BMC Structural Biology最新文献

{"title":"Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans","authors":"Laila Niiranen,&nbsp;Kjersti Lian,&nbsp;Kenneth A Johnson,&nbsp;Elin Moe","doi":"10.1186/s12900-015-0032-6","DOIUrl":"https://doi.org/10.1186/s12900-015-0032-6","url":null,"abstract":"<p>\u0000 <i>Deinococcus radiodurans</i> is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of <i>D. radiodurans</i> β-clamp (<i>Dr</i>β-clamp) at 2.0 ? resolution.</p><p>The sequence verification process revealed that at the time of the study the gene encoding <i>Dr</i>β-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution.</p><p>The structure of <i>Dr</i>β-clamp was determined to 2.0 ? resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in <i>D. radiodurans</i> upon exposure to high doses of ionizing irradiation or desiccation.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"15 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2015-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-015-0032-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5039602","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":"BMC Structural Biology reviewer acknowledgment 2014","authors":"Catherine J Potenski","doi":"10.1186/s12900-015-0029-1","DOIUrl":"https://doi.org/10.1186/s12900-015-0029-1","url":null,"abstract":"","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"15 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2015-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-015-0029-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4969351","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":"Crystal structure and biophysical characterization of the nucleoside diphosphate kinase from Leishmania braziliensis","authors":"Plínio Salmazo Vieira,&nbsp;Priscila Oliveira de Giuseppe,&nbsp;Mario Tyago Murakami,&nbsp;Arthur Henrique Cavalcante de Oliveira","doi":"10.1186/s12900-015-0030-8","DOIUrl":"https://doi.org/10.1186/s12900-015-0030-8","url":null,"abstract":"<p>Nucleoside diphosphate kinase (NDK) is a housekeeping enzyme that plays key roles in nucleotide recycling and homeostasis in trypanosomatids. It is also secreted by the intracellular parasite <i>Leishmania</i> to modulate the host response. These functions make NDK an attractive target for drug design and for studies aiming at a better understanding of the mechanisms mediating host-pathogen interactions.</p><p>We report the crystal structure and biophysical characterization of the NDK from <i>Leishmania braziliensis</i> (<i>Lb</i>NDK). The subunit consists of six α-helices along with a core of four β-strands arranged in a β2β3β1β4 antiparallel topology order. In contrast to the NDK from <i>L. major,</i> the <i>Lb</i>NDK C-terminal extension is partially unfolded. SAXS data showed that <i>Lb</i>NDK forms hexamers in solution in the pH range from 7.0 to 4.0, a hydrodynamic behavior conserved in most eukaryotic NDKs. However, DSF assays show that acidification and alkalization decrease the hexamer stability.</p><p>Our results support that <i>Lb</i>NDK remains hexameric in pH conditions akin to that faced by this enzyme when secreted by <i>Leishmania</i> amastigotes in the parasitophorous vacuoles (pH?4.7 to 5.3). The unusual unfolded conformation of <i>Lb</i>NDK C-terminus decreases the surface buried in the trimer interface exposing new regions that might be explored for the development of compounds designed to disturb enzyme oligomerization, which may impair the important nucleotide salvage pathway in these parasites.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"15 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2015-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-015-0030-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4116109","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":"Structural importance of the C-terminal region in pig aldo-keto reductase family 1 member C1 and their effects on enzymatic activity","authors":"Minky Son,&nbsp;Chanin Park,&nbsp;Seul Gi Kwon,&nbsp;Woo Young Bang,&nbsp;Sam Woong Kim,&nbsp;Chul Wook Kim,&nbsp;Keun Woo Lee","doi":"10.1186/s12900-014-0028-7","DOIUrl":"https://doi.org/10.1186/s12900-014-0028-7","url":null,"abstract":"<p>Pig aldo-keto reductase family 1 member C1 (AKR1C1) belongs to AKR superfamily which catalyzes the NAD(P)H-dependent reduction of various substrates including steroid hormones. Previously we have reported two paralogous pig AKR1C1s, wild-type AKR1C1 (C-type) and C-terminal-truncated AKR1C1 (T-type). Also, the C-terminal region significantly contributes to the NADPH-dependent reductase activity for 5α-DHT reduction. Molecular modeling studies combined with kinetic experiments were performed to investigate structural and enzymatic differences between wild-type AKR1C1 C-type and T-type.</p><p>The results of the enzyme kinetics revealed that <i>V</i>\u0000 _max and <i>k</i>\u0000 _cat values of the T-type were 2.9 and 1.6 folds higher than those of the C-type. Moreover, catalytic efficiency was also 1.9 fold higher in T-type compared to C-type. Since x-ray crystal structures of pig AKR1C1 were not available, three dimensional structures of the both types of the protein were predicted using homology modeling methodology and they were used for molecular dynamics simulations. The structural comparisons between C-type and T-type showed that 5α-DHT formed strong hydrogen bonds with catalytic residues such as Tyr55 and His117 in T-type. In particular, C3 ketone group of the substrate was close to Tyr55 and NADPH in T-type.