PDBsum entry 3ufb

Transferase

PDB id: 3ufb

Contents

Protein chain

484 a.a.

Waters ×542

PDB id:

3ufb

Name:

Transferase

Title:

Crystal structure of a modification subunit of a putative type i restriction enzyme from vibrio vulnificus yj016

Structure:

Type i restriction-modification system methyltransferase subunit. Chain: a. Engineered: yes

Source:

Vibrio vulnificus. Organism_taxid: 196600. Strain: yj016. Gene: vv0266. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.184 R-free: 0.215

Authors:

S.Y.Park,H.J.Lee,J.Sun,K.Nishi,J.M.Song,J.S.Kim

Key ref:

S.Y.Park et al. (2012). Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016. Acta Crystallogr D Biol Crystallogr, 68, 1570-1577. PubMed id: 23090406

Date:

01-Nov-11 Release date: 07-Nov-12

Protein chain

Q7MPU6  (Q7MPU6_VIBVY) -  site-specific DNA-methyltransferase (adenine-specific) from Vibrio vulnificus (strain YJ016)

Seq: 530 a.a.

Struc: 484 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.72 - site-specific DNA-methyltransferase (adenine-specific).
• Reaction: a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N₆-methyl- 2'-deoxyadenosine in DNA + S-adenosyl-L-homocysteine + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Acta Crystallogr D Biol Crystallogr 68:1570-1577 (2012)

PubMed id: 23090406

Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.

S.Y.Park, H.J.Lee, J.M.Song, J.Sun, H.J.Hwang, K.Nishi, J.S.Kim.

ABSTRACT

In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 Å. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an α/β-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.