Document Detail

Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
MedLine Citation:
PMID:  9705308     Owner:  NLM     Status:  MEDLINE    
The 2.1-A cocrystal structure of EcoRV endonuclease bound to 5'-CGGGATATCCC, in a crystal lattice isomorphous with the cocrystallized undecamer 5'-AAAGATATCTT previously determined, shows novel base recognition in the major groove of the DNA flanking the GATATC target site. Lys104 of the enzyme interacts through water molecules with the exocyclic N-4 amino groups of flanking cytosines. Steric exclusion of water molecule-binding sites by the 5-methyl group of thymine drives the adoption of alternative water-mediated contacts with AT versus GC flanks. This structure provides a rare example of structural adaptability in the recognition of different DNA sequences by a protein and suggests preferred strategies for the expansion of target site specificity by EcoRV.
N C Horton; J J Perona
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  The Journal of biological chemistry     Volume:  273     ISSN:  0021-9258     ISO Abbreviation:  J. Biol. Chem.     Publication Date:  1998 Aug 
Date Detail:
Created Date:  1998-09-17     Completed Date:  1998-09-17     Revised Date:  2008-08-29    
Medline Journal Info:
Nlm Unique ID:  2985121R     Medline TA:  J Biol Chem     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  21721-9     Citation Subset:  IM    
Department of Chemistry and Interdepartmental Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, California 93106-9510, USA.
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MeSH Terms
Binding Sites
Crystallography, X-Ray
DNA / metabolism*
Deoxyribonucleases, Type II Site-Specific / metabolism*
Models, Molecular
Molecular Sequence Data
Protein Conformation
Grant Support
Reg. No./Substance:
7732-18-5/Water; 9007-49-2/DNA; EC, Type II Site-Specific; EC type II deoxyribonucleases

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