› 2i9k

X-ray diffraction
2.65Å resolution

Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA Methyltransferase M.HhaI

Released:
DOI: 10.2210/pdb2i9k/pdb
PDB entry 2i9k coloured by chain, front view.
PDB entry 2i9k coloured by chain, side view.
PDB entry 2i9k coloured by chain, top view.
Source organism: Haemophilus haemolyticus
Primary publication:
Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HhaI.
Youngblood B, Shieh FK, De Los Rios S, Perona JJ, Reich NO
J Mol Biol 362 334-46 (2006)
PMID: 16919299

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-115387 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Type II methyltransferase M.HhaI Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 36.97 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*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3' Chains: C, D
Molecule details ›
Chains: C, D
Length: 13 nucleotides
Theoretical weight: 3.97 KDa
Source organism: Haemophilus haemolyticus
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 RU200
Spacegroup: R32
Unit cell:
a: 97.51Å b: 97.51Å c: 319.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.39 0.238 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 citation in other articles

The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI.
Shieh et al. (2006)
5 more

1 mention without citation

Single-base methylome profiling of the giant kelp Saccharina japonica reveals significant differences in DNA methylation to microalgae and plants.
Fan et al. (2020)