Proline racemase

In enzymology, a proline racemase (EC 5.1.1.4) is an enzyme that catalyzes the chemical reaction

L-proline D-proline
proline racemase
Identifiers
EC number5.1.1.4
CAS number9024-09-3
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Proline racemase
Identifiers
SymbolPro_racemase
PfamPF05544
InterProIPR008794

Hence, this enzyme has two substrates, L- and D-proline, and two products, D- and L- proline.

This enzyme belongs to the family of proline racemases acting on free amino acids. The systematic name of this enzyme class is proline racemase. This enzyme participates in arginine and proline metabolism. These enzymes catalyse the interconversion of L- and D-proline in bacteria.[1]

Species distribution

This first eukaryotic proline racemase was identified in Trypanosoma cruzi and fully characterized Q9NCP4. The parasite enzyme, TcPRAC, is as a co-factor-independent proline racemase and displays B-cell mitogenic properties when released by T. cruzi upon infection, contributing to parasite escape.[2][3]

Novel proline racemases of medical and veterinary importance were described respectively in Clostridium difficile (Q17ZY4)[4] and Trypanosoma vivax (B8LFE4).[5] These studies showed that a peptide motif used as a minimal pattern signature to identify putative proline racemases (motif III*) is insufficient stringent per se to discriminate proline racemases from 4-hydroxyproline epimerases (HyPRE). Also, additional, non-dissociated elements that account for the discrimination of these enzymes were identified, based for instance on polarity constraints imposed by specific residues of the catalytic pockets. Based on those elements, enzymes incorrectly described as proline racemases were biochemically proved to be hydroxyproline epimerases (i.e. HyPREs from Pseudomonas aeruginosa (Q9I476), Burkholderia pseudomallei (Q63NG7), Brucella abortus (Q57B94), Brucella suis (Q8FYS0) and Brucella melitensis (Q8YJ29).[4]

Structural studies

The biochemical mechanism of proline racemase was first put forward in the late sixties by Cardinale and Abeles[6] using the Clostridium sticklandii enzyme, CsPRAC. The catalytic mechanism of proline racemase was late revisited by Buschiazzo, Goytia and collaborators that, in 2006, resolved the structure of the parasite TcPRAC co-crystallyzed with its known competitive inhibitor - pyrrole carboxylic acid (PYC).[7] Those studies showed that each active enzyme contains two catalytic pockets. Isothermal titration calorimetry then showed that two molecules of PYC associate with TcPRAC in solution, and that this association is time-dependent and most probably based on mechanism of negative cooperativity. Complementary biochemical findings are consistent with the presence of two active catalytic sites per homodimer, each pertaining to one enzyme subunit, challenging the previously proposed mechanism of one catalytic site per homodimer previously proposed.[8]

Mechanism

The proline racemase active site contains two general bases, each of them a Cys, located on either side of the alpha-carbon of the substrate. In order to work properly, one Cys must be protonated (a thiol, RSH) and the other must be deprotonated (a thiolate, RS–).

Inhibition

Proline racemase is inhibited by pyrrole-2-carboxylic acid, a transition state analogue that is flat like the transition state.

References
  1. Fisher LM, Albery WJ, Knowles JR (May 1986). "Energetics of proline racemase: racemization of unlabeled proline in the unsaturated, saturated, and oversaturated regimes". Biochemistry. 25 (9): 2529–37. doi:10.1021/bi00357a037. PMID 3755058.
  2. Reina-San-Martín B, Degrave W, Rougeot C, Cosson A, Chamond N, Cordeiro-Da-Silva A, Arala-Chaves M, Coutinho A, Minoprio P (August 2000). "A B-cell mitogen from a pathogenic trypanosome is a eukaryotic proline racemase". Nature Medicine. 6 (8): 890–7. doi:10.1038/78651. PMID 10932226. S2CID 9163196.
  3. Chamond N, Goytia M, Coatnoan N, Barale JC, Cosson A, Degrave WM, Minoprio P (October 2005). "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity". Molecular Microbiology. 58 (1): 46–60. doi:10.1111/j.1365-2958.2005.04808.x. PMID 16164548. S2CID 28436244.
  4. Goytia M, Chamond N, Cosson A, Coatnoan N, Hermant D, Berneman A, Minoprio P (2007). "Molecular and structural discrimination of proline racemase and hydroxyproline-2-epimerase from nosocomial and bacterial pathogens". PLOS ONE. 2 (9): e885. Bibcode:2007PLoSO...2..885G. doi:10.1371/journal.pone.0000885. PMC 1964878. PMID 17849014.
  5. Chamond N, Cosson A, Coatnoan N, Minoprio P (June 2009). "Proline racemases are conserved mitogens: characterization of a Trypanosoma vivax proline racemase". Molecular and Biochemical Parasitology. 165 (2): 170–9. doi:10.1016/j.molbiopara.2009.02.002. PMID 19428664.
  6. Cardinale GJ, Abeles RH (November 1968). "Purification and mechanism of action of proline racemase". Biochemistry. 7 (11): 3970–8. doi:10.1021/bi00851a026. PMID 5722267.
  7. PDB: 1W61​ and PDB: 1W62​; Buschiazzo A, Goytia M, Schaeffer F, Degrave W, Shepard W, Grégoire C, Chamond N, Cosson A, Berneman A, Coatnoan N, Alzari PM, Minoprio P (February 2006). "Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase". Proceedings of the National Academy of Sciences. 103 (6): 1705–10. Bibcode:2006PNAS..103.1705B. doi:10.1073/pnas.0509010103. PMC 1413642. PMID 16446443.
  8. Albery WJ, Knowles JR (May 1986). "Energetics and mechanism of proline racemase". Biochemistry. 25 (9): 2572–7. doi:10.1021/bi00357a043. PMID 3718964.

Further reading
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