Acta crystallographica. Section D, Biological crystallography最新文献_第7页

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications. 结核分枝杆菌尿嘧啶- dna糖基酶(MtUng)的结构可塑性及其功能意义。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715009311

S M Arif, K Geethanandan, P Mishra, A Surolia, U Varshney, M Vijayan

{"title":"Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications.","authors":"S M Arif, K Geethanandan, P Mishra, A Surolia, U Varshney, M Vijayan","doi":"10.1107/S1399004715009311","DOIUrl":"https://doi.org/10.1107/S1399004715009311","url":null,"abstract":"17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 5' position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design. ","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1514-27"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715009311","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Structure of the catalytic phosphatase domain of MTMR8: implications for dimerization, membrane association and reversible oxidation. MTMR8催化磷酸酶结构域的结构:二聚化、膜结合和可逆氧化的意义。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S139900471500927X

Ki Young Yoo, Ji Young Son, Jee Un Lee, Woori Shin, Dong Won Im, Seung Jun Kim, Seong Eon Ryu, Yong Seok Heo

{"title":"Structure of the catalytic phosphatase domain of MTMR8: implications for dimerization, membrane association and reversible oxidation.","authors":"Ki Young Yoo, Ji Young Son, Jee Un Lee, Woori Shin, Dong Won Im, Seung Jun Kim, Seong Eon Ryu, Yong Seok Heo","doi":"10.1107/S139900471500927X","DOIUrl":"https://doi.org/10.1107/S139900471500927X","url":null,"abstract":"Myotubularin-related proteins are a large family of phosphoinositide phosphatases; their activity, stability and subcellular localization are regulated by dimeric interactions with other members of the family. Here, the crystal structure of the phosphatase domain of MTMR8 is reported. Conformational deviation of the two loops that mediate interaction with the PH-GRAM domain suggests that the PH-GRAM domain interacts differently with the phosphatase domain of each MTMR member. The protein exists as a dimer with twofold symmetry, providing insight into a novel mode of dimerization mediated by the phosphatase domain. Structural comparison and mutation studies suggest that Lys255 of MTMR8 interacts with the substrate diacylglycerol moiety, similar to Lys333 of MTMR2, although the positions of these residues are different. The catalytic activity of the MTMR8 phosphatase domain is inhibited by oxidation and is reversibly reactivated by reduction, suggesting the presence of an oxidation-protective intermediate other than a disulfide bond owing to the absence of a cysteine within a disulfide-bond distance from Cys338. ","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1528-39"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S139900471500927X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Protonation and geometry of histidine rings. 组氨酸环的质子化和几何形状

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715007816

Maura Malinska, Miroslawa Dauter, Marcin Kowiel, Mariusz Jaskolski, Zbigniew Dauter

{"title":"Protonation and geometry of histidine rings.","authors":"Maura Malinska, Miroslawa Dauter, Marcin Kowiel, Mariusz Jaskolski, Zbigniew Dauter","doi":"10.1107/S1399004715007816","DOIUrl":"10.1107/S1399004715007816","url":null,"abstract":"The presence of H atoms connected to either or both of the two N atoms of the imidazole moiety in a histidine residue affects the geometry of the five-membered ring. Analysis of the imidazole moieties found in histidine residues of atomic resolution protein crystal structures in the Protein Data Bank (PDB), and in small-molecule structures retrieved from the Cambridge Structural Database (CSD), identified characteristic patterns of bond lengths and angles related to the protonation state of the imidazole moiety. Using discriminant analysis, two functions could be defined, corresponding to linear combinations of the four most sensitive stereochemical parameters, two bond lengths (ND1-CE1 and CE1-NE2) and two endocyclic angles (-ND1- and -NE2-), that uniquely identify the protonation states of all imidazole moieties in the CSD and can be used to predict which N atom(s) of the histidine side chains in protein structures are protonated. Updated geometrical restraint target values are proposed for differently protonated histidine side chains for use in macromolecular refinement. ","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1444-54"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498602/pdf/d-71-01444.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34259855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protein secondary-structure description with a coarse-grained model. 用粗粒度模型描述蛋白质二级结构。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715007191

Gerald R Kneller, Konrad Hinsen

引用次数: 8

S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations. 结合多晶体和取向数据的流产布鲁氏菌单斜组氨酸激酶的S-SAD相位:数据收集策略的一个例子和不同数据组合的后验分析。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715007622

Sebastián Klinke, Nicolas Foos, Jimena J Rinaldi, Gastón Paris, Fernando A Goldbaum, Pierre Legrand, Beatriz G Guimarães, Andrew Thompson

