Journal of structural and functional genomics最新文献

{"title":"Expression, purification, and crystallization of Schizosaccharomyces pombe eIF2B","authors":"K. Kashiwagi, T. Shigeta, H. Imataka, Takuhiro Ito, S. Yokoyama","doi":"10.1007/s10969-016-9203-3","DOIUrl":"https://doi.org/10.1007/s10969-016-9203-3","url":null,"abstract":"","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"40 1","pages":"33 - 38"},"PeriodicalIF":0.0,"publicationDate":"2016-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76950343","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 impact of structural genomics: the first quindecennial","authors":"M. Grabowski, E. Niedzialkowska, M. Zimmerman, W. Minor","doi":"10.1007/s10969-016-9201-5","DOIUrl":"https://doi.org/10.1007/s10969-016-9201-5","url":null,"abstract":"","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"95 1","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2016-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83400821","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 of the MazG-related nucleoside triphosphate pyrophosphohydrolase from Thermotoga maritima MSB8.","authors":"Balasundaram Padmanabhan,&nbsp;Prashant Deshmukh,&nbsp;Shigeyuki Yokoyama,&nbsp;Yoshitaka Bessho","doi":"10.1007/s10969-015-9195-4","DOIUrl":"https://doi.org/10.1007/s10969-015-9195-4","url":null,"abstract":"<p><p>The MazG family proteins, which are highly conserved in bacteria, are nucleoside triphosphate pyrophosphohydrolases that hydrolyze all canonical nucleoside triphosphates, and are also involved in removing noncanonical nucleoside triphosphates to prevent their incorporation into DNA or RNA. The primary structure of TM0360 from Thermotoga maritima MSB8 suggested that TM0360 is a MazG-related nucleoside triphosphate pyrophosphohydrolase. The crystal structure of the TM0360 protein was determined by the MAD technique at 2.0 Å resolution. The asymmetric unit contains an intact dimer molecule. The overall structure of TM0360 is similar to the known structures of the dimeric MazG protein and dUTPases. The putative NTP binding pocket in TM0360, identified by considering the probable NTP-interacting residues and structural features, suggested that TM0360 resembles the C-terminal domain of Escherichia coli MazG, although TM0360 may be a truncated paralog of the N-terminal domain of T. maritima MazG (TM0913), according to its primary structure. The putative function of TM0360 is discussed, based on structural homology. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 2","pages":"81-9"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9195-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33119361","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":"Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.","authors":"Naoya Tochio,&nbsp;Takashi Umehara,&nbsp;Kazuhiko Nakabayashi,&nbsp;Misao Yoneyama,&nbsp;Kengo Tsuda,&nbsp;Mikako Shirouzu,&nbsp;Seizo Koshiba,&nbsp;Satoru Watanabe,&nbsp;Takanori Kigawa,&nbsp;Takehiko Sasazuki,&nbsp;Senji Shirasawa,&nbsp;Shigeyuki Yokoyama","doi":"10.1007/s10969-015-9196-3","DOIUrl":"https://doi.org/10.1007/s10969-015-9196-3","url":null,"abstract":"<p><p>ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4-ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4-ZF5 interfinger linker in the regulation of ZFAT function. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 2","pages":"55-65"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9196-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33155277","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":"Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies.","authors":"David J Aceti,&nbsp;Craig A Bingman,&nbsp;Russell L Wrobel,&nbsp;Ronnie O Frederick,&nbsp;Shin-Ichi Makino,&nbsp;Karl W Nichols,&nbsp;Sarata C Sahu,&nbsp;Lai F Bergeman,&nbsp;Paul G Blommel,&nbsp;Claudia C Cornilescu,&nbsp;Katarzyna A Gromek,&nbsp;Kory D Seder,&nbsp;Soyoon Hwang,&nbsp;John G Primm,&nbsp;Grzegorz Sabat,&nbsp;Frank C Vojtik,&nbsp;Brian F Volkman,&nbsp;Zsolt Zolnai,&nbsp;George N Phillips,&nbsp;John L Markley,&nbsp;Brian G Fox","doi":"10.1007/s10969-015-9198-1","DOIUrl":"https://doi.org/10.1007/s10969-015-9198-1","url":null,"abstract":"<p><p>Vectors designed for protein production in Escherichia coli and by wheat germ cell-free translation were tested using 21 well-characterized eukaryotic proteins chosen to serve as controls within the context of a structural genomics pipeline. The controls were carried through cloning, small-scale expression trials, large-scale growth or synthesis, and purification. Successfully purified proteins were also subjected to either crystallization trials or (1)H-(15)N HSQC NMR analyses. Experiments evaluated: (1) the relative efficacy of restriction/ligation and recombinational cloning systems; (2) the value of maltose-binding protein (MBP) as a solubility enhancement tag; (3) the consequences of in vivo proteolysis of the MBP fusion as an alternative to post-purification proteolysis; (4) the effect of the level of LacI repressor on the yields of protein obtained from E. coli using autoinduction; (5) the consequences of removing the His tag from proteins produced by the cell-free system; and (6) the comparative performance of E. coli cells or wheat germ cell-free translation. Optimal promoter/repressor and fusion tag configurations for each expression system are discussed. