Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts

Nancy C Horton, John J. Perona

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

The 2.1-Å 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.

Original languageEnglish (US)
Pages (from-to)21721-21729
Number of pages9
JournalJournal of Biological Chemistry
Volume273
Issue number34
DOIs
StatePublished - Aug 21 1998
Externally publishedYes

Fingerprint

DNA sequences
Water
Molecules
Thymine
Cytosine
Crystal lattices
Binding Sites
DNA
Enzymes
GATATC-specific type II deoxyribonucleases
Proteins

ASJC Scopus subject areas

  • Biochemistry

Cite this

Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts. / Horton, Nancy C; Perona, John J.

In: Journal of Biological Chemistry, Vol. 273, No. 34, 21.08.1998, p. 21721-21729.

Research output: Contribution to journalArticle

@article{b24618fe038d4badb6554ad43afdee97,
title = "Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts",
abstract = "The 2.1-{\AA} 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.",
author = "Horton, {Nancy C} and Perona, {John J.}",
year = "1998",
month = "8",
day = "21",
doi = "10.1074/jbc.273.34.21721",
language = "English (US)",
volume = "273",
pages = "21721--21729",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "34",

}

TY - JOUR

T1 - Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts

AU - Horton, Nancy C

AU - Perona, John J.

PY - 1998/8/21

Y1 - 1998/8/21

N2 - The 2.1-Å 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.

AB - The 2.1-Å 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.

UR - http://www.scopus.com/inward/record.url?scp=0032555574&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032555574&partnerID=8YFLogxK

U2 - 10.1074/jbc.273.34.21721

DO - 10.1074/jbc.273.34.21721

M3 - Article

C2 - 9705308

AN - SCOPUS:0032555574

VL - 273

SP - 21721

EP - 21729

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 34

ER -