{"title":"S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations.","authors":"Sebastián Klinke, Nicolas Foos, Jimena J Rinaldi, Gastón Paris, Fernando A Goldbaum, Pierre Legrand, Beatriz G Guimarães, Andrew Thompson","doi":"10.1107/S1399004715007622","DOIUrl":"https://doi.org/10.1107/S1399004715007622","url":null,"abstract":"The histidine kinase (HK) domain belonging to the light-oxygen-voltage histidine kinase (LOV-HK) from Brucella abortus is a member of the HWE family, for which no structural information is available, and has low sequence identity (20%) to the closest HK present in the PDB. The `off-edge' S-SAD method in macromolecular X-ray crystallography was used to solve the structure of the HK domain from LOV-HK at low resolution from crystals in a low-symmetry space group (P21) and with four copies in the asymmetric unit (∼108 kDa). Data were collected both from multiple crystals (diffraction limit varying from 2.90 to 3.25 Å) and from multiple orientations of the same crystal, using the κ-geometry goniostat on SOLEIL beamline PROXIMA 1, to obtain `true redundancy'. Data from three different crystals were combined for structure determination. An optimized HK construct bearing a shorter cloning artifact yielded crystals that diffracted X-rays to 2.51 Å resolution and that were used for final refinement of the model. Moreover, a thorough a posteriori analysis using several different combinations of data sets allowed us to investigate the impact of the data-collection strategy on the success of the structure determination. ","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1433-43"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715007622","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34259853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM. 原子分辨x射线衍射和混合QM/MM对人壳三酸苷酶(CHIT1)催化结构域酶促机制的新认识。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S139900471500783X

Firas Fadel, Yuguang Zhao, Raul Cachau, Alexandra Cousido-Siah, Francesc X Ruiz, Karl Harlos, Eduardo Howard, Andre Mitschler, Alberto Podjarny

{"title":"New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM.","authors":"Firas Fadel, Yuguang Zhao, Raul Cachau, Alexandra Cousido-Siah, Francesc X Ruiz, Karl Harlos, Eduardo Howard, Andre Mitschler, Alberto Podjarny","doi":"10.1107/S139900471500783X","DOIUrl":"https://doi.org/10.1107/S139900471500783X","url":null,"abstract":"Chitotriosidase (CHIT1) is a human chitinase belonging to the highly conserved glycosyl hydrolase family 18 (GH18). GH18 enzymes hydrolyze chitin, an N-acetylglucosamine polymer synthesized by lower organisms for structural purposes. Recently, CHIT1 has attracted attention owing to its upregulation in immune-system disorders and as a marker of Gaucher disease. The 39 kDa catalytic domain shows a conserved cluster of three acidic residues, Glu140, Asp138 and Asp136, involved in the hydrolysis reaction. Under an excess concentration of substrate, CHIT1 and other homologues perform an additional activity, transglycosylation. To understand the catalytic mechanism of GH18 chitinases and the dual enzymatic activity, the structure and mechanism of CHIT1 were analyzed in detail. The resolution of the crystals of the catalytic domain was improved from 1.65 Å (PDB entry 1waw) to 0.95-1.10 Å for the apo and pseudo-apo forms and the complex with chitobiose, allowing the determination of the protonation states within the active site. This information was extended by hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The results suggest a new mechanism involving changes in the conformation and protonation state of the catalytic triad, as well as a new role for Tyr27, providing new insights into the hydrolysis and transglycosylation activities. ","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":" ","pages":"1455-70"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S139900471500783X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34262925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

High-resolution crystal structures of the solubilized domain of porcine cytochrome b5. 猪细胞色素 b5 溶解域的高分辨率晶体结构。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715009438

Yu Hirano, Shigenobu Kimura, Taro Tamada

引用次数: 0

Two high-mobility group box domains act together to underwind and kink DNA. 两个高迁移率的组盒结构域共同作用，使DNA逆风和扭结。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715007452

R Sánchez-Giraldo, F J Acosta-Reyes, C S Malarkey, N Saperas, M E A Churchill, J L Campos

引用次数: 35

The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design. 磷脂酰肌醇4-激酶IIβ的高分辨率晶体结构和含有核苷类似物的磷脂酰肌醇4-激酶IIα的晶体结构为设计异构体特异性抑制剂提供了结构基础。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715009505

Martin Klima, Adriana Baumlova, Dominika Chalupska, Hubert Hřebabecký, Milan Dejmek, Radim Nencka, Evzen Boura

引用次数: 19

Intercalating dyes for enhanced contrast in second-harmonic generation imaging of protein crystals. 用于增强蛋白质晶体二次谐波成像对比度的夹杂染料。

Acta crystallographica. Section D, Biological crystallography Pub Date : 2015-07-01 Epub Date: 2015-06-30 DOI: 10.1107/S1399004715008287

Justin A Newman, Nicole M Scarborough, Nicholas R Pogranichniy, Rashmi K Shrestha, Richard G Closser, Chittaranjan Das, Garth J Simpson

引用次数: 0