› 2z6q

X-ray diffraction
2.79Å resolution

Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy

Released:
DOI: 10.2210/pdb2z6q/pdb
PDB entry 2z6q coloured by chain, front view.
PDB entry 2z6q coloured by chain, side view.
PDB entry 2z6q coloured by chain, top view.
Source organisms:
Primary publication:
The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI.
Shieh FK, Youngblood B, Reich NO
J Mol Biol 362 516-27 (2006)
PMID: 16926025

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115961 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Type II methyltransferase M.HhaI Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 36.96 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Escherichia coli
UniProt:
  • Canonical: P05102 (Residues: 1-327; Coverage: 100%)
Gene name: hhaIM
Sequence domains: C-5 cytosine-specific DNA methylase
Structure domains:
DNA (5'-D(*DGP*DAP*DTP*DAP*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DG)-3') Chain: D
Molecule details ›
Chain: D
Length: 6 nucleotides
Theoretical weight: 1.85 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DTP*DAP*DTP*DC)-3') Chain: E
Molecule details ›
Chain: E
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand DCZ 1 x DCZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: R32
Unit cell:
a: 92.924Å b: 92.924Å c: 315.781Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.209 0.269
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs.
Xu et al. (2010)
23 other articles