4-hydroxyproline betaine 2-epimerase

 

Catalyses the 2-epimerisation of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). These enzymes are involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilisation of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolised when it is needed as osmoprotectant. Can also catalyse the racemisation of L-proline betaine.

 

Reference Protein and Structure

Sequence
Q0FPQ4 UniProt (5.1.1.22) IPR029065 (Sequence Homologues) (PDB Homologues)
Biological species
Pelagibaca bermudensis HTCC2601 (Bacteria) Uniprot
PDB
4h2h - Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine) (1.7 Å) PDBe PDBsum 4h2h
Catalytic CATH Domains
3.20.20.120 CATHdb (see all for 4h2h)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:5.1.1.22)

trans-4-hydroxy-L-proline betaine
CHEBI:85533ChEBI
→
cis-4-hydroxy-D-proline betaine
CHEBI:85534ChEBI
Alternative enzyme names: HpbD (gene name), Hyp-B 2-epimerase, (4R)-4-hydroxyproline betaine 2-epimerase,

Enzyme Mechanism

Introduction

The exact mechanism of this protein has yet to be elucidated. However, as it is a member of the enolase superfamily the mechanism can be inferred as: initial abstraction of a proton from the carbon alpha to the carbonyl group. The intermediate is then reprotonated from the opposite face to complete the racemisation.

Catalytic Residues Roles

UniProt PDB* (4h2h)
Asp193, Glu218, Asp241 Asp193(202)A, Glu218(227)A, Asp241(250)A Form part of the magnesium binding site. metal ligand
Trp320 Trp320(329)A Forms pi-cation interaction with betaine, helping to stabilise the reactive intermediates and transition states formed during the course of the reaction. electrostatic stabiliser
Lys163, Lys265 Lys163(172)A, Lys265(274)A Acts as a general acid/base. One of these catalytic lysine residues abstracts the proton alpha to the carboxyl group (likely to be Lys163 based off similarity with other members of the mandelate racemase subgroup). The other lysine is responsible for donating the proton back to the substrate on the opposite side of the substrate to complete the racemisation. proton shuttle (general acid/base)
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Zhao S et al. (2013), Nature, 502, 698-702. Discovery of new enzymes and metabolic pathways by using structure and genome context. DOI:10.1038/nature12576. PMID:24056934.

Step 1.

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Catalytic Residues Roles

Residue Roles
Asp193(202)A metal ligand
Glu218(227)A metal ligand
Asp241(250)A metal ligand
Lys163(172)A proton shuttle (general acid/base)
Lys265(274)A proton shuttle (general acid/base)
Trp320(329)A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Shoshana Brown