Published online 9 February 2006
Article |
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion
Department of Biochemistry, Emory University School of Medicine 1510 Clifton Road, Atlanta, GA 30322, USA 1New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938-2723, USA
*To whom correspondence should be addressed. Tel: +1 404 727 8491; Fax: +1 404 727 3746; Email: xcheng{at}emory.edu
Received December 6, 2005. Revised January 4, 2006. Accepted January 16, 2006.
HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G
CGC in DNA. We report three structures of HinP1I–DNA complexes: in the presence of Ca2+ (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg2+ (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 (Ca2+ or Mg2+) 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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. L. Sanders, L. E. Catto, S. R. W. Bellamy, and S. E. Halford Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands Nucleic Acids Res., April 1, 2009; 37(7): 2105 - 2115. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Tessmer, Y. Yang, J. Zhai, C. Du, P. Hsieh, M. M. Hingorani, and D. A. Erie Mechanism of MutS Searching for DNA Mismatches and Signaling Repair J. Biol. Chem., December 26, 2008; 283(52): 36646 - 36654. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. L. Lorieau, L. A. Day, and A. E. McDermott Conformational dynamics of an intact virus: Order parameters for the coat protein of Pf1 bacteriophage PNAS, July 29, 2008; 105(30): 10366 - 10371. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Gao and J. Skolnick DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions Nucleic Acids Res., July 1, 2008; 36(12): 3978 - 3992. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Gasiunas, G. Sasnauskas, G. Tamulaitis, C. Urbanke, D. Razaniene, and V. Siksnys Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family Nucleic Acids Res., February 11, 2008; 36(3): 938 - 949. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kaus-Drobek, H. Czapinska, M. Sokolowska, G. Tamulaitis, R. H. Szczepanowski, C. Urbanke, V. Siksnys, and M. Bochtler Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically Nucleic Acids Res., March 19, 2007; 35(6): 2035 - 2046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Carpenter, P. Divvela, V. Pingoud, J. Bujnicki, and A. S. Bhagwat Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI Nucleic Acids Res., August 7, 2006; 34(13): 3762 - 3770. [Abstract] [Full Text] [PDF]
|
|