3H1T

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016

Summary for 3H1T

• Entry DOI: 10.2210/pdb3h1t/pdb
• Descriptor: Type I site-specific restriction-modification system, R (Restriction) subunit (2 entities in total)
• Functional Keywords: hydrolase, restriction enzyme hsdr, atp-binding, nucleotide-binding
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 1
• Total formula weight: 68077.24

Authors

Park, S.Y.,Lee, H.J.,Kim, J.S. (deposition date: 2009-04-13, release date: 2009-10-20, Last modification date: 2024-11-20)

Primary citation

Uyen, N.T.,Park, S.Y.,Choi, J.W.,Lee, H.J.,Nishi, K.,Kim, J.S.
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
Nucleic Acids Res., 2009

PubMed 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.

PubMed: 19625490
DOI: 10.1093/nar/gkp603

Experimental method

X-RAY DIFFRACTION (2.3 Å)