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Acta Crystallographica Section F-structural Biology and Crystallization Communications最新文献

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Crystal Structure of Thymidylate Synthase, Thy1, from Thermus thermophilus having an Extra C Terminal Domain 具有额外C末端结构域的嗜热热菌胸腺酸合酶Thy1的晶体结构
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2019-06-01 DOI: 10.2210/PDB6J61/PDB
A. Ogawa, G. Sampei, G. Kawai
{"title":"Crystal Structure of Thymidylate Synthase, Thy1, from Thermus thermophilus having an Extra C Terminal Domain","authors":"A. Ogawa, G. Sampei, G. Kawai","doi":"10.2210/PDB6J61/PDB","DOIUrl":"https://doi.org/10.2210/PDB6J61/PDB","url":null,"abstract":"The thymidylate synthases ThyA and Thy1 are enzymes that catalyse the formation of thymidine monophosphate from 2′-deoxyuridine monophosphate. Thy1 (or ThyX) requires flavin for catalytic reactions, while ThyA does not. In the present study, the crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus HB8 (TtThy1, TTHA1096) was determined in complex with FAD and phosphate at 2.5 A resolution. TtThy1 is a tetrameric molecule like other Thy1 proteins, to which four FAD molecules are bound. In the crystal of TtThy1, two phosphate ions were bound to each dUMP-binding site. The characteristic feature of TtThy1 is the existence of an extra C-terminal domain (CTD) consisting of three α-helices and a β-strand. The function of the CTD is unknown and database analysis showed that this CTD is only shared by part of the Deinococcus–Thermus phylum.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"360 1","pages":"450-454"},"PeriodicalIF":0.9,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76453767","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
The dimerization domain of human SFPQ in space group C2221 空间群C2221中人类SFPQ的二聚化域
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2019-06-01 DOI: 10.2210/PDB6NCQ/PDB
Thushara Welwelwela Hewage, Sofia Caria, Mihwa Lee
{"title":"The dimerization domain of human SFPQ in space group C2221","authors":"Thushara Welwelwela Hewage, Sofia Caria, Mihwa Lee","doi":"10.2210/PDB6NCQ/PDB","DOIUrl":"https://doi.org/10.2210/PDB6NCQ/PDB","url":null,"abstract":"Splicing factor proline/glutamine-rich (SFPQ) is an essential RNA-binding protein that is implicated in many aspects of nuclear function. The structures of SFPQ and two paralogs, non-POU domain-containing octamer-binding protein and paraspeckle component 1, from the Drosophila behavior human splicing protein family have previously been characterized. The unusual arrangement of the four domains, two RNA-recognition motifs (RRMs), a conserved region termed the NonA/paraspeckle (NOPS) domain and a C-terminal coiled coil, in the intertwined dimer provides a potentially unique RNA-binding surface. However, the molecular details of how the four RRMs in the dimeric SFPQ interact with RNA remain to be characterized. Here, a new crystal structure of the dimerization domain of human SFPQ in the C-centered orthorhombic space group C2221 with one monomer in the asymmetric unit is presented. Comparison of the new crystal structure with the previously reported structure of SFPQ and analysis of the solution small-angle X-scattering data revealed subtle domain movements in the dimerization domain of SFPQ, supporting the concept of multiple conformations of SFPQ in equilibrium in solution. The domain movement of RRM1, in particular, may reflect the complexity of the RNA substrates of SFPQ. Taken together, the crystal and solution structure analyses provide a molecular basis for further investigation into the plasticity of nucleic acid binding by SFPQ in the absence of the structure in complex with its cognate RNA-binding partners.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"96 1","pages":"439-449"},"PeriodicalIF":0.9,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89909202","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: 1
A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor RXR-ALPHA 人类核受体RXR-ALPHA的配体结合域的载脂蛋白结构的重新审视版本
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2019-02-01 DOI: 10.2210/PDB6HN6/PDB
Jérôme Eberhardt, A. McEwen, W. Bourguet, D. Moras, A. Dejaegere
