Acta Crystallographica Section F-structural Biology and Crystallization Communications最新文献_第5页

Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase. 铜绿假单胞菌肌苷5′-单磷酸脱氢酶的结构。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-03-01 Epub Date: 2013-02-22 DOI: 10.1107/S1744309113002352

Vincenzo A Rao, Sharon M Shepherd, Richard Owen, William N Hunter

{"title":"Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase.","authors":"Vincenzo A Rao, Sharon M Shepherd, Richard Owen, William N Hunter","doi":"10.1107/S1744309113002352","DOIUrl":"10.1107/S1744309113002352","url":null,"abstract":"Inosine 5'-monophosphate dehydrogenase (IMPDH) represents a potential antimicrobial drug target. The crystal structure of recombinant Pseudomonas aeruginosa IMPDH has been determined to a resolution of 2.25 Å. The structure is a homotetramer of subunits dominated by a (β/α)8-barrel fold, consistent with other known structures of IMPDH. Also in common with previous work, the cystathionine β-synthase domains, residues 92-204, are not present in the model owing to disorder. However, unlike the majority of available structures, clearly defined electron density exists for a loop that creates part of the active site. This loop, composed of residues 297-315, links α8 and β9 and carries the catalytic Cys304. P. aeruginosa IMPDH shares a high level of sequence identity with bacterial and protozoan homologues, with residues involved in binding substrate and the NAD+ cofactor being conserved. Specific differences that have been proven to contribute to selectivity against the human enzyme in a study of Cryptosporidium parvum IMPDH are also conserved, highlighting the potential value of IMPDH as a drug target.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 3","pages":"243-7"},"PeriodicalIF":0.9,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1744309113002352","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9625224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Some practical guidelines for UV imaging in the protein crystallization laboratory. 蛋白质结晶实验室中紫外成像的一些实用指南。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-02-01 Epub Date: 2013-01-26 DOI: 10.1107/S1744309112048634

Sebastien Desbois, Shane A Seabrook, Janet Newman

引用次数: 32

Crystallization and preliminary structure determination of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501. 革兰氏阳性结合质粒pIP501转移蛋白TraM的结晶及初步结构测定。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-02-01 Epub Date: 2013-01-31 DOI: 10.1107/S1744309113000134

Nikolaus Goessweiner-Mohr, Lukas Grumet, Tea Pavkov-Keller, Ruth Birner-Gruenberger, Elisabeth Grohmann, Walter Keller

{"title":"Crystallization and preliminary structure determination of the transfer protein TraM from the Gram-positive conjugative plasmid pIP501.","authors":"Nikolaus Goessweiner-Mohr, Lukas Grumet, Tea Pavkov-Keller, Ruth Birner-Gruenberger, Elisabeth Grohmann, Walter Keller","doi":"10.1107/S1744309113000134","DOIUrl":"10.1107/S1744309113000134","url":null,"abstract":"The major means of horizontal gene spread (e.g. of antibiotic resistance) is conjugative plasmid transfer. It presents a serious threat especially for hospitalized and immuno-suppressed patients, as it can lead to the accelerated spread of bacteria with multiple antibiotic resistances. Detailed information about the process is available only for bacteria of Gram-negative (G-) origin and little is known about the corresponding mechanisms in Gram-positive (G+) bacteria. Here we present the purification, biophysical characterization, crystallization and preliminary structure determination of the TraM C-terminal domain (TraMΔ, comprising residues 190-322 of the full-length protein), a putative transfer protein from the G+ conjugative model plasmid pIP501. The crystals diffracted to 2.5 Å resolution and belonged to space group P1, with unit-cell parameters a = 39.21, b = 54.98, c = 93.47 Å, α = 89.91, β = 86.44, γ = 78.63° and six molecules per asymmetric unit. The preliminary structure was solved by selenomethionine single-wavelength anomalous diffraction.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 2","pages":"178-83"},"PeriodicalIF":0.9,"publicationDate":"2013-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1107/S1744309113000134","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31218914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Expectation bias and information content. 期望偏差与信息内容。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-02-01 Epub Date: 2013-01-19 DOI: 10.1107/S1744309113001486

Zbigniew Dauter, Manfred S Weiss, Howard Einspahr, Edward N Baker

引用次数: 4

The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. 针对铜绿假单胞菌的 AEROPATH 项目：用于评估早期药物发现潜在目标的晶体学研究。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-01-01 Epub Date: 2012-12-25 DOI: 10.1107/S1744309112044739

