Pub Date : 2015-11-01DOI: 10.1107/S1399004715015825
C. M. Sousa, P. Carpentier, P. Matias, F. Testa, F. Pinho, P. Sarti, A. Giuffrè, Tiago M. Bandeiras, C. Romão
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.
{"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":null,"pages":null},"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}
Pub Date : 2015-11-01Epub Date: 2015-10-27DOI: 10.1107/S1399004715015679
Lada Biedermannová, Bohdan Schneider
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.
晶体学提供了有关蛋白质表面附近水分子排列的独特信息。利用一组分辨率优于 1.8 Å 的 2818 个非冗余蛋白质晶体结构，分析了所有 20 个标准氨基酸残基的水合外壳的范围和结构与残基构象、二级结构和溶剂可及性的函数关系。结果表明了水合如何取决于氨基酸构象和发生水合的环境。在对单个残基进行构象聚类后，对水分子的密度分布进行了汇编，并根据水分布的伪电子密度表示法中的最大值确定了首选水合位点。许多水合位点与主链和侧链氨基酸原子都有相互作用，此外还报告了一些水合位点的非典型接触，如碳-捐赠者氢键、OH-π 相互作用以及与芳香杂原子的平面外相互作用。有关根据经验确定的蛋白质首选水合位点的位置和相对重要性的信息可用于改进分子置换、ab initio 蛋白质结构预测和分子动力学模拟设置中的现有水合位点预测方法。
{"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":"<p><p>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.</p>","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"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}
H. Pedersen, K. Johnson, C. E. McVey, I. Leiros, E. Moe
{"title":"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","authors":"H. Pedersen, K. Johnson, C. E. McVey, I. Leiros, E. Moe","doi":"10.2210/PDB4UQM/PDB","DOIUrl":"https://doi.org/10.2210/PDB4UQM/PDB","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2015-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78221729","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}
R. R. Ruiz-Arellano, F. Medrano, A. Moreno, A. Romero
{"title":"Crystal Structure of Struthiocalcin-1, an Intramineral Protein from Struthio Camelus Eggshell, in Two Different Crystal Forms.","authors":"R. R. Ruiz-Arellano, F. Medrano, A. Moreno, A. Romero","doi":"10.2210/pdb4uww/pdb","DOIUrl":"https://doi.org/10.2210/pdb4uww/pdb","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2015-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87439389","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}
{"title":"Structural characterization of potential modulation sites in the extracellular domain of the prokaryotic pentameric proton-gated ion channel GLIC","authors":"Z. Fourati, M. Delarue, L. Sauguet","doi":"10.2210/PDB4QH1/PDB","DOIUrl":"https://doi.org/10.2210/PDB4QH1/PDB","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2015-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84894244","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}
{"title":"Structure of Human Saposin a at Lysosomal Ph.","authors":"C. Hill, R. Read, J. Deane","doi":"10.2210/PDB4UEX/PDB","DOIUrl":"https://doi.org/10.2210/PDB4UEX/PDB","url":null,"abstract":"","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83349528","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}
Pub Date : 2014-07-01DOI: 10.1107/S1399004714013613
B. Yoon, Yong-Hak Kim, Nahee Kim, Bo-Young Yun, Jin-Sik Kim, Joon-Hee Lee, Hyun-soo Cho, Kangseok Lee, N. Ha
The affiliation of two of the authors of Yoon et al. [(2013). D69, 1867–1875] is corrected.
Yoon等人[(2013)]的两位作者的隶属关系。D69, 1867-1875]是更正的。
{"title":"Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium. Corrigendum","authors":"B. Yoon, Yong-Hak Kim, Nahee Kim, Bo-Young Yun, Jin-Sik Kim, Joon-Hee Lee, Hyun-soo Cho, Kangseok Lee, N. Ha","doi":"10.1107/S1399004714013613","DOIUrl":"https://doi.org/10.1107/S1399004714013613","url":null,"abstract":"The affiliation of two of the authors of Yoon et al. [(2013). D69, 1867–1875] is corrected.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87903742","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}
Pub Date : 2014-03-26DOI: 10.1107/S1399004714005719
L. Chavas
A review of Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules by Dmitri I. Svergun, Michel H. J. Koch, Peter A. Timmins and Roland P. May.
Dmitri I. Svergun, Michel H. J. Koch, Peter A. Timmins和Roland P. May在生物大分子溶液中的小角x射线和中子散射研究综述
{"title":"Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules.","authors":"L. Chavas","doi":"10.1107/S1399004714005719","DOIUrl":"https://doi.org/10.1107/S1399004714005719","url":null,"abstract":"A review of Small Angle X-Ray and Neutron Scattering from Solutions of Biological Macromolecules by Dmitri I. Svergun, Michel H. J. Koch, Peter A. Timmins and Roland P. May.","PeriodicalId":6895,"journal":{"name":"Acta Crystallographica Section D: Biological Crystallography","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2014-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004714005719","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61948336","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}
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