› 1b5d

X-ray diffraction
2.2Å resolution

DCMP Hydroxymethylase from T4 (Intact)

Released:
DOI: 10.2210/pdb1b5d/pdb
PDB entry 1b5d coloured by chain, front view.
PDB entry 1b5d coloured by chain, side view.
PDB entry 1b5d coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
Song HK, Sohn SH, Suh SW
EMBO J 18 1104-13 (1999)
PMID: 10064578

Function and Biology Details

Reaction catalysed: 
5,10-methylenetetrahydrofolate + H(2)O + deoxycytidylate = tetrahydrofolate + 5-hydroxymethyldeoxycytidylate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140376 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxycytidylate 5-hydroxymethyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 246 amino acids
Theoretical weight: 28.52 KDa
Source organism: Escherichia virus T4
UniProt:
  • Canonical: P08773 (Residues: 1-246; Coverage: 100%)
Gene name: 42
Sequence domains: Thymidylate synthase
Structure domains: Thymidylate synthase/dCMP hydroxymethylase domain

Ligands and Environments

1 bound ligand:
Ligand DCM 2 x DCM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 176.23Å b: 53.29Å c: 75.86Å
α: 90° β: 115.54° γ: 90°
R-values:
R R work R free
0.16 0.16 0.208

Quick links

Citations

3 review citations

Evolutionary entanglement of mobile genetic elements and host defence systems: guns for hire.
Koonin et al. (2020)
2 more

2 mentions without citation

Bacteriophage T4 genome.
Miller et al. (2003)
1 more