{"title":"A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor RXR-ALPHA","authors":"Jérôme Eberhardt, A. McEwen, W. Bourguet, D. Moras, A. Dejaegere","doi":"10.2210/PDB6HN6/PDB","DOIUrl":"https://doi.org/10.2210/PDB6HN6/PDB","url":null,"abstract":"The retinoic X receptor (RXR) plays a crucial role in the superfamily of nuclear receptors (NRs) by acting as an obligatory partner of several nuclear receptors; its role as a transcription factor is thus critical in many signalling pathways, such as metabolism, cell development, differentiation and cellular death. The first published structure of the apo ligand-binding domain (LBD) of RXRα, which is still used as a reference today, contained inaccuracies. In the present work, these inaccuracies were corrected using modern crystallographic tools. The most important correction concerns the presence of a π-bulge in helix H7, which was originally built as a regular α-helix. The presence of several CHAPS molecules, which are visible for the first time in the electron-density map and which stabilize the H1–H3 loop, which contains helix H2, are also revealed. The apo RXR structure has played an essential role in deciphering the molecular mode of action of NR ligands and is still used in numerous biophysical studies. This refined structure should be used preferentially in the future in interpreting experiments as well as for modelling and structural dynamics studies of the apo RXRα LBD.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"1 1","pages":"98-104"},"PeriodicalIF":0.9,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82999963","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: 5
INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk 流感病毒神经氨酸酶亚型N9 (TERN)与四臂臂(TB)结构域柄
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2019-01-23 DOI: 10.2210/PDB6MCX/PDB
V. Streltsov, P. Schmidt, J. McKimm-Breschkin
{"title":"INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk","authors":"V. Streltsov, P. Schmidt, J. McKimm-Breschkin","doi":"10.2210/PDB6MCX/PDB","DOIUrl":"https://doi.org/10.2210/PDB6MCX/PDB","url":null,"abstract":"","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"1 1","pages":""},"PeriodicalIF":0.9,"publicationDate":"2019-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87304316","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
Glutathione reductase from Streptococcus pneumoniae 肺炎链球菌的谷胱甘肽还原酶
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2019-01-16 DOI: 10.2210/PDB6DU7/PDB
Mwilye Sikanyika, D. Aragão, C. McDevitt, M. Maher
{"title":"Glutathione reductase from Streptococcus pneumoniae","authors":"Mwilye Sikanyika, D. Aragão, C. McDevitt, M. Maher","doi":"10.2210/PDB6DU7/PDB","DOIUrl":"https://doi.org/10.2210/PDB6DU7/PDB","url":null,"abstract":"The glutathione reductase (GR) from Streptococcus pneumoniae is a flavo­enzyme that catalyzes the reduction of oxidized glutathione (GSSG) to its reduced form (GSH) in the cytoplasm of this bacterium. The maintenance of an intracellular pool of GSH is critical for the detoxification of reactive oxygen and nitrogen species and for intracellular metal tolerance to ions such as zinc. Here, S. pneumoniae GR (SpGR) was overexpressed and purified and its crystal structure determined at 2.56 A resolution. SpGR shows overall structural similarity to other characterized GRs, with a dimeric structure that includes an antiparallel β-sheet at the dimer interface. This observation, in conjunction with comparisons with the interface structures of other GR enzymes, allows the classification of these enzymes into three classes. Analyses of the kinetic properties of SpGR revealed a significantly higher value for Km(GSSG) (231.2 ± 24.7 µM) in comparison to other characterized GR enzymes.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"13 1","pages":"54-61"},"PeriodicalIF":0.9,"publicationDate":"2019-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88906141","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: 1
Crystal structure of RecR from Pseudomonas aeruginosa PAO1 铜绿假单胞菌PAO1中RecR的晶体结构
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2018-04-01 DOI: 10.2210/PDB5Z2V/PDB
S. Che, Yujing Chen, Yakun Liang, Qionglin Zhang, M. Bartlam
