› 2c7p

X-ray diffraction
1.7Å resolution

HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine opposite to the target base (GCGC:GMPC) and SAH

Released:
DOI: 10.2210/pdb2c7p/pdb
PDB entry 2c7p coloured by chain, front view.
PDB entry 2c7p coloured by chain, side view.
PDB entry 2c7p coloured by chain, top view.
Source organisms:
Primary publication:
Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DT, Klimasauskas S, Jones AC
Nucleic Acids Res 33 6953-60 (2005)
PMID: 16340006

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-115140 (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:
5'-D(*G*GP*AP*TP*GP*(5CM*2PR)*CP*TP*GP*AP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*G*TP*CP*AP*GP*CP*GP*CP*AP*TP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
3 bound ligands:
Ligand SO4 5 x SO4
Ligand EPE 1 x EPE
Ligand CIT 1 x CIT
2 modified residues:
Ligand 5CM 1 x 5CM
Ligand 2PR 1 x 2PR

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: R32
Unit cell:
a: 94.845Å b: 94.845Å c: 313.03Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.196 0.196 0.22
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Fluorescent DNA-based enzyme sensors.
Dai et al. (2011)
6 more

3 mentions without citation

CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Wojciechowski et al. (2013)
2 more