› 2v9d

X-ray diffraction
2.15Å resolution

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12

Released:
DOI: 10.2210/pdb2v9d/pdb
PDB entry 2v9d coloured by chain, front view.
PDB entry 2v9d coloured by chain, side view.
PDB entry 2v9d coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
Manicka S, Peleg Y, Unger T, Albeck S, Dym O, Greenblatt HM, Bourenkov G, Lamzin V, Krishnaswamy S, Sussman JL
Proteins 71 2102-8 (2008)
PMID: 18361457

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: 37.25 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

No bound ligands
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 56.279Å b: 149.806Å c: 78.967Å
α: 90° β: 108.42° γ: 90°
R-values:
R R work R free
0.168 0.166 0.218
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms.
Valdehuesa et al. (2018)
1 other article

1 mention without citation

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