› 3ijq

X-ray diffraction
2Å resolution

Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Ala-D-Glu; productive substrate binding.

Released:
DOI: 10.2210/pdb3ijq/pdb
Model geometry
Fit model/data
PDB entry 3ijq coloured by chain, front view.
PDB entry 3ijq coloured by chain, side view.
PDB entry 3ijq coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron
Primary publication:
Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP
Proc Natl Acad Sci U S A 109 4122-7 (2012)
PMID: 22392983

Function and Biology Details

Reaction catalysed: 
L-alanyl-D-glutamate = L-alanyl-L-glutamate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183749 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-Ala-D/L-Glu epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 338 amino acids
Theoretical weight: 37.53 KDa
Source organism: Bacteroides thetaiotaomicron
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8A861 (Residues: 46-383; Coverage: 88%)
Gene name: BT_1313
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ALA 2 x ALA
Ligand DGL 2 x DGL
Ligand MG 2 x MG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: NSLS BEAMLINE X4A
Spacegroup: C2
Unit cell:
a: 141.71Å b: 99.865Å c: 60.851Å
α: 90° β: 90.32° γ: 90°
R-values:
R R work R free
0.247 0.247 0.287
Expression system: Escherichia coli

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Citations

8 review citations

Bacterial cell-wall recycling.
Johnson et al. (2013)
7 more

1 mention without citation

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Lukk et al. (2012)