› 2c7o

X-ray diffraction
1.9Å resolution

HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH

Released:
DOI: 10.2210/pdb2c7o/pdb
PDB entry 2c7o coloured by chain, front view.
PDB entry 2c7o coloured by chain, side view.
PDB entry 2c7o 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-115139 (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(*T*GP*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP *C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.91 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand SO4 4 x SO4
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: 95.18Å b: 95.18Å c: 312.547Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.194 0.215
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

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