</p><p>Our results showed that 5α-DHT binding in T-type was more favorable for catalytic reaction to facilitate hydride transfer from the cofactor, and were consistent with experimental results. We believe that our study provides valuable information to understand important role of C-terminal region that affects enzymatic properties for 5α-DHT, and further molecular mechanism for the enzyme kinetics of AKR1C1 proteins.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"15 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2015-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0028-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4532458","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":"In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L","authors":"Masayo Morishita,&nbsp;Damiaan Mevius,&nbsp;Eric di Luccio","doi":"10.1186/s12900-014-0025-x","DOIUrl":"https://doi.org/10.1186/s12900-014-0025-x","url":null,"abstract":"<p>Histone lysine methylation has a pivotal role in regulating the chromatin. Histone modifiers, including histone methyl transferases (HMTases), have clear roles in human carcinogenesis but the extent of their functions and regulation are not well understood. The NSD family of HMTases comprised of three members (NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L) are oncogenes aberrantly expressed in several cancers, suggesting their potential to serve as novel therapeutic targets. However, the substrate specificity of the NSDs and the molecular mechanism of histones H3 and H4 recognition and methylation have not yet been established.</p><p>Herein, we investigated the <i>in vitro</i> mechanisms of histones H3 and H4 recognition and modifications by the catalytic domain of NSD family members. In this study, we quantified <i>in vitro</i> mono-, di- and tri- methylations on H3K4, H3K9, H3K27, H3K36, H3K79, and H4K20 by the carboxyl terminal domain (CTD) of NSD1, NSD2 and NSD3, using histone as substrate. Next, we used a molecular modelling approach and docked 6-mer peptides H3K4 a.a. 1-7; H3K9 a.a. 5-11; H3K27 a.a. 23-29; H3K36 a.a. 32-38; H3K79 a.a. 75-81; H4K20 a.a. 16-22 with the catalytic domain of the NSDs to provide insight into lysine-marks recognition and methylation on histones H3 and H4.</p><p>Our data highlight the versatility of NSD1, NSD2, and NSD3 for recognizing and methylating several histone lysine marks on histones H3 and H4. Our work provides a basis to design selective and specific NSDs inhibitors. We discuss the relevance of our findings for the development of NSD inhibitors amenable for novel chemotherapies.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0025-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4484654","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 insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering","authors":"Hunho Jo,&nbsp;Eui Young Jeong,&nbsp;Jinseong Jeon,&nbsp;Changill Ban","doi":"10.1186/s12900-014-0024-y","DOIUrl":"https://doi.org/10.1186/s12900-014-0024-y","url":null,"abstract":"<p>Polymyxin B resistance protein D (PmrD) plays a key role in the polymyxin B-resistance pathway, as it is the signaling protein that can act as a specific connecter between PmrA/PmrB and PhoP/PhoQ. We conducted structural analysis to characterize <i>Escherichia coli</i> (<i>E. coli</i>) PmrD, which exhibits different features compared with PmrD in other bacteria.</p><p>The X-ray crystal structure of <i>E. coli</i> PmrD was determined at a 2.00?? resolution, revealing novel information such as the unambiguous secondary structures of the protein and the presence of a disulfide bond. Furthermore, various assays such as native gel electrophoresis, surface plasmon resonance (SPR), size-exclusion chromatography, dynamic light scattering (DLS), and small-angle X-ray scattering (SAXS) measurements, were performed to elucidate the structural and functional role of the internal disulfide bond in <i>E. coli</i> PmrD.</p><p>The structural characteristics of <i>E. coli</i> PmrD were clearly identified via diverse techniques. The findings help explain the different protective mechanism of <i>E. coli</i> compared to other Gram-negative bacteria.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0024-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4200509","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":"Structure and functional characterization of pyruvate decarboxylase from Gluconacetobacter diazotrophicus","authors":"Leonardo J van Zyl,&nbsp;Wolf-Dieter Schubert,&nbsp;Marla I Tuffin,&nbsp;Don A Cowan","doi":"10.1186/s12900-014-0021-1","DOIUrl":"https://doi.org/10.1186/s12900-014-0021-1","url":null,"abstract":"<p>Bacterial pyruvate decarboxylases (PDC) are rare. Their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. PDCs from <i>Zymomonas mobilis</i> (ZmPDC), <i>Zymobacter palmae</i> (ZpPDC) and <i>Sarcina ventriculi</i> (SvPDC) have been characterized and ZmPDC has been produced successfully in a range of heterologous hosts. PDCs from the <i>Acetobacteraceae</i> and their role in metabolism have not been characterized to the same extent<i>.</i> Examples include <i>Gluconobacter oxydans</i> (GoPDC), <i>G. diazotrophicus</i> (GdPDC) and <i>Acetobacter pasteutrianus</i> (ApPDC). All of these organisms are of commercial importance.</p><p>This study reports the kinetic characterization and the crystal structure of a PDC from <i>Gluconacetobacter diazotrophicus</i> (GdPDC). Enzyme kinetic analysis indicates a high affinity for pyruvate (<i>K</i>_{\u0000 <i>M</i>\u0000} 0.06 mM at pH 5), high catalytic efficiencies (1.3 ? 