› 5u7v

X-ray diffraction
2.15Å resolution

Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Trifolium repens in complex with AMP

Released:
DOI: 10.2210/pdb5u7v/pdb
PDB entry 5u7v coloured by chain, front view.
PDB entry 5u7v coloured by chain, side view.
PDB entry 5u7v coloured by chain, top view.
Source organism: Trifolium repens
Primary publication:
Structures and kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion catalytic mechanism.
Summers EL, Cumming MH, Oulavallickal T, Roberts NJ, Arcus VL
Protein Sci 26 1627-1638 (2017)
PMID: 28543850

Function and Biology Details

Reaction catalysed: 
(1a) a nucleoside 5'-triphosphate + H(2)O = a nucleoside 5'-diphosphate + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110890 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Apyrase Chain: A
Molecule details ›
Chain: A
Length: 426 amino acids
Theoretical weight: 46.99 KDa
Source organism: Trifolium repens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B9U139 (Residues: 38-455; Coverage: 96%)
Sequence domains: GDA1/CD39 (nucleoside phosphatase) family

Ligands and Environments

1 bound ligand:
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P21
Unit cell:
a: 53.83Å b: 51.91Å c: 69.46Å
α: 90° β: 108.46° γ: 90°
R-values:
R R work R free
0.199 0.195 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

Crystal structure of the nucleotide-metabolizing enzyme NTPDase4.
Gorelik et al. (2020)
2 more

2 mentions without citation

Recent Advances Clarifying the Structure and Function of Plant Apyrases (Nucleoside Triphosphate Diphosphohydrolases).
Clark et al. (2021)
1 more