› 2z6a

X-ray diffraction
2.88Å resolution

S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation

Released:
DOI: 10.2210/pdb2z6a/pdb
PDB entry 2z6a coloured by chain, front view.
PDB entry 2z6a coloured by chain, side view.
PDB entry 2z6a coloured by chain, top view.
Source organisms:
Primary publication:
S-adenosyl-L-methionine-dependent methyl transfer: observable precatalytic intermediates during DNA cytosine methylation.
Youngblood B, Shieh FK, Buller F, Bullock T, Reich NO
Biochemistry 46 8766-75 (2007)
PMID: 17616174

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115960 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Type II methyltransferase M.HhaI Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 37.01 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*DGP*DCP*DGP*DCP*DTP*DAP*DTP*DC)-3') Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.97 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: R32
Unit cell:
a: 98.49Å b: 98.49Å c: 323.61Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.297 0.22 0.28
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Mammalian DNA methyltransferases: a structural perspective.
Cheng et al. (2008)
2 more

2 mentions without citation

Replication origin-flanking roadblocks reveal origin-licensing dynamics and altered sequence dependence.
Warner et al. (2017)
1 more