› 3r1z

X-ray diffraction
1.9Å resolution

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Complex with L-Ala-L-Glu and L-Ala-D-Glu

Released:
DOI: 10.2210/pdb3r1z/pdb
PDB entry 3r1z coloured by chain, front view.
PDB entry 3r1z coloured by chain, side view.
PDB entry 3r1z coloured by chain, top view.
Source organism: Francisella philomiragia subsp. philomiragia ATCC 25017
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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109217 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-amino acid-D/L-Glu epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 379 amino acids
Theoretical weight: 42.46 KDa
Source organism: Francisella philomiragia subsp. philomiragia ATCC 25017
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0TZW0 (Residues: 2-356; Coverage: 100%)
Gene name: Fphi_1647
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ALA 2 x ALA
Ligand GLU 1 x GLU
Ligand SO4 6 x SO4
Ligand GOL 4 x GOL
Ligand DGL 1 x DGL
1 modified residue:
Ligand MSE 18 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P41212
Unit cell:
a: 121.19Å b: 121.19Å c: 149.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.157 0.185
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

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

2 mentions without citation

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