› 4oe7

X-ray diffraction
1.99Å resolution

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

Released:
DOI: 10.2210/pdb4oe7/pdb
PDB entry 4oe7 coloured by chain, front view.
PDB entry 4oe7 coloured by chain, side view.
PDB entry 4oe7 coloured by chain, top view.
Source organism: Escherichia coli K-12
Entry authors: Manoj Kumar P, Baskar 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

7 bound ligands:
Ligand EDO 27 x EDO
Ligand GOL 5 x GOL
Ligand MG 4 x MG
Ligand GXT 1 x GXT
Ligand PYR 2 x PYR
Ligand GXP 2 x GXP
Ligand GXS 2 x GXS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21212
Unit cell:
a: 141.24Å b: 155.14Å c: 55.58Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.233
Expression system: Escherichia coli BL21(DE3)

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