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 2","pages":"67-80"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9198-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33075194","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":"Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.","authors":"Thomas E Edwards,&nbsp;Loren Baugh,&nbsp;Jameson Bullen,&nbsp;Ruth O Baydo,&nbsp;Pam Witte,&nbsp;Kaitlin Thompkins,&nbsp;Isabelle Q H Phan,&nbsp;Jan Abendroth,&nbsp;Matthew C Clifton,&nbsp;Banumathi Sankaran,&nbsp;Wesley C Van Voorhis,&nbsp;Peter J Myler,&nbsp;Bart L Staker,&nbsp;Christoph Grundner,&nbsp;Donald D Lorimer","doi":"10.1007/s10969-015-9197-2","DOIUrl":"https://doi.org/10.1007/s10969-015-9197-2","url":null,"abstract":"<p><p>The methylmalonyl Co-A mutase-associated GTPase MeaB from Methylobacterium extorquens is involved in glyoxylate regulation and required for growth. In humans, mutations in the homolog methylmalonic aciduria associated protein (MMAA) cause methylmalonic aciduria, which is often fatal. The central role of MeaB from bacteria to humans suggests that MeaB is also important in other, pathogenic bacteria such as Mycobacterium tuberculosis. However, the identity of the mycobacterial MeaB homolog is presently unclear. Here, we identify the M. tuberculosis protein Rv1496 and its homologs in M. smegmatis and M. thermoresistibile as MeaB. The crystal structures of all three homologs are highly similar to MeaB and MMAA structures and reveal a characteristic three-domain homodimer with GDP bound in the G domain active site. A structure of Rv1496 obtained from a crystal grown in the presence of GTP exhibited electron density for GDP, suggesting GTPase activity. These structures identify the mycobacterial MeaB and provide a structural framework for therapeutic targeting of M. tuberculosis MeaB. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 2","pages":"91-9"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9197-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33180961","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":"Annotation of proteins of unknown function: initial enzyme results.","authors":"Talia McKay,&nbsp;Kaitlin Hart,&nbsp;Alison Horn,&nbsp;Haeja Kessler,&nbsp;Greg Dodge,&nbsp;Keti Bardhi,&nbsp;Kostandina Bardhi,&nbsp;Jeffrey L Mills,&nbsp;Herbert J Bernstein,&nbsp;Paul A Craig","doi":"10.1007/s10969-015-9194-5","DOIUrl":"https://doi.org/10.1007/s10969-015-9194-5","url":null,"abstract":"<p><p>Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having \"unknown function\". Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 1","pages":"43-54"},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9194-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33335063","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":"X-ray structure of the mature ectodomain of phogrin.","authors":"Martín E Noguera,&nbsp;María E Primo,&nbsp;Jean Jakoncic,&nbsp;Edgardo Poskus,&nbsp;Michele Solimena,&nbsp;Mario R Ermácora","doi":"10.1007/s10969-014-9191-0","DOIUrl":"https://doi.org/10.1007/s10969-014-9191-0","url":null,"abstract":"<p><p>Phogrin/IA-2β and ICA512/IA-2 are two paralogs receptor-type protein-tyrosine phosphatases (RPTP) that localize in secretory granules of various neuroendocrine cells. In pancreatic islet β-cells, they participate in the regulation of insulin secretion, ensuring proper granulogenesis, and β-cell proliferation. The role of their cytoplasmic tail has been partially unveiled, while that of their luminal region remains unclear. To advance the understanding of its structure-function relationship, the X-ray structure of the mature ectodomain of phogrin (ME phogrin) at pH 7.4 and 4.6 has been solved at 1.95- and 2.01-Å resolution, respectively. Similarly to the ME of ICA512, ME phogrin adopts a ferredoxin-like fold: a sheet of four antiparallel β-strands packed against two α-helices. Sequence conservation among vertebrates, plants and insects suggests that the structural similarity extends to all the receptor family. Crystallized ME phogrin is monomeric, in agreement with solution studies but in striking contrast with the behavior of homodimeric ME ICA512. The structural details that may cause the quaternary structure differences are analyzed. The results provide a basis for building models of the overall orientation and oligomerization state of the receptor in biological membranes. