› 2o5w

X-ray diffraction
2.6Å resolution

Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex with Sm+3 and pyrophosphate

Released:
DOI: 10.2210/pdb2o5w/pdb
PDB entry 2o5w coloured by chain, front view.
PDB entry 2o5w coloured by chain, side view.
PDB entry 2o5w coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis.
Gabelli SB, Bianchet MA, Xu W, Dunn CA, Niu ZD, Amzel LM, Bessman MJ
Structure 15 1014-22 (2007)
PMID: 17698004

Function and Biology Details

Reaction catalysed: 
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 7,8-dihydroneopterin 3'-phosphate + 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-142705 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydroneopterin triphosphate diphosphatase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 150 amino acids
Theoretical weight: 17.33 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AFC0 (Residues: 1-150; Coverage: 100%)
Gene names: JW1854, b1865, ntpA, nudB
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand SO4 4 x SO4
Ligand SM 3 x SM
Ligand NA 2 x NA
Ligand PPV 2 x PPV
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 124.416Å b: 42.909Å c: 108.328Å
α: 90° β: 115.19° γ: 90°
R-values:
R R work R free
0.2 0.195 0.287
Expression system: Escherichia coli

Quick links

Citations

4 review citations

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.
Hanson et al. (2009)
3 more

1 mention without citation

Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism.
Hill et al. (2017)