› 3nev

X-ray diffraction
2.19Å resolution

Crystal structure of YagE, a prophage protein from E. coli K12 in complex with KDGal

Released:
DOI: 10.2210/pdb3nev/pdb
PDB entry 3nev coloured by chain, front view.
PDB entry 3nev coloured by chain, side view.
PDB entry 3nev coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis.
Bhaskar V, Kumar M, Manicka S, Tripathi S, Venkatraman A, Krishnaswamy S
Proteins 79 1132-42 (2011)
PMID: 21294156

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: 298 amino acids
Theoretical weight: 32.12 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P75682 (Residues: 5-302; Coverage: 99%)
Gene names: JW0261, b0268, yagE
Sequence domains: Dihydrodipicolinate synthetase family
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand EDO 8 x EDO
Ligand RSH 4 x RSH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM14
Spacegroup: P21212
Unit cell:
a: 141.86Å b: 155.13Å c: 55.71Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.237
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives.
Francois et al. (2020)
2 other articles

2 mentions without citation

Structure and function of aldopentose catabolism enzymes involved in oxidative non-phosphorylative pathways.
Ren et al. (2022)
1 more