› 6a9b

X-ray diffraction
2.01Å resolution

T4 dCMP hydroxymethylase structure solved by I-SAD using a home source

Released:
DOI: 10.2210/pdb6a9b/pdb
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PDB entry 6a9b coloured by chain, front view.
PDB entry 6a9b coloured by chain, side view.
PDB entry 6a9b coloured by chain, top view.
Source organism: Escherichia virus T4
Primary publication:
A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate.
Park SH, Suh SW, Song HK
OpenAccess logo IUCrJ 6 206-217 (2019)
PMID: 30867918

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140376 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxycytidylate 5-hydroxymethyltransferase Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 28.52 KDa
Source organism: Escherichia virus T4
Expression system: Escherichia coli BL21(DE3)
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

2 bound ligands:
Ligand IOD 1 x IOD
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU
Spacegroup: I222
Unit cell:
a: 52.603Å b: 74.982Å c: 155.345Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.16 0.192
Expression system: Escherichia coli BL21(DE3)

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Citations

2 citation in other articles

A Novel Broad Host Range Phage Infecting Alteromonas.
Feng et al. (2021)
1 more

1 mention without citation

A cytosine modification mechanism revealed by the structure of a ternary complex of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate.
Park et al. (2019)

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