› 2uz4

X-ray diffraction
2.1Å resolution

HhaI DNA methyltransferase R165N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH

Released:
DOI: 10.2210/pdb2uz4/pdb
PDB entry 2uz4 coloured by chain, front view.
PDB entry 2uz4 coloured by chain, side view.
PDB entry 2uz4 coloured by chain, top view.
Source organism: Haemophilus parahaemolyticus
Entry authors: Daujotyte D, Leinartaite L, Grazulis S

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-115857 (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 KDa
Source organism: Haemophilus parahaemolyticus
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*GP*GP*AP*TP*GP*5CMP*GP*CP*TP*GP *AP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Haemophilus parahaemolyticus
Expression system: Not provided
5'-D(*GP*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: Haemophilus parahaemolyticus
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
2 bound ligands:
Ligand SO4 4 x SO4
Ligand GOL 2 x GOL
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: R32
Unit cell:
a: 95.177Å b: 95.177Å c: 312.355Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.21 0.235
Expression systems:
  • Escherichia coli
  • Not provided

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