10⁶ M^?1?s^?1 at pH 5), pH_opt of 5.5 and T_opt at 45°C. The enzyme is not thermostable (T_? of 18 minutes at 60°C) and the calculated number of bonds between monomers and dimers do not give clear indications for the relatively lower thermostability compared to other PDCs. The structure is highly similar to those described for <i>Z. mobilis</i> (ZmPDC) and <i>A. pasteurianus</i> PDC (ApPDC) with a rmsd value of 0.57 ? for Cα when comparing GdPDC to that of ApPDC. Indole-3-pyruvate does not serve as a substrate for the enzyme. Structural differences occur in two loci, involving the regions Thr341 to Thr352 and Asn499 to Asp503.</p><p>This is the first study of the PDC from <i>G. diazotrophicus</i> (PAL5) and lays the groundwork for future research into its role in this endosymbiont. The crystal structure of GdPDC indicates the enzyme to be evolutionarily closely related to homologues from <i>Z. mobilis</i> and <i>A. pasteurianus</i> and suggests strong selective pressure to keep the enzyme characteristics in a narrow range. The pH optimum together with reduced thermostability likely reflect the host organisms niche and conditions under which these properties have been naturally selected for. The lack of activity on indole-3-pyruvate excludes this decarboxylase as the enzyme responsible for indole acetic acid production in <i>G. diazotrophicus.</i></p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0021-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4225598","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":"Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species","authors":"Kirill E. Medvedev,&nbsp;Nikolay A. Alemasov,&nbsp;Yuri N. Vorobjev,&nbsp;Elena V. Boldyreva,&nbsp;Nikolay A. Kolchanov,&nbsp;Dmitry A. Afonnikov","doi":"10.1186/s12900-014-0023-z","DOIUrl":"https://doi.org/10.1186/s12900-014-0023-z","url":null,"abstract":"<p>The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (<i>P. furiosus</i>) and the deep-water (<i>P. abyssi</i>) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures.</p><p>The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the <i>P. abyssi</i> Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.</p><p>The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0023-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4628411","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":"Buried chloride stereochemistry in the Protein Data Bank","authors":"Oliviero Carugo","doi":"10.1186/s12900-014-0019-8","DOIUrl":"https://doi.org/10.1186/s12900-014-0019-8","url":null,"abstract":"<p>Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres.</p><p>The analysis of a non-redundant set (pairwise sequence identity?&lt;?30%) of 1739 high resolution (&lt;2??) crystal structures that contain at least one chloride anion shows that the first coordination spheres of the chlorides are essentially constituted by hydrogen bond donors. Amongst the side-chains positively charged, arginine interacts with chlorides much more frequently than lysine. Although the most common coordination number is 4, the coordination stereochemistry is closer to the expected geometry when the coordination number is 5, suggesting that this is the coordination number towards which the chlorides tend when they interact with proteins.</p><p>The results of these analyses are useful in interpreting, describing, and validating new protein crystal structures that contain chloride anions.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0019-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4911338","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 recognition of amino-acylated initiator tRNA by eIF5B in the 80S initiation complex","authors":"Bernhard Kuhle,&nbsp;Ralf Ficner","doi":"10.1186/s12900-014-0020-2","DOIUrl":"https://doi.org/10.1186/s12900-014-0020-2","url":null,"abstract":"<p>From bacteria to eukarya, the specific recognition of the amino-acylated initiator tRNA by the universally conserved translational GTPase eIF5B/IF2 is one of the most central interactions in the process of translation initiation. However, the molecular details, particularly also in the context of ribosomal initiation complexes, are only partially understood.</p><p>A reinterpretation of the 6.6 ? resolution cryo-electron microscopy (cryo-EM) structure of the eukaryal 80S initiation complex using the recently published crystal structure of eIF5B reveals that domain IV of eIF5B forms extensive interaction interfaces with the Met-tRNA_i, which, in contrast to the previous model, directly involve the methionylated 3′ CCA-end of the acceptor stem. These contacts are mediated by a conserved surface area, which is homologous to the surface areas mediating the interactions between IF2 and fMet-tRNA^fMet as well as between domain II of EF-Tu and amino-acylated elongator tRNAs.</p><p>The reported observations provide novel direct structural insight into the specific recognition of the methionylated acceptor stem by eIF5B domain IV and demonstrate its universality among eIF5B/IF2 orthologs in the three domains of life.</p>","PeriodicalId":498,"journal":{"name":"BMC Structural Biology","volume":"14 1","pages":""},"PeriodicalIF":2.222,"publicationDate":"2014-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12900-014-0020-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4703017","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}