› 5b5u

X-ray diffraction
2.61Å resolution

Crystal structure of truncated Pyrococcus furiosus L-asparaginase with peptide

Released:
DOI: 10.2210/pdb5b5u/pdb
PDB entry 5b5u coloured by chain, front view.
PDB entry 5b5u coloured by chain, side view.
PDB entry 5b5u coloured by chain, top view.
Source organisms:
Primary publication:
Heat induces end to end repetitive association in P. furiosus L-asparaginase which enables its thermophilic property.
Sharma P, Tomar R, Yadav SS, Badmalia MD, Nath SK, Kundu B
Sci Rep 10 21702 (2020)
PMID: 33303914

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165454 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
L-asparaginase Chain: A
Molecule details ›
Chain: A
Length: 178 amino acids
Theoretical weight: 19.47 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TZE8 (Residues: 1-178; Coverage: 55%)
Gene name: PF2047
Sequence domains: Asparaginase, N-terminal
Structure domains: L-asparaginase, N-terminal domain
L-asparaginase Chain: B
Molecule details ›
Chain: B
Length: 127 amino acids
Theoretical weight: 13.9 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TZE8 (Residues: 202-326; Coverage: 38%)
Gene name: PF2047
Sequence domains: Glutaminase/Asparaginase C-terminal domain
Structure domains: Rossmann fold
LEU-VAL-VAL-ASN Chains: C, E
Molecule details ›
Chains: C, E
Length: 4 amino acids
Theoretical weight: 444 Da
Source organism: Pyrococcus furiosus
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ASP 1 x ASP
Ligand CL 2 x CL
Ligand IPA 2 x IPA
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P6522
Unit cell:
a: 91.31Å b: 91.31Å c: 186.971Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.205 0.203 0.242
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Thermo-L-Asparaginases: From the Role in the Viability of Thermophiles and Hyperthermophiles at High Temperatures to a Molecular Understanding of Their Thermoactivity and Thermostability.
Dumina et al. (2023)

2 mentions without citation

Geometric considerations support the double-displacement catalytic mechanism of l-asparaginase.
Lubkowski et al. (2019)
1 more