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DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.

Abstract：

:HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Horton JR,Zhang X,Maunus R,Yang Z,Wilson GG,Roberts RJ,Cheng X

doi

10.1093/nar/gkj484

keywords:

subject

Has Abstract

pub_date

2006-02-09 00:00:00

pages

939-48

issue

3

eissn

0305-1048

issn

1362-4962

pii

34/3/939

journal_volume

34

pub_type

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