› 2xjd

X-ray diffraction
2Å resolution

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate

Released:
DOI: 10.2210/pdb2xjd/pdb
PDB entry 2xjd coloured by chain, front view.
PDB entry 2xjd coloured by chain, side view.
PDB entry 2xjd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for the allosteric regulation and substrate recognition of human cytosolic 5'-nucleotidase II.
Walldén K, Nordlund P
J Mol Biol 408 684-96 (2011)
PMID: 21396942

Function and Biology Details

Reactions catalysed: 
A nucleotide + a 2'-deoxynriboucleoside = a nucleoside + a 2'-deoxyribonucleoside 5'-phosphate
A 5'-ribonucleotide + H(2)O = a ribonucleoside + phosphate
IMP + H(2)O = inosine + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156075 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cytosolic purine 5'-nucleotidase Chain: A
Molecule details ›
Chain: A
Length: 554 amino acids
Theoretical weight: 63.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49902 (Residues: 1-536; Coverage: 96%)
Gene names: NT5B, NT5C2, NT5CP, PNT5
Sequence domains: 5' nucleotidase family

Ligands and Environments

4 bound ligands:
Ligand ATP 1 x ATP
Ligand GOL 6 x GOL
Ligand PO4 1 x PO4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: I222
Unit cell:
a: 92.299Å b: 128.432Å c: 131.201Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.176 0.208
Expression system: Escherichia coli BL21(DE3)

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Citations

9 review citations

Enzyme promiscuity: engine of evolutionary innovation.
Pandya et al. (2014)
8 more