orengo_annrevbioch2005_foldclass

orengo_annrevbioch2005_foldclass - Annu. Rev. Biochem....

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Unformatted text preview: Annu. Rev. Biochem. 2005. 74:867–900 doi: 10.1146/annurev.biochem.74.082803.133029 Copyright c ° 2005 by Annual Reviews. All rights reserved P ROTEIN F AMILIES AND T HEIR E VOLUTION —A S TRUCTURAL P ERSPECTIVE Christine A. Orengo 1 and Janet M. Thornton 2 1 Department of Biochemistry and Molecular Biology, University College, London WC1E 6BT, United Kingdom; email: [email protected] 2 European Bioinformatics Institute, Hinxton Campus, Cambridge CB10 1SD, United Kingdom; email: [email protected] Key Words protein classifications, comparative genomics, bioinformatics ■ Abstract We can now assign about two thirds of the sequences from completed genomes to as few as 1400 domain families for which structures are known and thus more ancient evolutionary relationships established. About 200 of these domain fami- lies are common to all kingdoms of life and account for nearly 50% of domain structure annotations in the genomes. Some of these domain families have been very extensively duplicated within a genome and combined with different domain partners giving rise to different multidomain proteins. The ways in which these domain combinations evolve tend to be specific to the organism so that less than 15% of the protein families found within a genome appear to be common to all kingdoms of life. Recent analyses of completed genomes, exploiting the structural data, have revealed the extent to which duplication of these domains and modifications of their functions can expand the func- tional repertoire of the organism, contributing to increasing complexity. CONTENTS INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 868 CLASSIFYING AND CHARACTERIZING PROTEIN FAMILIES . . . . . . . . . . . . . . 871 Families and Superfamilies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871 Fold Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 872 Domain Structure Architectures and Classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 872 Orthologous and Paralogous Relatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 873 HOW DO WE FIND PROTEIN RELATIVES? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 873 Finding Close Relatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 873 Finding Distant Relatives in the Twilight Zone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 875 Finding Very Distant Relatives in the Midnight Zone . . . . . . . . . . . . . . . . . . . . . . . . 875 WHAT DO THE CURRENT CLASSIFICATIONS REVEAL ABOUT THE NUMBER AND NATURE OF DOMAIN FAMILIES? . . . . . . . . . . . . . . . . . . . 878 How Many Domain Families Can Be Identified in Sequence Databases? . . . . . . . . . 878 How Many Domain Families Are Currently Identified Using Structural Data?How Many Domain Families Are Currently Identified Using Structural Data?...
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This note was uploaded on 05/28/2010 for the course WE BIBI010000 taught by Professor Marnikvuylsteke during the Spring '10 term at Ghent University.

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orengo_annrevbioch2005_foldclass - Annu. Rev. Biochem....

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