› 4pu6

X-ray diffraction
2.3Å resolution

Crystal structure of potassium-dependent plant-type L-asparaginase from Phaseolus vulgaris in complex with K+ cations

Released:
DOI: 10.2210/pdb4pu6/pdb
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PDB entry 4pu6 coloured by chain, front view.
PDB entry 4pu6 coloured by chain, side view.
PDB entry 4pu6 coloured by chain, top view.
Source organism: Phaseolus vulgaris
Primary publication:
Na⁺/K⁺ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase.
Bejger M, Imiolczyk B, Clavel D, Gilski M, Pajak A, Marsolais F, Jaskolski M
Acta Crystallogr D Biol Crystallogr 70 1854-72 (2014)
PMID: 25004963

Function and Biology Details

Reaction catalysed: 
L-asparagine + H(2)O = L-aspartate + NH(3)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197678 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Isoaspartyl peptidase/L-asparaginase 2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 197 amino acids
Theoretical weight: 21.02 KDa
Source organism: Phaseolus vulgaris
Expression system: Escherichia coli
UniProt:
  • Canonical: V7CU13 (Residues: 1-195; Coverage: 60%)
Gene name: PHAVU_001G025000g
Sequence domains: Asparaginase
Isoaspartyl peptidase/L-asparaginase 2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 131 amino acids
Theoretical weight: 13.62 KDa
Source organism: Phaseolus vulgaris
Expression system: Escherichia coli
UniProt:
  • Canonical: V7CU13 (Residues: 196-326; Coverage: 40%)
Gene name: PHAVU_001G025000g
Sequence domains: Asparaginase
Structure domains: (Glycosyl)asparaginase

Ligands and Environments

2 bound ligands:
Ligand K 4 x K
Ligand ASP 1 x ASP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P212121
Unit cell:
a: 56.938Å b: 102.672Å c: 127.035Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.231
Expression system: Escherichia coli

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Citations

4 review citations

Microbial L-asparaginase for Application in Acrylamide Mitigation from Food: Current Research Status and Future Perspectives.
Jia et al. (2021)
3 more

2 mentions without citation

Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.
Loch et al. (2022)
1 more

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