Acta crystallographica. Section D, Biological crystallography最新文献

{"title":"A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime.","authors":"Patricia M Legler,&nbsp;Iswarduth Soojhawon,&nbsp;Charles B Millard","doi":"10.1107/S1399004715011281","DOIUrl":"https://doi.org/10.1107/S1399004715011281","url":null,"abstract":"<p><p>As part of ongoing efforts to design improved nerve agent antidotes, two X-ray crystal structures of Torpedo californica acetylcholinesterase (TcAChE) bound to the bis-pyridinium oxime, Ortho-7, or its experimental bis-imidazolium analogue, 2BIM-7, were determined. Bis-oximes contain two oxime groups connected by a hydrophobic linker. One oxime group of Ortho-7 binds at the entrance to the active-site gorge near Trp279, and the second binds at the bottom near Trp84 and Phe330. In the Ortho-7-TcAChE complex the oxime at the bottom of the gorge was directed towards the nucleophilic Ser200. In contrast, the oxime group of 2BIM-7 was rotated away from Ser200 and the oxime at the entrance induced a significant conformational change in the peripheral anionic site (PAS) residue Trp279. The conformational change alters the surface of the PAS and positions the imidazolium oxime of 2BIM-7 further from Ser200. The relatively weaker binding and poorer reactivation of VX-inhibited, tabun-inhibited or sarin-inhibited human acetylcholinesterase by 2BIM-7 compared with Ortho-7 may in part be owing to the unproductively bound states caught in crystallo. Overall, the reactivation efficiency of 2BIM-7 was comparable to that of 2-pyridine aldoxime methyl chloride (2-PAM), but unlike 2-PAM the bis-imidazolium oxime lacks a fixed charge, which may affect its membrane permeability. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1788-98"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715011281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33968102","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":"Refining a model electron-density map via the Phantom Derivative method.","authors":"Maria Cristina Burla,&nbsp;Benedetta Carrozzini,&nbsp;Giovanni Luca Cascarano,&nbsp;Carmelo Giacovazzo,&nbsp;Giampiero Polidori","doi":"10.1107/S1399004715013024","DOIUrl":"https://doi.org/10.1107/S1399004715013024","url":null,"abstract":"<p><p>The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1864-71"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34034513","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":"ARCIMBOLDO_LITE: single-workstation implementation and use.","authors":"Massimo Sammito,&nbsp;Claudia Millán,&nbsp;Dawid Frieske,&nbsp;Eloy Rodríguez-Freire,&nbsp;Rafael J Borges,&nbsp;Isabel Usón","doi":"10.1107/S1399004715010846","DOIUrl":"https://doi.org/10.1107/S1399004715010846","url":null,"abstract":"<p><p>ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1921-30"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715010846","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33965227","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":"Structures of the methyltransferase component of Desulfitobacterium hafniense DCB-2 O-demethylase shed light on methyltetrahydrofolate formation.","authors":"Hanno Sjuts,&nbsp;Mark S Dunstan,&nbsp;Karl Fisher,&nbsp;David Leys","doi":"10.1107/S1399004715013061","DOIUrl":"https://doi.org/10.1107/S1399004715013061","url":null,"abstract":"<p><p>O-Demethylation by acetogenic or organohalide-respiring bacteria leads to the formation of methyltetrahydrofolate from aromatic methyl ethers. O-Demethylases, which are cobalamin-dependent, three-component enzyme systems, catalyse methyl-group transfers from aromatic methyl ethers to tetrahydrofolate via methylcobalamin intermediates. In this study, crystal structures of the tetrahydrofolate-binding methyltransferase module from a Desulfitobacterium hafniense DCB-2 O-demethylase were determined both in complex with tetrahydrofolate and the product methyltetrahydrofolate. While these structures are similar to previously determined methyltransferase structures, the position of key active-site residues is subtly altered. A strictly conserved Asn is displaced to establish a putative proton-transfer network between the substrate N5 and solvent. It is proposed that this supports the efficient catalysis of methyltetrahydrofolate formation, which is necessary for efficient O-demethylation. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1900-8"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33965225","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 conformational switching in the copper metalloregulator CsoR from Streptomyces lividans.","authors":"Tatiana V Porto,&nbsp;Michael A Hough,&nbsp;Jonathan A R Worrall","doi":"10.1107/S1399004715013012","DOIUrl":"https://doi.org/10.1107/S1399004715013012","url":null,"abstract":"<p><p>Copper-sensitive operon repressors (CsoRs) act to sense cuprous ions and bind them with a high affinity under copper stress in many bacteria. The binding of copper(I) leads to a conformational change in their homotetramer structure, causing disassembly of the operator DNA-CsoR complex and evoking a transcriptional response. Atomic-level structural insight into the conformational switching mechanism between the apo and metal-bound states is lacking. Here, a new X-ray crystal structure of the CsoR from Streptomyces lividans is reported and compared with a previously reported S. lividans CsoR X-ray structure crystallized under different conditions. Based on evidence from this new X-ray structure, it is revealed that the conformational switching between states centres on a concertina effect at the C-terminal end of each α2 helix in the homotetramer. This drives the Cys104 side chain, a copper(I)-ligating residue, into a position enabling copper(I) coordination and as a result disrupts the α2-helix geometry, leading to a compacting and twisting of the homotetramer structure. Strikingly, the conformational switching induces a redistribution of electrostatic surface potential on the tetrameric DNA-binding face, which in the copper(I)-bound state would no longer favour interaction with the mode of operator DNA binding. