PDBsum entry 3h1t

Hydrolase

PDB id: 3h1t

Contents

Protein chain

515 a.a. *

Waters ×343

* Residue conservation analysis

PDB id:

3h1t

Name:

Hydrolase

Title:

The fragment structure of a putative hsdr subunit of a type i restriction enzyme from vibrio vulnificus yj016

Structure:

Type i site-specific restriction-modification system, r (restriction) subunit. Chain: a. Fragment: unp residues 1-590. Engineered: yes

Source:

Vibrio vulnificus. Organism_taxid: 196600. Strain: yj016. Gene: vv0265. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.30Å R-factor: 0.218 R-free: 0.242

Authors:

S.Y.Park,H.J.Lee,J.S.Kim

Key ref:

N.T.Uyen et al. (2009). 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, 37, 6960-6969. PubMed id: 19625490

Date:

13-Apr-09 Release date: 20-Oct-09

Protein chain

Q7MPU7  (Q7MPU7_VIBVY) -  Type I site-specific restriction-modification system, R (Restriction) subunit from Vibrio vulnificus (strain YJ016)

Seq: 817 a.a.

Struc: 515 a.a.

Nucleic Acids Res 37:6960-6969 (2009)

PubMed id: 19625490

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.

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

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.