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      Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

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          Abstract

          To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence–structure–function relationships.

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          The online version of this article (doi:10.1007/s10969-008-9056-5) contains supplementary material, which is available to authorized users.

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          The Universal Protein Resource (UniProt): an expanding universe of protein information

          The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .
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            Database resources of the National Center for Biotechnology Information

            In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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              The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

              The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.
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                Author and article information

                Contributors
                +1-415-5144227 , +1-415-5144231 , ursula@salilab.org
                +1-415-5144227 , +1-415-5144231 , sali@salilab.org
                Journal
                J Struct Funct Genomics
                Journal of Structural and Functional Genomics
                Springer Netherlands (Dordrecht )
                1345-711X
                1570-0267
                14 February 2009
                April 2009
                : 10
                : 2
                : 107-125
                Affiliations
                [1 ]Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, Byers Hall at Mission Bay, Office 501-32, 1700 4th Street, San Francisco, CA 94158 USA
                [2 ]Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, Byers Hall at Mission Bay, Office 501, 1700 4th Street, San Francisco, CA 94158 USA
                [3 ]Department of Biopharmaceutical Sciences, California Institute for Quantitative Biosciences, University of California at San Francisco, Byers Hall at Mission Bay, Office 501C, 1700 4th Street, San Francisco, CA 94158 USA
                [4 ]SGX Pharmaceuticals Inc, 10505 Roselle Street, San Diego, CA 92121 USA
                [5 ]Departments of Biochemistry and Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
                [6 ]Biology Department, Brookhaven National Laboratory, Upton, NY 11973 USA
                [7 ]Case Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106 USA
                [8 ]Departments of Biochemistry and Chemistry, University of Illinois, Urbana, IL 61801 USA
                [9 ]Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, TX 77842-3012 USA
                [10 ]Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, 600 16th St., Box 2240, Genentech Hall at Mission Bay, Room N472C, San Francisco, CA 94158-2517 USA
                [11 ]Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, Byers Hall at Mission Bay, Office 508E, 1700 4th Street, San Francisco, CA 94158 USA
                [12 ]Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, Byers Hall at Mission Bay, Office 503B, 1700 4th Street, San Francisco, CA 94158 USA
                Article
                9056
                10.1007/s10969-008-9056-5
                2693957
                19219566
                e4841d14-fb4b-443a-83a1-35539edc5e28
                © The Author(s) 2009
                History
                : 8 August 2008
                : 12 December 2008
                Categories
                Article
                Custom metadata
                © Springer Science+Business Media B.V. 2009

                Genetics
                structural genomics,amidohydrolase and enolase superfamilies,structure annotation,target selection

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