Lucille Moynie, Robert Schnell, Stephen A McMahon, Tatyana Sandalova, Wassila Abdelli Boulkerou, Jason W Schmidberger, Magnus Alphey, Cyprian Cukier, Fraser Duthie, Jolanta Kopec, Huanting Liu, Agata Jacewicz, William N Hunter, James H Naismith, Gunter Schneider

{"title":"The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.","authors":"Lucille Moynie, Robert Schnell, Stephen A McMahon, Tatyana Sandalova, Wassila Abdelli Boulkerou, Jason W Schmidberger, Magnus Alphey, Cyprian Cukier, Fraser Duthie, Jolanta Kopec, Huanting Liu, Agata Jacewicz, William N Hunter, James H Naismith, Gunter Schneider","doi":"10.1107/S1744309112044739","DOIUrl":"10.1107/S1744309112044739","url":null,"abstract":"Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"69 Pt 1","pages":"25-34"},"PeriodicalIF":0.9,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40218058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystals on the cover 2013. 2013年封面上的水晶。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2013-01-01 Epub Date: 2012-12-31 DOI: 10.1107/S1744309112051950

Howard Einspahr, Manfred S Weiss

引用次数: 1

Complex of myoglobin with phenol bound in a proximal cavity. 肌红蛋白与苯酚结合在近端空腔中的复合物。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-12-01 Epub Date: 2012-11-19 DOI: 10.1107/S1744309112045514

Xiao Huang, Chunxue Wang, Lesa R Celeste, Leslie L Lovelace, Shenfang Sun, John H Dawson, Lukasz Lebioda

{"title":"Complex of myoglobin with phenol bound in a proximal cavity.","authors":"Xiao Huang, Chunxue Wang, Lesa R Celeste, Leslie L Lovelace, Shenfang Sun, John H Dawson, Lukasz Lebioda","doi":"10.1107/S1744309112045514","DOIUrl":"10.1107/S1744309112045514","url":null,"abstract":"Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with Cβ and Cγ of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 12","pages":"1465-71"},"PeriodicalIF":0.9,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509966/pdf/f-68-01465.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31081142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex. Mn2+与非自互补的z型DNA双工的相互作用。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-12-01 Epub Date: 2012-11-14 DOI: 10.1107/S1744309112041759

P K Mandal, S Venkadesh, N Gautham

引用次数: 7

Purification, crystallization and preliminary X-ray analysis of two hydrogen sulfide-producing enzymes from Fusobacterium nucleatum. 核酸镰刀菌两种硫化氢产生酶的纯化、结晶和初步 X 射线分析。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-12-01 Epub Date: 2012-11-14 DOI: 10.1107/S1744309112042546

Yuichiro Kezuka, Naoto Abe, Yasuo Yoshida, Takamasa Nonaka

引用次数: 0

Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana. 拟南芥四吡咯生物合成酶卟啉原脱氨酶的结晶和初步 X 射线表征。

IF 0.9 4区生物学

Acta Crystallographica Section F-structural Biology and Crystallization Communications Pub Date : 2012-12-01 Epub Date: 2012-11-14 DOI: 10.1107/S1744309112042212

A Roberts, R Gill, R J Hussey, H Mikolajek, P T Erskine, J B Cooper, S P Wood, E J T Chrystal, P M Shoolingin-Jordan

{"title":"Crystallization and preliminary X-ray characterization of the tetrapyrrole-biosynthetic enzyme porphobilinogen deaminase from Arabidopsis thaliana.","authors":"A Roberts, R Gill, R J Hussey, H Mikolajek, P T Erskine, J B Cooper, S P Wood, E J T Chrystal, P M Shoolingin-Jordan","doi":"10.1107/S1744309112042212","DOIUrl":"10.1107/S1744309112042212","url":null,"abstract":"The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step of the haem-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor which is covalently linked by a thioether bridge to an invariant cysteine residue. Since PBGD catalyses a reaction which is common to the biosynthesis of both haem and chlorophyll, structural studies of a plant PBGD enzyme offer great potential for the discovery of novel herbicides. Until recently, structural data have only been available for the Escherichia coli and human forms of the enzyme. Expression in E. coli of a codon-optimized gene for Arabidopsis thaliana PBGD has permitted for the first time the crystallization and preliminary X-ray analysis of the enzyme from a plant species at high resolution.","PeriodicalId":7310,"journal":{"name":"Acta Crystallographica Section F-structural Biology and Crystallization Communications","volume":"68 Pt 12","pages":"1491-3"},"PeriodicalIF":0.9,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509971/pdf/f-68-01491.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31079216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0