› 6v2g

X-ray diffraction
1.9Å resolution

Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp. Covalent acyl-enzyme intermediate and tetrahedral intermediate.

Released:
DOI: 10.2210/pdb6v2g/pdb
PDB entry 6v2g coloured by chain, front view.
PDB entry 6v2g coloured by chain, side view.
PDB entry 6v2g coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Mechanism of Catalysis by l-Asparaginase.
Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S, Fushman D, Rempe S, Anishkin A, Wlodawer A
Biochemistry 59 1927-1945 (2020)
PMID: 32364696

Function and Biology Details

Reaction catalysed: 
L-asparagine + H(2)O = L-aspartate + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133590 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-asparaginase 2 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 333 amino acids
Theoretical weight: 35.7 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00805 (Residues: 23-348; Coverage: 100%)
Gene names: JW2924, ansB, b2957
Sequence domains:

Ligands and Environments

No bound ligands
2 modified residues:
Ligand AEI 4 x AEI
Ligand QNY 2 x QNY

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 62.097Å b: 125.971Å c: 76.376Å
α: 90° β: 96.7° γ: 90°
R-values:
R R work R free
0.151 0.149 0.207
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

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

2 mentions without citation

Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity.
Loch et al. (2021)
1 more