moesin) proteins provide a regulated linkage between membrane proteins and the cortical cytoskeleton and also participate in signal transduction pathways. Ezrin is localized to the apical membrane of parietal cells and couples the protein kinase A activation cascade to regulated HCl secretion in gastric parietal cells. Here, we show that the integrity of ezrin is essential for parietal cell activation and provide the first evidence that ezrin interacts with PALS1, an evolutionarily conserved PDZ and SH3 domain-containing protein. Our biochemical study verifies that ezrin binds to PALS1 via its N terminus and is co-localized with PALS1 to the apical membrane of gastric parietal cells. Furthermore, our study shows that PALS1 is essential for the apical localization of ezrin, as either suppression of PALS1 protein accumulation or deletion of the PALS1-binding domain of ezrin eliminated the apical localization of ezrin. Finally, our study demonstrates the essential role of ezrin-PALS1 interaction in the apical membrane remodeling associated with parietal cell secretion. Taken together, these results define a novel molecular mechanism linking ezrin to the conserved apical polarity complexes and their roles in polarized epithelial secretion of gastric parietal cells.
- Published
- 2005
99. Design and performance of U7B beamline and X-ray diffraction and scattering station at NSRL and its preliminary experiments in protein crystallography
- Author
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Chen Gao, Liwen Niu, Xiaohua Lou, Rong Fan, Qingqiu Huang, Guoqiang Pan, Maikun Teng, and Chaoyin Xu
- Subjects
Diffraction ,Physics ,Nuclear and High Energy Physics ,Scattering ,business.industry ,Plate detector ,Synchrotron radiation ,law.invention ,Optics ,Beamline ,law ,X-ray crystallography ,business ,Instrumentation ,Single crystal ,Monochromator - Abstract
This publication describes the design and performance of the U7B beamline and X-ray diffraction and diffuse scattering station at National Synchrotron Radiation Laboratory (NSRL). The beamline optics comprise a Pt-coated toroidal focusing mirror and a double-crystal Si(1 1 1) monochromator. A preliminary experiment of diffraction data collection and processing was carried out using a commercial imaging plate detector system (Mar345). The data collected from one single crystal of acutohaemolysin, a Lys49-type PLA2 from Agkistrodon acutus venom, are of high quality.
- Published
- 2005
100. Crystal Structures and Amidolytic Activities of Two Glycosylated Snake Venom Serine Proteinases
- Author
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Weihua Xu, Maikun Teng, Zhiqiang Zhu, Zhi Liang, Tianyi Zhang, Zhongliang Zhu, and Liwen Niu
- Subjects
Models, Molecular ,Amyloid ,DNA, Complementary ,Glycosylation ,Protein Conformation ,Trypsin inhibitor ,Molecular Sequence Data ,Carbohydrates ,Oligosaccharides ,Venom ,Biology ,Crystallography, X-Ray ,Biochemistry ,Species Specificity ,Sequence Homology, Nucleic Acid ,Hydrolase ,medicine ,Animals ,Trimeresurus ,Trypsin ,Amino Acid Sequence ,Trisaccharide ,Molecular Biology ,chemistry.chemical_classification ,Aspartic Acid ,Binding Sites ,Base Sequence ,Sequence Homology, Amino Acid ,Kunitz STI protease inhibitor ,Reverse Transcriptase Polymerase Chain Reaction ,Monosaccharides ,Serine Endopeptidases ,Cell Biology ,Kinetics ,chemistry ,Snake venom ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Mutagenesis, Site-Directed ,Agkistrodon ,Asparagine ,Trypsin Inhibitor, Kunitz Soybean ,Plasminogen activator ,Snake Venoms ,medicine.drug - Abstract
We deduced that Agkistrodon actus venom serine proteinases I and II, previously isolated from the venom of A. acutus (Zhu, Z., Gong, P., Teng, M., and Niu, L. (2003) Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 547-550), are encoded by two almost identical genes, with only the single substitution Asp for Asn at residue 62. Amidolytic assays indicated that they possess slightly different enzymatic properties. Crystal structures of A. actus venom serine proteinases I and II were determined at resolution of 2.0 and 2.1 A with the identification of trisaccharide (NAG(301)-FUC(302)-NAG(303)) and monosaccharide (NAG(301)) residues in them, respectively. The substrate binding sites S3 of the two proteinases appear much shallower than that of Trimeresurus stejnegeri venom plasminogen activator despite the overall structural similarity. Based on structural analysis, we showed that these Asn(35)-linked oligosaccharides collide spatially with some inhibitors, such as soybean trypsin inhibitor, and would therefore hinder their inhibitory binding. Difference of the carbohydrates in both the proteinases might also lead to their altered catalytic activities.
- Published
- 2005
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