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1872-8"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34034514","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 the novel inhibition mechanism of Trypanosoma cruzi spermidine synthase.","authors":"Yasushi Amano,&nbsp;Ichiji Namatame,&nbsp;Yukihiro Tateishi,&nbsp;Kazuya Honboh,&nbsp;Eiki Tanabe,&nbsp;Tatsuya Niimi,&nbsp;Hitoshi Sakashita","doi":"10.1107/S1399004715013048","DOIUrl":"https://doi.org/10.1107/S1399004715013048","url":null,"abstract":"<p><p>Trypanosoma cruzi causes Chagas disease, a severe disease affecting 8-10 million people in Latin America. While nifurtimox and benznidazole are used to treat this disease, their efficacy is limited and adverse effects are observed. New therapeutic targets and novel drugs are therefore urgently required. Enzymes in the polyamine-trypanothione pathway are promising targets for the treatment of Chagas disease. Spermidine synthase is a key enzyme in this pathway that catalyzes the transfer of an aminopropyl group from decarboxylated S-adenosylmethionine (dcSAM) to putrescine. Fragment-based drug discovery was therefore conducted to identify novel, potent inhibitors of spermidine synthase from T. cruzi (TcSpdSyn). Here, crystal structures of TcSpdSyn in complex with dcSAM, trans-4-methylcyclohexylamine and hit compounds from fragment screening are reported. The structure of dcSAM complexed with TcSpdSyn indicates that dcSAM stabilizes the conformation of the `gatekeeping' loop to form the putrescine-binding pocket. The structures of fragments bound to TcSpdSyn revealed two fragment-binding sites: the putrescine-binding pocket and the dimer interface. The putrescine-binding pocket was extended by an induced-fit mechanism. The crystal structures indicate that the conformation of the dimer interface is required to stabilize the gatekeeping loop and that fragments binding to this interface inhibit TcSpdSyn by disrupting its conformation. These results suggest that utilizing the dynamic structural changes in TcSpdSyn that occur upon inhibitor binding will facilitate the development of more selective and potent inhibitors. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1879-89"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33965223","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":"Response from Tanley et al. to Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.","authors":"Simon W M Tanley,&nbsp;Kay Diederichs,&nbsp;Loes M J Kroon-Batenburg,&nbsp;Colin Levy,&nbsp;Antoine M M Schreurs,&nbsp;John R Helliwell","doi":"10.1107/S1399004715014340","DOIUrl":"https://doi.org/10.1107/S1399004715014340","url":null,"abstract":"Clearly cisplatin and carboplatin and their interactions with proteins are important as is shown by the various research groups that are actively involved studying these X-ray crystal structures, and which are focused on in the critique article by Shabalin et al. (2015). We welcome this detailed interest by Shabalin et al. in these various crystal structures in the PDB and for harnessing the processed structure factor and derived atomic coordinates data. We have also made available numerous raw diffraction image data sets as due diligence for researchers in this area. Some of these have been harnessed. We aim to complete the availability of the full suite of raw data sets as soon as possible. The suggestions of Shabalin et al. (2015) of the need for improved tools in model validation, especially for metal protein ligand complexes, we also support. Some of the tools that are discussed by Shabalin et al. (2015) are not yet available in e.g the CCP4 suite, which we use predominantly. We also have used the SHELX suite for metal occupancy refinements as a complement to CCP4. The predominant criticisms of our publications by Shabalin et al. (2015) involve our model refinements of hen egg-white lysozyme with various platin metal ligand types. These model refinements are the work and responsibility of SWMT and JRH. We wish to note that we did not use the incorrect PDB ligand for cisplatin cited by Shabalin et al. (2015) and instead used individual atom placements not least for the tendency for the chemical transformation of these two platins that we observed. Shabalin et al. (2015) shared with us their three new refinements, with a brief e-mail commentary, ahead of their publication. These three new model refinements showed differences in approach between our and their methods, namely a larger placement of split occupancy side chains than we had made and placement of a larger number of bound waters. We did not accept the bulk of these changes as there was insufficient, if any, electron-density evidence. However, we do agree with their critical scrutiny of our bound solvent/ solute molecules, highlighted in their article, and the need for some assignment changes or deletion. We note that on these the PDB annotators were very thorough and did offer queries in some cases. SWMT and JRH discussed these but thought that the precision of their placement was