› 4onv

X-ray diffraction
2.57Å resolution

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

Released:
DOI: 10.2210/pdb4onv/pdb
PDB entry 4onv coloured by chain, front view.
PDB entry 4onv coloured by chain, side view.
PDB entry 4onv coloured by chain, top view.
Source organism: Escherichia coli K-12
Entry authors: Manoj Kumar P, Bhaskar V, Manicka S, Krishnaswamy S

Function and Biology Details

Reactions catalysed: 
2-dehydro-3-deoxy-D-pentonate = pyruvate + glycolaldehyde
2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159987 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 343 amino acids
Theoretical weight: 37.01 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P75682 (Residues: 1-302; Coverage: 100%)
Gene names: JW0261, b0268, yagE
Sequence domains: Dihydrodipicolinate synthetase family
Structure domains: Aldolase class I

Ligands and Environments

3 bound ligands:
Ligand EDO 15 x EDO
Ligand GOL 13 x GOL
Ligand KDG 4 x KDG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21212
Unit cell:
a: 141.17Å b: 155.41Å c: 55.51Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.247 0.284
Expression system: Escherichia coli BL21(DE3)

Quick links