Acta Crystallographica Section D: Biological Crystallography最新文献_第4页

Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum. 海洋植物髋臼紫红质I光循环慢、质子释放晚的结构基础。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 DOI: 10.1107/S1399004715015722

M. Furuse, Jun Tamogami, T. Hosaka, T. Kikukawa, N. Shinya, M. Hato, N. Ohsawa, S. Kim, K. Jung, M. Demura, S. Miyauchi, N. Kamo, K. Shimono, T. Kimura-Someya, S. Yokoyama, M. Shirouzu

{"title":"Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.","authors":"M. Furuse, Jun Tamogami, T. Hosaka, T. Kikukawa, N. Shinya, M. Hato, N. Ohsawa, S. Kim, K. Jung, M. Demura, S. Miyauchi, N. Kamo, K. Shimono, T. Kimura-Someya, S. Yokoyama, M. Shirouzu","doi":"10.1107/S1399004715015722","DOIUrl":"https://doi.org/10.1107/S1399004715015722","url":null,"abstract":"Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 Å) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"25 1","pages":"2203-16"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85361849","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: 19

Deformable complex network for refining low-resolution X-ray structures. 用于精炼低分辨率x射线结构的可变形复杂网络。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-27 DOI: 10.1107/S139900471501528X

Chong Zhang, Qinghua Wang, Jianpeng Ma

引用次数: 1

Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex. 结核分枝杆菌邻氨基甲酸合酶复合体I亚基的结构、抑制及活性复合体的表达。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 DOI: 10.1107/S1399004715017216

G. Bashiri, J. Johnston, G. Evans, E. M. Bulloch, David C. Goldstone, E.N.M. Jirgis, S. Kleinboelting, A. Castell, R. J. Ramsay, Alexandra Manos-Turvey, Richard J. Payne, J. Lott, Edward N. Baker

{"title":"Structure and inhibition of subunit I of the anthranilate synthase complex of Mycobacterium tuberculosis and expression of the active complex.","authors":"G. Bashiri, J. Johnston, G. Evans, E. M. Bulloch, David C. Goldstone, E.N.M. Jirgis, S. Kleinboelting, A. Castell, R. J. Ramsay, Alexandra Manos-Turvey, Richard J. Payne, J. Lott, Edward N. Baker","doi":"10.1107/S1399004715017216","DOIUrl":"https://doi.org/10.1107/S1399004715017216","url":null,"abstract":"The tryptophan-biosynthesis pathway is essential for Mycobacterium tuberculosis (Mtb) to cause disease, but not all of the enzymes that catalyse this pathway in this organism have been identified. The structure and function of the enzyme complex that catalyses the first committed step in the pathway, the anthranilate synthase (AS) complex, have been analysed. It is shown that the open reading frames Rv1609 (trpE) and Rv0013 (trpG) encode the chorismate-utilizing (AS-I) and glutamine amidotransferase (AS-II) subunits of the AS complex, respectively. Biochemical assays show that when these subunits are co-expressed a bifunctional AS complex is obtained. Crystallization trials on Mtb-AS unexpectedly gave crystals containing only AS-I, presumably owing to its selective crystallization from solutions containing a mixture of the AS complex and free AS-I. The three-dimensional structure reveals that Mtb-AS-I dimerizes via an interface that has not previously been seen in AS complexes. As is the case in other bacteria, it is demonstrated that Mtb-AS shows cooperative allosteric inhibition by tryptophan, which can be rationalized based on interactions at this interface. Comparative inhibition studies on Mtb-AS-I and related enzymes highlight the potential for single inhibitory compounds to target multiple chorismate-utilizing enzymes for TB drug discovery.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"71 Pt 11 1","pages":"2297-308"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87516121","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: 17

Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning. 在低分辨率、各向异性数据和晶体孪晶的情况下，MATE转运体的晶体学研究在结构确定方面存在困难。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 DOI: 10.1107/S1399004715016995

J. Symerský, Yi Guo, Jimin Wang, Min Lu

引用次数: 1

The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase. 来自假单胞菌 CAM 质粒的 3,6-二酮樟脑单加氧酶的加氧成分：II 型 Baeyer-Villiger 单加氧酶的首个晶体结构。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-31 DOI: 10.1107/S1399004715017939

Michail N Isupov, Ewald Schröder, Robert P Gibson, Jean Beecher, Giuliana Donadio, Vahid Saneei, Stephlina A Dcunha, Emma J McGhie, Christopher Sayer, Colin F Davenport, Peter C Lau, Yoshie Hasegawa, Hiroaki Iwaki, Maria Kadow, Kathleen Balke, Uwe T Bornscheuer, Gleb Bourenkov, Jennifer A Littlechild

{"title":"The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.","authors":"Michail N Isupov, Ewald Schröder, Robert P Gibson, Jean Beecher, Giuliana Donadio, Vahid Saneei, Stephlina A Dcunha, Emma J McGhie, Christopher Sayer, Colin F Davenport, Peter C Lau, Yoshie Hasegawa, Hiroaki Iwaki, Maria Kadow, Kathleen Balke, Uwe T Bornscheuer, Gleb Bourenkov, Jennifer A Littlechild","doi":"10.1107/S1399004715017939","DOIUrl":"10.1107/S1399004715017939","url":null,"abstract":"The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"71 1","pages":"2344-53"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61948478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures. 蛋白质中氨基酸有序水合的结构：晶体结构分析。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-27 DOI: 10.1107/S1399004715015679

