› 1skm

X-ray diffraction
2.2Å resolution

HhaI methyltransferase in complex with DNA containing an abasic south carbocyclic sugar at its target site

Released:
DOI: 10.2210/pdb1skm/pdb
PDB entry 1skm coloured by chain, front view.
PDB entry 1skm coloured by chain, side view.
PDB entry 1skm coloured by chain, top view.
Source organism: Haemophilus haemolyticus
Primary publication:
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.
Horton JR, Ratner G, Banavali NK, Huang N, Choi Y, Maier MA, Marquez VE, MacKerell AD, Cheng X
Nucleic Acids Res 32 3877-86 (2004)
PMID: 15273274

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-114596 (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(*TP*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.93 KDa
Source organism: Haemophilus haemolyticus
Expression system: Not provided
5'-D(*T*GP*TP*CP*AP*GP*(HCX)P*GP*CP*AP*TP*GP*G)-3' Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 3.89 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: NSLS BEAMLINE X26C
Spacegroup: R32
Unit cell:
a: 95.681Å b: 95.681Å c: 315.683Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.183 0.221
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Eukaryotic cytosine methyltransferases.
Goll et al. (2005)
23 other articles

2 mentions without citation

An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.
Laurino et al. (2016)
1 more