› 2bdu

X-ray diffraction
2.35Å resolution

X-Ray Structure of a Cytosolic 5'-Nucleotidase III from Mus Musculus MM.158936

Released:
DOI: 10.2210/pdb2bdu/pdb
PDB entry 2bdu coloured by chain, front view.
PDB entry 2bdu coloured by chain, side view.
PDB entry 2bdu coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.
Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN
J Biol Chem 281 20521-9 (2006)
PMID: 16672222

Function and Biology Details

Reactions catalysed: 
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
CMP + H(2)O = cytidine + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190033 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic 5'-nucleotidase 3A Chains: A, B
Molecule details ›
Chains: A, B
Length: 297 amino acids
Theoretical weight: 34.16 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9D020 (Residues: 37-43, 44-331; Coverage: 89%)
Gene names: Nt5c3, Nt5c3a
Sequence domains: Pyrimidine 5'-nucleotidase (UMPH-1)
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand EPE 2 x EPE
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P32
Unit cell:
a: 133.674Å b: 133.674Å c: 38.889Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.166 0.163 0.22
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.
Phillips et al. (2007)
11 other articles

5 mentions without citation

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)
4 more