poor and the rather","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1982-3"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33967367","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":"Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1.","authors":"Jooyoung Park, Ann M Guggisberg, Audrey R Odom, Niraj H Tolia","doi":"10.1107/S1399004715012067","DOIUrl":"10.1107/S1399004715012067","url":null,"abstract":"<p><p>Haloacid dehalogenases (HADs) are a large enzyme superfamily of more than 500,000 members with roles in numerous metabolic pathways. Plasmodium falciparum HAD1 (PfHAD1) is a sugar phosphatase that regulates the methylerythritol phosphate (MEP) pathway for isoprenoid synthesis in malaria parasites. However, the structural determinants for diverse substrate recognition by HADs are unknown. Here, crystal structures were determined of PfHAD1 in complex with three sugar phosphates selected from a panel of diverse substrates that it utilizes. Cap-open and cap-closed conformations are observed, with cap closure facilitating substrate binding and ordering. These structural changes define the role of cap movement within the major subcategory of C2 HAD enzymes. The structures of an HAD bound to multiple substrates identifies binding and specificity-determining residues that define the structural basis for substrate recognition and catalysis within the HAD superfamily. While the substrate-binding region of the cap domain is flexible in the open conformations, this region becomes ordered and makes direct interactions with the substrate in the closed conformations. These studies further inform the structural and biochemical basis for catalysis within a large superfamily of HAD enzymes with diverse functions.</p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1824-34"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556313/pdf/d-71-01824.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34034509","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":"Crystallographic studies of two variants of Pseudomonas aeruginosa IMPDH with impaired allosteric regulation.","authors":"Gilles Labesse,&nbsp;Thomas Alexandre,&nbsp;Muriel Gelin,&nbsp;Ahmed Haouz,&nbsp;Hélène Munier-Lehmann","doi":"10.1107/S1399004715013115","DOIUrl":"https://doi.org/10.1107/S1399004715013115","url":null,"abstract":"<p><p>Inosine-5'-monophosphate dehydrogenases (IMPDHs), which are the rate-limiting enzymes in guanosine-nucleotide biosynthesis, are important therapeutic targets. Despite in-depth functional and structural characterizations of various IMPDHs, the role of the Bateman domain containing two CBS motifs remains controversial. Their involvement in the allosteric regulation of Pseudomonas aeruginosa IMPDH by Mg-ATP has recently been reported. To better understand the function of IMPDH and the importance of the CBS motifs, the structure of a variant devoid of these modules (ΔCBS) was solved at high resolution in the apo form and in complex with IMP. In addition, a single amino-acid substitution variant, D199N, was also structurally characterized: the mutation corresponds to the autosomal dominant mutant D226N of human IMPDH1, which is responsible for the onset of the retinopathy adRP10. These new structures shed light onto the possible mechanism of regulation of the IMPDH enzymatic activity. In particular, three conserved loops seem to be key players in this regulation as they connect the tetramer-tetramer interface with the active site and show significant modification upon substrate binding. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1890-9"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013115","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33965224","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":"Iron binding to human heavy-chain ferritin.","authors":"Cecilia Pozzi,&nbsp;Flavio Di Pisa,&nbsp;Caterina Bernacchioni,&nbsp;Silvia Ciambellotti,&nbsp;Paola Turano,&nbsp;Stefano Mangani","doi":"10.1107/S1399004715013073","DOIUrl":"https://doi.org/10.1107/S1399004715013073","url":null,"abstract":"<p><p>Maxi-ferritins are ubiquitous iron-storage proteins with a common cage architecture made up of 24 identical subunits of five α-helices that drive iron biomineralization through catalytic iron(II) oxidation occurring at oxidoreductase sites (OS). Structures of iron-bound human H ferritin were solved at high resolution by freezing ferritin crystals at different time intervals after exposure to a ferrous salt. Multiple binding sites were identified that define the iron path from the entry ion channels to the oxidoreductase sites. Similar data are available for another vertebrate ferritin: the M protein from Rana catesbeiana. A comparative analysis of the iron sites in the two proteins identifies new reaction intermediates and underlines clear differences in the pattern of ligands that define the additional iron sites that precede the oxidoreductase binding sites along this path. Stopped-flow kinetics assays revealed that human H ferritin has different levels of activity compared with its R. catesbeiana counterpart. The role of the different pattern of transient iron-binding sites in the OS is discussed with respect to the observed differences in activity across the species. </p>","PeriodicalId":7047,"journal":{"name":"Acta crystallographica. Section D, Biological crystallography","volume":"71 Pt 9","pages":"1909-20"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1399004715013073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33965226","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}