title: 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.
abstract: 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.
authors.affiliation: Interdisciplinary Graduate Program in Molecular Medicine, Gwangju 501-746, Korea.
authors.forename: Nguyen To
authors.initials: NT
authors.lastname: Uyen
authors.forename: Suk-Youl
authors.initials: SY
authors.lastname: Park
authors.forename: Ji-Woo
authors.initials: JW
authors.lastname: Choi
authors.forename: Hyun-Ju
authors.initials: HJ
authors.lastname: Lee
authors.forename: Kosuke
authors.initials: K
authors.lastname: Nishi
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Kim
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry; D000595:Amino Acid Sequence; D004247:DNA / Q000378:metabolism; D053837:DNA Cleavage; D015253:Deoxyribonucleases, Type I Site-Specific / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000378:metabolism; D041261:Vibrio vulnificus / Q000201:enzymology*
chemical_list: D021122:Protein Subunits; D004247:DNA; D015253:Deoxyribonucleases, Type I Site-Specific; D000251:Adenosine Triphosphatases