Acta crystallographica. Section D, Biological crystallography最新文献

{"title":"DATASW, a tool for HPLC-SAXS data analysis.","authors":"Alexander V Shkumatov,&nbsp;Sergei V Strelkov","doi":"10.1107/S1399004715007154","DOIUrl":"https://doi.org/10.1107/S1399004715007154","url":null,"abstract":"<p><p>Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement the high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiments using a sliding window of a user-specified size, calculates overall parameters [I(0), Rg, Dmax and molecular weight] and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviours recorded on different beamlines. DATASW binaries for major operating systems can be downloaded from http://datasw.sourceforge.net/. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1347-50"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715007154","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33253298","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}

{"title":"Structural analysis of the α-glucosidase HaG provides new insights into substrate specificity and catalytic mechanism.","authors":"Xing Shen,&nbsp;Wataru Saburi,&nbsp;Zuoqi Gai,&nbsp;Koji Kato,&nbsp;Teruyo Ojima-Kato,&nbsp;Jian Yu,&nbsp;Keisuke Komoda,&nbsp;Yusuke Kido,&nbsp;Hirokazu Matsui,&nbsp;Haruhide Mori,&nbsp;Min Yao","doi":"10.1107/S139900471500721X","DOIUrl":"https://doi.org/10.1107/S139900471500721X","url":null,"abstract":"<p><p>α-Glucosidases, which catalyze the hydrolysis of the α-glucosidic linkage at the nonreducing end of the substrate, are important for the metabolism of α-glucosides. Halomonas sp. H11 α-glucosidase (HaG), belonging to glycoside hydrolase family 13 (GH13), only has high hydrolytic activity towards the α-(1 → 4)-linked disaccharide maltose among naturally occurring substrates. Although several three-dimensional structures of GH13 members have been solved, the disaccharide specificity and α-(1 → 4) recognition mechanism of α-glucosidase are unclear owing to a lack of corresponding substrate-bound structures. In this study, four crystal structures of HaG were solved: the apo form, the glucosyl-enzyme intermediate complex, the E271Q mutant in complex with its natural substrate maltose and a complex of the D202N mutant with D-glucose and glycerol. These structures explicitly provide insights into the substrate specificity and catalytic mechanism of HaG. A peculiar long β → α loop 4 which exists in α-glucosidase is responsible for the strict recognition of disaccharides owing to steric hindrance. Two residues, Thr203 and Phe297, assisted with Gly228, were found to determine the glycosidic linkage specificity of the substrate at subsite +1. Furthermore, an explanation of the α-glucosidase reaction mechanism is proposed based on the glucosyl-enzyme intermediate structure.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1382-91"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S139900471500721X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33253302","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}

{"title":"Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis.","authors":"Aik Hong Teh,&nbsp;Masatomo Makino,&nbsp;Takeshi Hoshino,&nbsp;Seiki Baba,&nbsp;Nobutaka Shimizu,&nbsp;Masaki Yamamoto,&nbsp;Takashi Kumasaka","doi":"10.1107/S1399004715007166","DOIUrl":"https://doi.org/10.1107/S1399004715007166","url":null,"abstract":"<p><p>In the general stress response of Bacillus subtilis, which is governed by the sigma factor σ(B), stress signalling is relayed by a cascade of Rsb proteins that regulate σ(B) activity. RsbX, a PPM II phosphatase, halts the response by dephosphorylating the stressosome composed of RsbR and RsbS. The crystal structure of RsbX reveals a reorganization of the catalytic centre, with the second Mn(2+) ion uniquely coordinated by Gly47 O from the β4-α1 loop instead of a water molecule as in PPM I phosphatases. An extra helical turn of α1 tilts the loop towards the metal-binding site, and the β2-β3 loop swings outwards to accommodate this tilting. The residues critical for this defining feature of the PPM II phosphatases are highly conserved. Formation of the catalytic centre is metal-specific, as crystallization with Mg(2+) ions resulted in a shift of the β4-α1 loop that led to loss of the second ion. RsbX also lacks the flap subdomain characteristic of PPM I phosphatases. On the basis of a stressosome model, the activity of RsbX towards RsbR-P and RsbS-P may be influenced by the different accessibilities of their phosphorylation sites.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1392-9"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715007166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33253303","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}

