› 10mh

X-ray diffraction
2.55Å resolution

TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH ADOHCY AND HEMIMETHYLATED DNA CONTAINING 5,6-DIHYDRO-5-AZACYTOSINE AT THE TARGET

Released:
DOI: 10.2210/pdb10mh/pdb
PDB entry 10mh coloured by chain, front view.
PDB entry 10mh coloured by chain, side view.
PDB entry 10mh coloured by chain, top view.
Source organism: Haemophilus haemolyticus
Primary publication:
Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine.
Sheikhnejad G, Brank A, Christman JK, Goddard A, Alvarez E, Ford H, Marquez VE, Marasco CJ, Sufrin JR, O'gara M, Cheng X
J Mol Biol 285 2021-34 (1999)
PMID: 9925782

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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113301 (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: 37.04 KDa
Source organism: Haemophilus haemolyticus
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(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Haemophilus haemolyticus
Expression system: Not provided
DNA (5'-D(P*GP*TP*CP*AP*GP*5NCP*GP*CP*AP*TP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Haemophilus haemolyticus
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
No bound ligands
2 modified residues:
Ligand 5CM 1 x 5CM
Ligand 5NC 1 x 5NC

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: R32
Unit cell:
a: 99.86Å b: 99.86Å c: 325.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.205 not available
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

5-Azacytidine and 5-aza-2'-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy.
Christman JK. (2002)
8 more

6 mentions without citation

Many paths to methyltransfer: a chronicle of convergence.
Schubert et al. (2003)
5 more