› 2vws

X-ray diffraction
1.39Å resolution

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12

Released:
DOI: 10.2210/pdb2vws/pdb
PDB entry 2vws coloured by chain, front view.
PDB entry 2vws coloured by chain, side view.
PDB entry 2vws coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12.
Rea D, Hovington R, Rakus JF, Gerlt JA, Fülöp V, Bugg TD, Roper DI
Biochemistry 47 9955-65 (2008)
PMID: 18754683

Function and Biology Details

Reaction catalysed: 
2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160093 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-keto-3-deoxy-L-rhamnonate aldolase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 267 amino acids
Theoretical weight: 28.94 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P76469 (Residues: 1-267; Coverage: 100%)
Gene names: JW2239, b2245, rhmA, yfaU
Sequence domains: HpcH/HpaI aldolase/citrate lyase family
Structure domains: Phosphoenolpyruvate-binding domains

Ligands and Environments

2 bound ligands:
Ligand PO4 4 x PO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX14.2
Spacegroup: C2221
Unit cell:
a: 105.2Å b: 136.8Å c: 123.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.191
Expression system: Escherichia coli

Quick links

Citations

1 review citation

DHAP-dependent aldolases from (hyper)thermophiles: biochemistry and applications.
Falcicchio et al. (2014)
14 other articles

4 mentions without citation

Broad Analysis of Vicinal Disulfides: Occurrences, Conformations with Cis or with Trans Peptides, and Functional Roles Including Sugar Binding.
Richardson et al. (2017)
3 more