{"title":"In meso in situ serial X-ray crystallography of soluble and membrane proteins.","authors":"Chia Ying Huang, Vincent Olieric, Pikyee Ma, Ezequiel Panepucci, Kay Diederichs, Meitian Wang, Martin Caffrey","doi":"10.1107/S1399004715005210","DOIUrl":"10.1107/S1399004715005210","url":null,"abstract":"<p><p>The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β2-adrenoreceptor-Gs protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1238-56"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715005210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33374784","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}

{"title":"A revised partiality model and post-refinement algorithm for X-ray free-electron laser data.","authors":"Helen Mary Ginn, Aaron S Brewster, Johan Hattne, Gwyndaf Evans, Armin Wagner, Jonathan M Grimes, Nicholas K Sauter, Geoff Sutton, David Ian Stuart","doi":"10.1107/S1399004715006902","DOIUrl":"10.1107/S1399004715006902","url":null,"abstract":"<p><p>Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the R(split) value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1400-10"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33253304","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}

{"title":"The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket.","authors":"Claire F Dickson,&nbsp;David A Jacques,&nbsp;Robert T Clubb,&nbsp;J Mitchell Guss,&nbsp;David A Gell","doi":"10.1107/S1399004715005817","DOIUrl":"10.1107/S1399004715005817","url":null,"abstract":"<p><p>Staphylococcus aureus is a common and serious cause of infection in humans. The bacterium expresses a cell-surface receptor that binds to, and strips haem from, human haemoglobin (Hb). The binding interface has previously been identified; however, the structural changes that promote haem release from haemoglobin were unknown. Here, the structure of the receptor-Hb complex is reported at 2.6 Å resolution, which reveals a conformational change in the α-globin F helix that disrupts the haem-pocket structure and alters the Hb quaternary interactions. These features suggest potential mechanisms by which the S. aureus Hb receptor induces haem release from Hb.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1295-306"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715005817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33248378","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}

{"title":"Full-length structure of the major autolysin LytA.","authors":"Qiong Li,&nbsp;Wang Cheng,&nbsp;Cécile Morlot,&nbsp;Xiao Hui Bai,&nbsp;Yong Liang Jiang,&nbsp;Wenjia Wang,&nbsp;David I Roper,&nbsp;Thierry Vernet,&nbsp;Yu Hui Dong,&nbsp;Yuxing Chen,&nbsp;Cong Zhao Zhou","doi":"10.1107/S1399004715007403","DOIUrl":"https://doi.org/10.1107/S1399004715007403","url":null,"abstract":"<p><p>LytA is responsible for the autolysis of many Streptococcus species, including pathogens such as S. pneumoniae, S. pseudopneumoniae and S. mitis. However, how this major autolysin achieves full activity remains unknown. Here, the full-length structure of the S. pneumoniae LytA dimer is reported at 2.1 Å resolution. Each subunit has an N-terminal amidase domain and a C-terminal choline-binding domain consisting of six choline-binding repeats, which form five canonical and one single-layered choline-binding sites. Site-directed mutageneses combined with enzymatic activity assays indicate that dimerization and binding to choline are two independent requirements for the autolytic activity of LytA in vivo. Altogether, it is suggested that dimerization and full occupancy of all choline-binding sites through binding to choline-containing TA chains enable LytA to adopt a fully active conformation which allows the amidase domain to cleave two lactyl-amide bonds located about 103 Å apart on the peptidoglycan.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1373-81"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715007403","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33253301","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}

