› 4h2h

X-ray diffraction
1.7Å resolution

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)

Released:
DOI: 10.2210/pdb4h2h/pdb
PDB entry 4h2h coloured by chain, front view.
PDB entry 4h2h coloured by chain, side view.
PDB entry 4h2h coloured by chain, top view.
Source organism: Salipiger bermudensis HTCC2601
Primary publication:
Discovery of new enzymes and metabolic pathways by using structure and genome context.
Zhao S, Kumar R, Sakai A, Vetting MW, Wood BM, Brown S, Bonanno JB, Hillerich BS, Seidel RD, Babbitt PC, Almo SC, Sweedler JV, Gerlt JA, Cronan JE, Jacobson MP
Nature 502 698-702 (2013)
PMID: 24056934

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-170924 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxyproline betaine 2-epimerase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 376 amino acids
Theoretical weight: 40.7 KDa
Source organism: Salipiger bermudensis HTCC2601
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0FPQ4 (Residues: 2-367; Coverage: 100%)
Gene names: R2601_01638, hpbD
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MG 8 x MG
Ligand NI 2 x NI
Ligand 0XW 8 x 0XW
Ligand IOD 61 x IOD
Ligand MPD 3 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 91.035Å b: 152.824Å c: 113.027Å
α: 90° β: 105.2° γ: 90°
R-values:
R R work R free
0.16 0.159 0.192
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

21 review citations

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt et al. (2015)
20 more

1 mention without citation

Discovery of new enzymes and metabolic pathways by using structure and genome context.
Zhao et al. (2013)