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      The evolution of enzyme function in the isomerases

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          Highlights

          • •

            Isomerases usually evolve to become enzymes from other EC classes.

          • •

            Conservation of substrates is more common than conservation of bond changes.

          • •

            The relationship between functional similarity and sequence similarity is not linear.

          Abstract

          The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.

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          The ENZYME database in 2000.

          A Bairoch (2000)
          The ENZYME database is a repository of information related to the nomenclature of enzymes. In recent years it has became an indispensable resource for the development of metabolic databases. The current version contains information on 3705 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/enzyme/ ).
          Article 0 comments Cited 356 times – based on 0 reviews     Review now
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            Update on activities at the Universal Protein Resource (UniProt) in 2013

            Claire O'Donovan, emmanuel boutet (2012)
            The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
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              Evolution of function in protein superfamilies, from a structural perspective.

              A Todd, C. A. Orengo, J Thornton (2001)
              The recent growth in protein databases has revealed the functional diversity of many protein superfamilies. We have assessed the functional variation of homologous enzyme superfamilies containing two or more enzymes, as defined by the CATH protein structure classification, by way of the Enzyme Commission (EC) scheme. Combining sequence and structure information to identify relatives, the majority of superfamilies display variation in enzyme function, with 25 % of superfamilies in the PDB having members of different enzyme types. We determined the extent of functional similarity at different levels of sequence identity for 486,000 homologous pairs (enzyme/enzyme and enzyme/non-enzyme), with structural and sequence relatives included. For single and multi-domain proteins, variation in EC number is rare above 40 % sequence identity, and above 30 %, the first three digits may be predicted with an accuracy of at least 90 %. For more distantly related proteins sharing less than 30 % sequence identity, functional variation is significant, and below this threshold, structural data are essential for understanding the molecular basis of observed functional differences. To explore the mechanisms for generating functional diversity during evolution, we have studied in detail 31 diverse structural enzyme superfamilies for which structural data are available. A large number of variations and peculiarities are observed, at the atomic level through to gross structural rearrangements. Almost all superfamilies exhibit functional diversity generated by local sequence variation and domain shuffling. Commonly, substrate specificity is diverse across a superfamily, whilst the reaction chemistry is maintained. In many superfamilies, the position of catalytic residues may vary despite playing equivalent functional roles in related proteins. The implications of functional diversity within supefamilies for the structural genomics projects are discussed. More detailed information on these superfamilies is available at http://www.biochem.ucl.ac.uk/bsm/FAM-EC/. Copyright 2001 Academic Press.
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                Author and article information

                Contributors
                Sergio Martinez Cuesta
                Janet M Thornton
                Journal
                Journal ID (nlm-ta): Curr Opin Struct Biol
                Journal ID (iso-abbrev): Curr. Opin. Struct. Biol
                Title: Current Opinion in Structural Biology
                Publisher: Elsevier Science
                ISSN (Print): 0959-440X
                ISSN (Electronic): 1879-033X
                Publication date PMC-release: 1 June 2014
                Publication date (Print): June 2014
                Volume: 26
                Issue: 100
                Pages: 121-130
                Affiliations
                [1 ]European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
                [2 ]Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
                [3 ]Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
                Article
                Publisher ID: S0959-440X(14)00066-9
                DOI: 10.1016/j.sbi.2014.06.002
                PMC ID: 4139412
                PubMed ID: 25000289
                SO-VID: 078a66b9-b7ff-432f-88ed-1e9f6c333925
                Copyright © © 2014 The Authors
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                Subject: Article

                ScienceOpen disciplines: Biophysics
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                ScienceOpen disciplines: Biophysics

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