{"title":"The structure of the giant haemoglobin from Glossoscolex paulistus.","authors":"José Fernando Ruggiero Bachega,&nbsp;Fernando Vasconcelos Maluf,&nbsp;Babak Andi,&nbsp;Humberto D'Muniz Pereira,&nbsp;Marcelo Falsarella Carazzollea,&nbsp;Allen M Orville,&nbsp;Marcel Tabak,&nbsp;José Brandão-Neto,&nbsp;Richard Charles Garratt,&nbsp;Eduardo Horjales Reboredo","doi":"10.1107/S1399004715005453","DOIUrl":"https://doi.org/10.1107/S1399004715005453","url":null,"abstract":"<p><p>The sequences of all seven polypeptide chains from the giant haemoglobin of the free-living earthworm Glossoscolex paulistus (HbGp) are reported together with the three-dimensional structure of the 3.6 MDa complex which they form. The refinement of the full particle, which has been solved at 3.2 Å resolution, the highest resolution reported to date for a hexagonal bilayer haemoglobin composed of 12 protomers, is reported. This has allowed a more detailed description of the contacts between subunits which are essential for particle stability. Interpretation of features in the electron-density maps suggests the presence of metal-binding sites (probably Zn(2+) and Ca(2+)) and glycosylation sites, some of which have not been reported previously. The former appear to be important for the integrity of the particle. The crystal structure of the isolated d chain (d-HbGp) at 2.1 Å resolution shows different interchain contacts between d monomers compared with those observed in the full particle. Instead of forming trimers, as seen in the complex, the isolated d chains associate to form dimers across a crystallographic twofold axis. These observations eliminate the possibility that trimers form spontaneously in solution as intermediates during the formation of the dodecameric globin cap and contribute to understanding of the possible ways in which the particle self-assembles.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1257-71"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715005453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33248375","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}

{"title":"The structure of Aquifex aeolicus FtsH in the ADP-bound state reveals a C2-symmetric hexamer.","authors":"Marina Vostrukhina,&nbsp;Alexander Popov,&nbsp;Elena Brunstein,&nbsp;Martin A Lanz,&nbsp;Renato Baumgartner,&nbsp;Christoph Bieniossek,&nbsp;Magdalena Schacherl,&nbsp;Ulrich Baumann","doi":"10.1107/S1399004715005945","DOIUrl":"https://doi.org/10.1107/S1399004715005945","url":null,"abstract":"<p><p>The crystal structure of a truncated, soluble quadruple mutant of FtsH from Aquifex aeolicus comprising the AAA and protease domains has been determined at 2.96 Å resolution in space group I222. The protein crystallizes as a hexamer, with the protease domain forming layers in the ab plane. Contacts between these layers are mediated by the AAA domains. These are highly disordered in one crystal form, but are clearly visible in a related form with a shorter c axis. Here, adenosine diphosphate (ADP) is bound to each subunit and the AAA ring exhibits twofold symmetry. The arrangement is different from the ADP-bound state of an analogously truncated, soluble FtsH construct from Thermotoga maritima. The pore is completely closed and the phenylalanine residues in the pore line a contiguous path. The protease hexamer is very similar to those described for other FtsH structures. To resolve certain open issues regarding a conserved glycine in the linker between the AAA and protease domains, as well as the active-site switch β-strand, mutations have been introduced in the full-length membrane-bound protein. Activity analysis of these point mutants reveals the crucial importance of these residues for proteolytic activity and is in accord with previous interpretation of the active-site switch and the importance of the linker glycine residue.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 6","pages":"1307-18"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715005945","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33248379","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}

{"title":"Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus.","authors":"Hironaga Akita,&nbsp;Tomonari Seto,&nbsp;Toshihisa Ohshima,&nbsp;Haruhiko Sakuraba","doi":"10.1107/S1399004715003673","DOIUrl":"https://doi.org/10.1107/S1399004715003673","url":null,"abstract":"<p><p>Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those of Symbiobacterium thermophilum DAPDH. However, the subunit arrangement of U. thermosphaericus DAPDH (a dimer) was totally different from that of the S. thermophilum enzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophile Corynebacterium glutamicum revealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability of U. thermosphaericus DAPDH. This differs from S. thermophilum DAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site of U. thermosphaericus DAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akita et al. (2012). Biotechnol. Lett. 34, 1693-1699; 1701-1702]. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 5","pages":"1136-46"},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715003673","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33152974","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}