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Nucleic Acids Research Advance Access published online on July 22, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp603
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity

Nguyen To Uyen1, Suk-Youl Park2, Ji-Woo Choi2, Hyun-Ju Lee2, Kosuke Nishi2 and Jeong-Sun Kim1,2,*

1Interdisciplinary Graduate Program in Molecular Medicine, Gwangju 501-746 and 2Department of Chemistry, Chonnam National University, Gwangju 500-757, Korea

*To whom correspondence should be addressed. Tel: +82 62 530 3384; Fax: +82 62 530 3389; Email: jsunkim{at}chonnam.ac.kr

Received February 4, 2009. Revised June 26, 2009. Accepted July 2, 2009.

Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is located close to the probable DNA-binding site for translocation, which is far from the NTD nucleolytic core. Comparison of relative domain arrangements with other functionally related ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that a linker helix connecting two RDs and an extended region within the nuclease domain may play a central role in switching the DNA translocation into the restriction activity.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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