› 7ww7

X-ray diffraction
1.67Å resolution

Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 1 hr in 5 mM Mn2+

Released:
DOI: 10.2210/pdb7ww7/pdb
PDB entry 7ww7 coloured by chain, front view.
PDB entry 7ww7 coloured by chain, side view.
PDB entry 7ww7 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase.
Nakamura T, Yamagata Y
OpenAccess logo Proc Natl Acad Sci U S A 119 e2203118119 (2022)
PMID: 35594391

Function and Biology Details

Reaction catalysed: 
8-oxo-dGTP + H(2)O = 8-oxo-dGMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140099 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
8-oxo-dGTP diphosphatase Chain: A
Molecule details ›
Chain: A
Length: 129 amino acids
Theoretical weight: 14.95 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P08337 (Residues: 1-129; Coverage: 100%)
Gene names: JW0097, b0099, mutT
Sequence domains: NUDIX domain

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
4 bound ligands:
Ligand 8DG 1 x 8DG
Ligand MN 3 x MN
Ligand NA 1 x NA
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 38.278Å b: 55.968Å c: 59.181Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.159 0.198
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

New insights into DNA polymerase mechanisms provided by time-lapse crystallography.
Weaver et al. (2022)
2 other articles