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9191-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32834126","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":"Expression, purification, crystallization, and preliminary X-ray crystallographic studies of the human adiponectin receptors, AdipoR1 and AdipoR2.","authors":"Hiroaki Tanabe,&nbsp;Kanna Motoyama,&nbsp;Mariko Ikeda,&nbsp;Motoaki Wakiyama,&nbsp;Takaho Terada,&nbsp;Noboru Ohsawa,&nbsp;Toshiaki Hosaka,&nbsp;Masakatsu Hato,&nbsp;Yoshifumi Fujii,&nbsp;Yoshihiro Nakamura,&nbsp;Satoshi Ogasawara,&nbsp;Tomoya Hino,&nbsp;Takeshi Murata,&nbsp;So Iwata,&nbsp;Miki Okada-Iwabu,&nbsp;Masato Iwabu,&nbsp;Kunio Hirata,&nbsp;Yoshiaki Kawano,&nbsp;Masaki Yamamoto,&nbsp;Tomomi Kimura-Someya,&nbsp;Mikako Shirouzu,&nbsp;Toshimasa Yamauchi,&nbsp;Takashi Kadowaki,&nbsp;Shigeyuki Yokoyama","doi":"10.1007/s10969-014-9192-z","DOIUrl":"https://doi.org/10.1007/s10969-014-9192-z","url":null,"abstract":"<p><p>The adiponectin receptors (AdipoR1 and AdipoR2) are membrane proteins with seven transmembrane helices. These receptors regulate glucose and fatty acid metabolism, thereby ameliorating type 2 diabetes. The full-length human AdipoR1 and a series of N-terminally truncated mutants of human AdipoR1 and AdipoR2 were expressed in insect cells. In small-scale size exclusion chromatography, the truncated mutants AdipoR1Δ88 (residues 89-375) and AdipoR2Δ99 (residues 100-386) eluted mostly in the intact monodisperse state, while the others eluted primarily as aggregates. However, gel filtration chromatography of the large-scale preparation of the tag-affinity-purified AdipoR1Δ88 revealed the presence of an excessive amount of the aggregated state over the intact state. Since aggregation due to contaminating nucleic acids may have occurred during the sample concentration step, anion-exchange column chromatography was performed immediately after affinity chromatography, to separate the intact AdipoR1Δ88 from the aggregating species. The separated intact AdipoR1Δ88 did not undergo further aggregation, and was successfully purified to homogeneity by gel filtration chromatography. The purified AdipoR1Δ88 and AdipoR2Δ99 proteins were characterized by thermostability assays with 7-diethylamino-3-(4-maleimidophenyl)-4-methyl coumarin, thin layer chromatography of bound lipids, and surface plasmon resonance analysis of ligand binding, demonstrating their structural integrities. The AdipoR1Δ88 and AdipoR2Δ99 proteins were crystallized with the anti-AdipoR1 monoclonal antibody Fv fragment, by the lipidic mesophase method. X-ray diffraction data sets were obtained at resolutions of 2.8 and 2.4 Å, respectively. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 1","pages":"11-23"},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9192-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32963923","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 SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.).","authors":"Tatsuo Yanagisawa, Ryohei Ishii, Yasushi Hikida, Ryuya Fukunaga, Toru Sengoku, Shun-ichi Sekine, Shigeyuki Yokoyama","doi":"10.1007/s10969-015-9193-6","DOIUrl":"10.1007/s10969-015-9193-6","url":null,"abstract":"<p><p>The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu (\"EF-Pyl\"). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r.m.s.d. < 0.1 Å). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu/SelB/aIF2γ, are packed against one another to form a closed architecture. The MM1309 structures resemble those of bacterial/archaeal SelB, bacterial EF-Tu in the GTP-bound form, and archaeal initiation factor aIF2γ, in this order. The GMPPNP and GDP molecules are visible in their co-crystal structures. Isothermal titration calorimetry measurements of MM1309·GTP·Mg(2+), MM1309·GDP·Mg(2+), and MM1309·GMPPNP·Mg(2+) provided dissociation constants of 0.43, 26.2, and 222.2 μM, respectively. Therefore, the affinities of MM1309 for GTP and GDP are similar to those of SelB rather than those of EF-Tu. Furthermore, the switch I and II regions of MM1309 are involved in domain-domain interactions, rather than nucleotide binding. The putative binding pocket for the aminoacyl moiety on MM1309 is too small to accommodate the pyrrolysyl moiety, based on a comparison of the present MM1309 structures with that of the EF-Tu·GMPPNP·aminoacyl-tRNA ternary complex. A hydrolysis protection assay revealed that MM1309 binds cysteinyl (Cys)-tRNA(Cys) and protects the aminoacyl bond from non-enzymatic hydrolysis. Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNA(Cys). </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"16 1","pages":"25-41"},"PeriodicalIF":0.0,"publicationDate":"2015-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4329189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33000899","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}