{"title":"Crystal structure of RecR from Pseudomonas aeruginosa PAO1","authors":"S. Che, Yujing Chen, Yakun Liang, Qionglin Zhang, M. Bartlam","doi":"10.2210/PDB5Z2V/PDB","DOIUrl":"https://doi.org/10.2210/PDB5Z2V/PDB","url":null,"abstract":"DNA damage is usually lethal to all organisms. Homologous recombination plays an important role in the DNA damage-repair process in prokaryotic organisms. Two pathways are responsible for homologous recombination in Pseudomonas aeruginosa: the RecBCD pathway and the RecFOR pathway. RecR is an important regulator in the RecFOR homologous recombination pathway in P. aeruginosa. It forms complexes with RecF and RecO that can facilitate the loading of RecA onto ssDNA in the RecFOR pathway. Here, the crystal structure of RecR from P. aeruginosa PAO1 (PaRecR) is reported. PaRecR crystallizes in space group P6122, with two monomers per asymmetric unit. Analytical ultracentrifugation data show that PaRecR forms a stable dimer, but can exist as a tetramer in solution. The crystal structure shows that dimeric PaRecR forms a ring-like tetramer architecture via crystal symmetry. The presence of a ligand in the Walker B motif of one RecR subunit suggests a putative nucleotide-binding site.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"26 1","pages":"222-230"},"PeriodicalIF":0.9,"publicationDate":"2018-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75107134","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
Structures of Bovine Cytochrome c Oxidase in the Fully Oxidized and Ligand-Free Reduced States at Neutral pH 中性pH下完全氧化和无配体还原状态下牛细胞色素c氧化酶的结构
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2018-02-07 DOI: 10.2210/PDB5XDX/PDB
F. Luo, K. Shinzawa-Itoh, N. Hagimoto, A. Shimada, S. Shimada, E. Yamashita, S. Yoshikawa, T. Tsukihara
{"title":"Structures of Bovine Cytochrome c Oxidase in the Fully Oxidized and Ligand-Free Reduced States at Neutral pH","authors":"F. Luo, K. Shinzawa-Itoh, N. Hagimoto, A. Shimada, S. Shimada, E. Yamashita, S. Yoshikawa, T. Tsukihara","doi":"10.2210/PDB5XDX/PDB","DOIUrl":"https://doi.org/10.2210/PDB5XDX/PDB","url":null,"abstract":"","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"4 1","pages":""},"PeriodicalIF":0.9,"publicationDate":"2018-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83026912","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 a DNA sequence d (CGTGAATTCACG) with DAPI 具有DAPI的DNA序列d (CGTGAATTCACG)的晶体结构
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2017-08-23 DOI: 10.2210/PDB5T4W/PDB
H. Sbirkova, B. Schivachev
{"title":"Crystal structure of a DNA sequence d (CGTGAATTCACG) with DAPI","authors":"H. Sbirkova, B. Schivachev","doi":"10.2210/PDB5T4W/PDB","DOIUrl":"https://doi.org/10.2210/PDB5T4W/PDB","url":null,"abstract":"","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"34 1","pages":""},"PeriodicalIF":0.9,"publicationDate":"2017-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90485628","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
Malonate in the nucleotide-binding site traps human AKAP18 gamma / delta in a novel conformational state. 核苷酸结合位点的丙二酸盐使人类AKAP18 γ / delta处于一种新的构象状态。
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2016-08-03 DOI: 10.2210/pdb5jj2/pdb
K. Bjerregaard-Andersen, E. stensen, John D. Scott, K. Taskén, J. P. Morth
{"title":"Malonate in the nucleotide-binding site traps human AKAP18 gamma / delta in a novel conformational state.","authors":"K. Bjerregaard-Andersen, E. stensen, John D. Scott, K. Taskén, J. P. Morth","doi":"10.2210/pdb5jj2/pdb","DOIUrl":"https://doi.org/10.2210/pdb5jj2/pdb","url":null,"abstract":"","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"41 1","pages":"591-597"},"PeriodicalIF":0.9,"publicationDate":"2016-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88979006","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: 3
Crystal structure of the bile salt hydrolase from Lactobacillus salivarius 唾液乳杆菌胆盐水解酶的晶体结构
IF 0.9 4区 生物学
Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2016-05-11 DOI: 10.2210/pdb5hke/pdb
F. Xu, Fangfang Guo, Xiao-Jian Hu, Jun Lin
{"title":"Crystal structure of the bile salt hydrolase from Lactobacillus salivarius","authors":"F. Xu, Fangfang Guo, Xiao-Jian Hu, Jun Lin","doi":"10.2210/pdb5hke/pdb","DOIUrl":"https://doi.org/10.2210/pdb5hke/pdb","url":null,"abstract":"","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"39 8 1","pages":"376-381"},"PeriodicalIF":0.9,"publicationDate":"2016-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85637616","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
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