Acta Crystallographica Section D: Biological Crystallography最新文献

Crystal structure of Hen Egg White Lysozyme in complex with I3C 蛋清溶菌酶与I3C配合物的晶体结构

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2019-07-01 DOI: 10.2210/PDB6PBB/PDB

J. Truong, S. Panjikar, L. Shearwin-Whyatt, J. Bruning, K. Shearwin

引用次数: 0

ADP bound to K46bE mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase ADP与人胚囊虫琥珀酰辅酶a合成酶K46bE突变体atp把握褶结合

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2019-07-01 DOI: 10.2210/PDB6NO1/PDB

J. Huang, V. H. Nguyen, K. A. Hamblin, R. Maytum, M. V. D. Glezen, M. Fraser

{"title":"ADP bound to K46bE mutant ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase","authors":"J. Huang, V. H. Nguyen, K. A. Hamblin, R. Maytum, M. V. D. Glezen, M. Fraser","doi":"10.2210/PDB6NO1/PDB","DOIUrl":"https://doi.org/10.2210/PDB6NO1/PDB","url":null,"abstract":"Succinyl-CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate-level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide-specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure of the nucleotide-binding domain in complex with Mg2+-ADP was determined, as well as the structures of four proteins with single mutations, K46βE, K114βD, V113βL and L227βF, and one with two mutations, K46βE/K114βD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide-specificity is provided by hydrogen-bonding interactions between the adenine base and Gln20β, Gly111β and Val113β. The O atom of the side chain of Gln20β interacts with N6 of ADP, while the side-chain N atom interacts with the carbonyl O atom of Gly111β. It is the different conformations of the backbone at Gln20β, of the side chain of Gln20β and of the linker that make the enzyme ATP-specific. This linker connects the two subdomains of the ATP-grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227βF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46βE/K114βD double mutant of Blastocystis hominis SCS binds GTP better than ATP according to kinetic assays, only the complex with Mg2+-ADP was obtained.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"18 1","pages":"647-659"},"PeriodicalIF":2.2,"publicationDate":"2019-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87506171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae. 霍乱弧菌cmp - n -乙酰神经胺酸合成酶的结构和功能表征。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2019-06-01 DOI: 10.2210/PDB6IFI/PDB

S. Bose, D. Purkait, D. Joseph, V. Nayak, R. Subramanian

{"title":"Structural and functional characterization of CMP-N-acetylneuraminate synthetase from Vibrio cholerae.","authors":"S. Bose, D. Purkait, D. Joseph, V. Nayak, R. Subramanian","doi":"10.2210/PDB6IFI/PDB","DOIUrl":"https://doi.org/10.2210/PDB6IFI/PDB","url":null,"abstract":"Several pathogenic bacteria utilize sialic acid, including host-derived N-acetylneuraminic acid (Neu5Ac), in at least two ways: they use it as a nutrient source and as a host-evasion strategy by coating themselves with Neu5Ac. Given the significant role of sialic acid in pathogenesis and host-gut colonization by various pathogenic bacteria, including Neisseria meningitidis, Haemophilus influenzae, Pasteurella multocida and Vibrio cholerae, several enzymes of the sialic acid catabolic, biosynthetic and incorporation pathways are considered to be potential drug targets. In this work, findings on the structural and functional characterization of CMP-N-acetylneuraminate synthetase (CMAS), a key enzyme in the incorporation pathway, from Vibrio cholerae are reported. CMAS catalyzes the synthesis of CMP-sialic acid by utilizing CTP and sialic acid. Crystal structures of the apo and the CDP-bound forms of the enzyme were determined, which allowed the identification of the metal cofactor Mg2+ in the active site interacting with CDP and the invariant Asp215 residue. While open and closed structural forms of the enzyme from eukaryotic and other bacterial species have already been characterized, a partially closed structure of V. cholerae CMAS (VcCMAS) observed upon CDP binding, representing an intermediate state, is reported here. The kinetic data suggest that VcCMAS is capable of activating the two most common sialic acid derivatives, Neu5Ac and Neu5Gc. Amino-acid sequence and structural comparison of the active site of VcCMAS with those of eukaryotic and other bacterial counterparts reveal a diverse hydrophobic pocket that interacts with the C5 substituents of sialic acid. Analyses of the thermodynamic signatures obtained from the binding of the nucleotide (CTP) and the product (CMP-sialic acid) to VcCMAS provide fundamental information on the energetics of the binding process.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"2018 1","pages":"564-577"},"PeriodicalIF":2.2,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74947778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long wavelength Mesh&Collect native SAD phasing on microcrystals 长波长网格&收集微晶体上的原生SAD相位

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2019-02-01 DOI: 10.2210/PDB6H2M/PDB

