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Nucleic Acids Research 2005 33(11):3598-3605; doi:10.1093/nar/gki676
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Published online 22 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

Lisa N. Kinch1,*, Krzysztof Ginalski1,2, Leszek Rychlewski3 and Nick V. Grishin1

1Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Boulevard, Dallas, TX 75390-9050, USA 2Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University Pawinskiego 5a, 02-106 Warsaw, Poland 3BioInfoBank Institute Limanowskiego 24A, 60-744 Poznan, Poland

*To whom correspondence should be addressed. Tel: +1 214 648 6432; Fax: +1 214 648-9099; Email: lkinch{at}chop.swmed.edu

Received April 12, 2005. Revised May 5, 2005. Accepted June 8, 2005.

Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. The lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. Using the consensus fold recognition method Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we identify nine new restriction endonuclease-like fold families among previously uncharacterized proteins and predict these proteins to cleave nucleic acid substrates. Application of transitive searches combined with gene neighborhood analysis allow us to confidently link these unknown families to a number of known restriction endonuclease-like structures and thus assign folds to the uncharacterized proteins. Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database.


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