Literature DB >> 15159570

Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution.

Izabela Janda1, Yancho Devedjiev, David Cooper, Maksymilian Chruszcz, Urszula Derewenda, Aleksandra Gabrys, Wladek Minor, Andrzej Joachimiak, Zygmunt S Derewenda.   

Abstract

High-throughput (HT) protein crystallography is severely impeded by the relatively low success rate of protein crystallization. Proteins whose structures are not solved in the HT pipeline owing to attrition in any phase of the project are referred to as the high-hanging fruit, in contrast to those proteins that yielded good-quality crystals and crystal structures, which are referred to as low-hanging fruit. It has previously been shown that proteins that do not crystallize in the wild-type form can have their surfaces engineered by site-directed mutagenesis in order to create patches of low conformational entropy that are conducive to forming intermolecular interactions. The application of this method to selected proteins from the Bacillus subtilis genome which failed to crystallize in the HT mode is now reported. In this paper, the crystal structure of the product of the YdeN gene is reported. Of three prepared double mutants, i.e. E124A/K127A, E167A/E169A and K88A/Q89A, the latter gave high-quality crystals and the crystal structure was solved by SAD at 1.8 angstroms resolution. The protein is a canonical alpha/beta hydrolase, with an active site that is accessible to solvent. Copyright 2004 International Union of Crystallography

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Year:  2004        PMID: 15159570      PMCID: PMC2792027          DOI: 10.1107/S0907444904007188

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  37 in total

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2.  3D-Jury: a simple approach to improve protein structure predictions.

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3.  Substructure solution with SHELXD.

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4.  Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

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Journal:  Proteins       Date:  2003-02-15

5.  Methods used in the structure determination of bovine mitochondrial F1 ATPase.

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6.  Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent.

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8.  Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A.

Authors:  Y Devedjiev; Z Dauter; S R Kuznetsov; T L Jones; Z S Derewenda
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9.  Shotgun crystallization strategy for structural genomics: an optimized two-tiered crystallization screen against the Thermotoga maritima proteome.

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10.  The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5-A resolution. Crystal structure of a fatty acid synthase component.

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  12 in total

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2.  The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism.

Authors:  Izabela Janda; Yancho Devedjiev; Urszula Derewenda; Zbigniew Dauter; Jakub Bielnicki; David R Cooper; Paul C F Graf; Andrzej Joachimiak; Ursula Jakob; Zygmunt S Derewenda
Journal:  Structure       Date:  2004-10       Impact factor: 5.006

3.  Structure of XC6422 from Xanthomonas campestris at 1.6 A resolution: a small serine alpha/beta-hydrolase.

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Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2006-05-31

4.  Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.

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Journal:  Protein Sci       Date:  2007-08       Impact factor: 6.725

5.  Distinctive structural motifs co-ordinate the catalytic nucleophile and the residues of the oxyanion hole in the alpha/beta-hydrolase fold enzymes.

Authors:  Polytimi S Dimitriou; Alexander I Denesyuk; Toru Nakayama; Mark S Johnson; Konstantin Denessiouk
Journal:  Protein Sci       Date:  2018-11-12       Impact factor: 6.725

6.  RBBP9: a tumor-associated serine hydrolase activity required for pancreatic neoplasia.

Authors:  David J Shields; Sherry Niessen; Eric A Murphy; Ainhoa Mielgo; Jay S Desgrosellier; Steven K M Lau; Leo A Barnes; Jacqueline Lesperance; Michael Bouvet; David Tarin; Benjamin F Cravatt; David A Cheresh
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7.  Polymer-driven crystallization.

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8.  Systematic replacement of lysine with glutamine and alanine in Escherichia coli malate synthase G: effect on crystallization.

Authors:  David M Anstrom; Leslie Colip; Brian Moshofsky; Eric Hatcher; S James Remington
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9.  Crystal structure of human retinoblastoma binding protein 9.

Authors:  Sergey M Vorobiev; Min Su; Jayaraman Seetharaman; Yuanpeng Janet Huang; Chen X Chen; Melissa Maglaqui; Haleema Janjua; Michael Proudfoot; Alexander Yakunin; Rong Xiao; Thomas B Acton; Gaetano T Montelione; Liang Tong
Journal:  Proteins       Date:  2009-02-01

10.  SCMCRYS: predicting protein crystallization using an ensemble scoring card method with estimating propensity scores of P-collocated amino acid pairs.

Authors:  Phasit Charoenkwan; Watshara Shoombuatong; Hua-Chin Lee; Jeerayut Chaijaruwanich; Hui-Ling Huang; Shinn-Ying Ho
Journal:  PLoS One       Date:  2013-09-03       Impact factor: 3.240

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