› 1z4i

X-ray diffraction
1.98Å resolution

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyribouridine 5'-monophosphate

Released:
DOI: 10.2210/pdb1z4i/pdb
PDB entry 1z4i coloured by chain, front view.
PDB entry 1z4i coloured by chain, side view.
PDB entry 1z4i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase.
Walldén K, Ruzzenente B, Rinaldo-Matthis A, Bianchi V, Nordlund P
Structure 13 1081-8 (2005)
PMID: 16004879

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192472 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'(3')-deoxyribonucleotidase, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 197 amino acids
Theoretical weight: 22.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NPB1 (Residues: 32-228; Coverage: 86%)
Gene names: DNT2, NT5M
Sequence domains: 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand UMP 1 x UMP
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P43212
Unit cell:
a: 73.7Å b: 73.7Å c: 106.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.164 0.206
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 citation in other articles

Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
Zimmerman et al. (2008)
9 more

1 mention without citation

Crystal structures of the novel cytosolic 5'-nucleotidase IIIB explain its preference for m7GMP.
Monecke et al. (2014)