› 3q45

X-ray diffraction
3Å resolution

Crystal structure of Dipeptide Epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Val

Released:
DOI: 10.2210/pdb3q45/pdb
PDB entry 3q45 coloured by chain, front view.
PDB entry 3q45 coloured by chain, side view.
PDB entry 3q45 coloured by chain, top view.
Source organism: Cytophaga hutchinsonii ATCC 33406
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

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171272 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-Ala-D/L-Ala epimerase Chains: A, B, C, D, E, F, G, H, I
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I
Length: 368 amino acids
Theoretical weight: 40.35 KDa
Source organism: Cytophaga hutchinsonii ATCC 33406
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q11T61 (Residues: 1-368; Coverage: 100%)
Gene names: CHU_2140, tfdD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 9 x MG
Ligand DAL 9 x DAL
Ligand VAL 9 x VAL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: P21
Unit cell:
a: 94Å b: 158.2Å c: 182.74Å
α: 90° β: 100.28° γ: 90°
R-values:
R R work R free
0.274 0.227 0.251
Expression system: Escherichia coli BL21(DE3)

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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)