› 5ghm

X-ray diffraction
1.5Å resolution

Crystal structure of human MTH1(G2K/D120N mutant) in complex with 8-oxo-dGTP at pH 7.0

Released:
DOI: 10.2210/pdb5ghm/pdb
PDB entry 5ghm coloured by chain, front view.
PDB entry 5ghm coloured by chain, side view.
PDB entry 5ghm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity.
Waz S, Nakamura T, Hirata K, Koga-Ogawa Y, Chirifu M, Arimori T, Tamada T, Ikemizu S, Nakabeppu Y, Yamagata Y
OpenAccess logo J Biol Chem 292 2785-2794 (2017)
PMID: 28035004

Function and Biology Details

Reaction catalysed: 
2-hydroxy-dATP + H(2)O = 2-hydroxy-dAMP + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153202 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oxidized purine nucleoside triphosphate hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 156 amino acids
Theoretical weight: 18.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36639 (Residues: 1-156; Coverage: 100%)
Gene names: MTH1, NUDT1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand 8DG 2 x 8DG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P212121
Unit cell:
a: 45.79Å b: 47.778Å c: 123.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.196
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Oxidative Stress Gene Expression Profile Correlates with Cancer Patient Poor Prognosis: Identification of Crucial Pathways Might Select Novel Therapeutic Approaches.
Leone et al. (2017)
11 other articles

1 mention without citation

Structural and Kinetic Studies of the Human Nudix Hydrolase MTH1 Reveal the Mechanism for Its Broad Substrate Specificity.
Waz et al. (2017)