Lada Biedermannová, Bohdan Schneider

{"title":"Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.","authors":"Lada Biedermannová, Bohdan Schneider","doi":"10.1107/S1399004715015679","DOIUrl":"10.1107/S1399004715015679","url":null,"abstract":"Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"71 1","pages":"2192-202"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61948402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase. 肠道沙门氏菌AadA的结构:一个单体氨基糖苷(3”)(9)腺苷转移酶。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 Epub Date: 2015-10-31 DOI: 10.1107/S1399004715016429

Yang Chen, Joakim Näsvall, Shiying Wu, Dan I Andersson, Maria Selmer

{"title":"Structure of AadA from Salmonella enterica: a monomeric aminoglycoside (3'')(9) adenyltransferase.","authors":"Yang Chen, Joakim Näsvall, Shiying Wu, Dan I Andersson, Maria Selmer","doi":"10.1107/S1399004715016429","DOIUrl":"10.1107/S1399004715016429","url":null,"abstract":"Aminoglycoside resistance is commonly conferred by enzymatic modification of drugs by aminoglycoside-modifying enzymes such as aminoglycoside nucleotidyltransferases (ANTs). Here, the first crystal structure of an ANT(3'')(9) adenyltransferase, AadA from Salmonella enterica, is presented. AadA catalyses the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. The structure was solved using selenium SAD phasing and refined to 2.5 Å resolution. AadA consists of a nucleotidyltransferase domain and an α-helical bundle domain. AadA crystallizes as a monomer and is a monomer in solution as confirmed by small-angle X-ray scattering, in contrast to structurally similar homodimeric adenylating enzymes such as kanamycin nucleotidyltransferase. Isothermal titration calorimetry experiments show that ATP binding has to occur before binding of the aminoglycoside substrate, and structure analysis suggests that ATP binding repositions the two domains for aminoglycoside binding in the interdomain cleft. Candidate residues for ligand binding and catalysis were subjected to site-directed mutagenesis. In vivo resistance and in vitro binding assays support the role of Glu87 as the catalytic base in adenylation, while Arg192 and Lys205 are shown to be critical for ATP binding.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"71 1","pages":"2267-77"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715016429","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61948413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 16

Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction. 来自肠贾第虫的超氧化物还原酶:来自真核生物的第一个SOR的结构特征显示铁中心对光还原高度敏感。

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-11-01 DOI: 10.1107/S1399004715015825

C. M. Sousa, P. Carpentier, P. Matias, F. Testa, F. Pinho, P. Sarti, A. Giuffrè, Tiago M. Bandeiras, C. Romão

{"title":"Superoxide reductase from Giardia intestinalis: structural characterization of the first SOR from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction.","authors":"C. M. Sousa, P. Carpentier, P. Matias, F. Testa, F. Pinho, P. Sarti, A. Giuffrè, Tiago M. Bandeiras, C. Romão","doi":"10.1107/S1399004715015825","DOIUrl":"https://doi.org/10.1107/S1399004715015825","url":null,"abstract":"Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2.0 Å resolution. By collecting several diffraction data sets at 100 K from the same flash-cooled protein crystal using synchrotron X-ray radiation, photoreduction of the iron centre was observed. Reduction was monitored using an online UV-visible microspectrophotometer, following the decay of the 647 nm absorption band characteristic of the iron site in the glutamate-bound, oxidized state. Similarly to other 1Fe-SORs structurally characterized to date, the enzyme displays a tetrameric quaternary-structure arrangement. As a distinctive feature, the N-terminal loop of the protein, containing the characteristic EKHxP motif, revealed an unusually high flexibility regardless of the iron redox state. At variance with previous evidence collected by X-ray crystallography and Fourier transform infrared spectroscopy of prokaryotic SORs, iron reduction did not lead to dissociation of glutamate from the catalytic metal or other structural changes; however, the glutamate ligand underwent X-ray-induced chemical changes, revealing high sensitivity of the GiSOR active site to X-ray radiation damage.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":"16 1","pages":"2236-47"},"PeriodicalIF":2.2,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85659597","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: 7

Crystal Structure Determination of Uracil-DNA N-Glycosylase (Ung) from Deinococcus Radiodurans in Complex with DNA - New Insights Into the Role of the Leucine-Loop for Damage Recognition and Repair 耐辐射球菌与DNA复合物中尿嘧啶-DNA n -糖基酶(Ung)晶体结构的测定——亮氨酸环在损伤识别和修复中的作用的新认识

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-08-12 DOI: 10.2210/PDB4UQM/PDB

H. Pedersen, K. Johnson, C. E. McVey, I. Leiros, E. Moe

引用次数: 0

Crystal Structure of Struthiocalcin-1, an Intramineral Protein from Struthio Camelus Eggshell, in Two Different Crystal Forms. 鹿角蛋壳蛋白-1的两种不同晶体结构

IF 2.2 4区生物学

Acta Crystallographica Section D: Biological Crystallography Pub Date : 2015-04-08 DOI: 10.2210/pdb4uww/pdb

R. R. Ruiz-Arellano, F. Medrano, A. Moreno, A. Romero

引用次数: 0