M. Cianci, M. Nanao, T. Schneider

{"title":"Long wavelength Mesh&Collect native SAD phasing on microcrystals","authors":"M. Cianci, M. Nanao, T. Schneider","doi":"10.2210/PDB6H2M/PDB","DOIUrl":"https://doi.org/10.2210/PDB6H2M/PDB","url":null,"abstract":"Harnessing the anomalous signal from macromolecular crystals with volumes of less than 10 000 µm3 for native phasing requires careful experimental planning. The type of anomalous scatterers that are naturally present in the sample, such as sulfur, phosphorus and calcium, will dictate the beam energy required and determine the level of radiation sensitivity, while the crystal size will dictate the beam size and the sample-mounting technique, in turn indicating the specifications of a suitable beamline. On the EMBL beamline P13 at PETRA III, Mesh&Collect data collection from concanavalin A microcrystals with linear dimensions of ∼20 µm or less using an accordingly sized microbeam at a wavelength of 1.892 A (6.551 keV, close to the Mn edge at 6.549 keV) increases the expected Bijvoet ratio to 2.1% from an expected 0.7% at 12.6 keV (Se K edge), thus allowing experimental phase determination using the anomalous signal from naturally present Mn2+ and Ca2+ ions. Dozens of crystals were harvested and flash-cryocooled in micro-meshes, rapidly screened for diffraction (less than a minute per loop) and then used for serial Mesh&Collect collection of about 298 partial data sets (10° of crystal rotation per sample). The partial data sets were integrated and scaled. A genetic algorithm for combining partial data sets was used to select those to be merged into a single data set. This final data set showed high completeness, high multiplicity and sufficient anomalous signal to locate the anomalous scatterers, and provided phasing information which allowed complete auto-tracing of the polypeptide chain. To allow the complete experiment to run in less than 2 h, a practically acceptable time frame, the diffractometer and detector had to run together with limited manual intervention. The combination of several cutting-edge components allowed accurate anomalous signal to be measured from small crystals.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"62 1","pages":"192-199"},"PeriodicalIF":2.2,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89829720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mycobacterium tuberculosis LexA C-domain K197A 结核分枝杆菌LexA c结构域K197A

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2019-01-23 DOI: 10.2210/PDB6A2T/PDB

A. Chandran, R. Srikalaivani, A. Paul, M. Vijayan

{"title":"Mycobacterium tuberculosis LexA C-domain K197A","authors":"A. Chandran, R. Srikalaivani, A. Paul, M. Vijayan","doi":"10.2210/PDB6A2T/PDB","DOIUrl":"https://doi.org/10.2210/PDB6A2T/PDB","url":null,"abstract":"LexA is a protein that is involved in the SOS response. The protein from Mycobacterium tuberculosis and its mutants have been biochemically characterized and the structures of their catalytic segments have been determined. The protein is made up of an N-terminal segment, which includes the DNA-binding domain, and a C-terminal segment encompassing much of the catalytic domain. The two segments are defined by a cleavage site. Full-length LexA, the two segments, two point mutants involving changes in the active-site residues (S160A and K197A) and another mutant involving a change at the cleavage site (G126D) were cloned and purified. The wild-type protein autocleaves at basic pH, while the mutants do not. The wild-type and the mutant proteins dimerize and bind DNA with equal facility. The C-terminal segment also dimerizes, and it also shows a tendency to form tetramers. The C-terminal segment readily crystallized. The crystals obtained from attempts involving the full-length protein and its mutants contained only the C-terminal segment including the catalytic core and a few residues preceding it, in a dimeric or tetrameric form, indicating protein cleavage during the long period involved in crystal formation. Modes of tetramerization of the full-length protein similar to those observed for the catalytic core are feasible. A complex of M. tuberculosis LexA and the cognate SOS box could be modeled in which the mutual orientation of the two N-terminal domains differs from that in the Escherichia coli LexA–DNA complex. These results represent the first thorough characterization of M. tuberculosis LexA and provide definitive information on its structure and assembly. They also provide leads for further exploration of this important protein.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"20 1","pages":"41-55"},"PeriodicalIF":2.2,"publicationDate":"2019-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80397336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystal structure of FAS1 domain of hyaluronic acid receptor stabilin-2 透明质酸受体稳定蛋白-2 FAS1结构域的晶体结构

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2018-06-27 DOI: 10.2210/PDB5N86/PDB

Aleksandra Twarda-Clapa, Beata Labuzek, Dobrosława Krzemień, B. Musielak, P. Grudnik, G. Dubin, T. Holak

引用次数: 0

Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis Beta-keto-acyl-ACP reductase MabA 耻垢分枝杆菌β -酮酰基- acp还原酶MabA在辅因子结合时发生的结构重排

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2018-02-28 DOI: 10.2210/pdb5ovl/pdb

T. Kussau, Marion Flipo, N. Wyk, Albertus Viljoen, V. Olieric, L. Kremer, M. Blaise

引用次数: 0

Crystal structure of the Zika virus NS3 helicase. 寨卡病毒NS3解旋酶的晶体结构。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2016-05-25 DOI: 10.2210/pdb5vi7/pdb

S. Nocadello, S. Light, G. Minasov, L. Shuvalova, A. CARDONA-CORREA, Isabel Ojeda, J. Vargas, Michael E. Johnson, Hyun Lee, W. Anderson

引用次数: 0

Sent packing: Protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 suitable for fragment-based lead discovery. 发送包装:蛋白质工程产生了一种新的铜绿假单胞菌DsbA1晶体形式，适合基于片段的先导发现。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-12-09 DOI: 10.2210/pdb4zl7/pdb

R. McMahon, J. Martin

引用次数: 1

Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis. 假丝酵素分泌的天冬氨酸蛋白酶Sapp2p的原子分辨率晶体结构。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-12-01 DOI: 10.1107/S1399004715019392

J. Dostál, Adam Pecina, O. Hrušková-Heidingsfeldová, L. Marečková, I. Pichová, P. Řezáčová, M. Lepšík, J. Brynda

引用次数: 10