› 4izg

X-ray diffraction
1.7Å resolution

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound cis-4oh-d-proline betaine (product)

Released:
DOI: 10.2210/pdb4izg/pdb
PDB entry 4izg coloured by chain, front view.
PDB entry 4izg coloured by chain, side view.
PDB entry 4izg coloured by chain, top view.
Source organism: Paracoccus denitrificans PD1222
Primary publication:
Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE
mBio 5 e00933-13 (2014)
PMID: 24520058

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106557 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxyproline betaine 2-epimerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 391 amino acids
Theoretical weight: 41.98 KDa
Source organism: Paracoccus denitrificans PD1222
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1B198 (Residues: 1-369; Coverage: 100%)
Gene names: Pden_1187, hpbD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand IOD 27 x IOD
Ligand MG 5 x MG
Ligand 4OP 2 x 4OP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P4212
Unit cell:
a: 117.463Å b: 117.463Å c: 111.049Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.167 0.165 0.197
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.
Jacobson et al. (2014)
8 other articles

1 mention without citation

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.
Kumar et al. (2014)