Biology:Proline racemase
| proline racemase | |||||||||
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| Identifiers | |||||||||
| EC number | 5.1.1.4 | ||||||||
| CAS number | 9024-09-3 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
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| Proline racemase | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||||
| Symbol | Pro_racemase | ||||||||||
| Pfam | PF05544 | ||||||||||
| InterPro | IPR008794 | ||||||||||
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In enzymology, a proline racemase (EC 5.1.1.4) is an enzyme that catalyzes the chemical reaction
- L-proline [math]\displaystyle{ \rightleftharpoons }[/math] D-proline
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
- ↑ "Energetics of proline racemase: racemization of unlabeled proline in the unsaturated, saturated, and oversaturated regimes". Biochemistry 25 (9): 2529–37. May 1986. doi:10.1021/bi00357a037. PMID 3755058.
- ↑ "A B-cell mitogen from a pathogenic trypanosome is a eukaryotic proline racemase". Nature Medicine 6 (8): 890–7. August 2000. doi:10.1038/78651. PMID 10932226.
- ↑ "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity". Molecular Microbiology 58 (1): 46–60. October 2005. doi:10.1111/j.1365-2958.2005.04808.x. PMID 16164548.
- ↑ 4.0 4.1 "Molecular and structural discrimination of proline racemase and hydroxyproline-2-epimerase from nosocomial and bacterial pathogens". PLOS ONE 2 (9): e885. 2007. doi:10.1371/journal.pone.0000885. PMID 17849014. Bibcode: 2007PLoSO...2..885G.
- ↑ "Proline racemases are conserved mitogens: characterization of a Trypanosoma vivax proline racemase". Molecular and Biochemical Parasitology 165 (2): 170–9. June 2009. doi:10.1016/j.molbiopara.2009.02.002. PMID 19428664.
- ↑ "Purification and mechanism of action of proline racemase". Biochemistry 7 (11): 3970–8. November 1968. doi:10.1021/bi00851a026. PMID 5722267.
- ↑ PDB: 1W61 and PDB: 1W62; "Crystal structure, catalytic mechanism, and mitogenic properties of Trypanosoma cruzi proline racemase". Proceedings of the National Academy of Sciences 103 (6): 1705–10. February 2006. doi:10.1073/pnas.0509010103. PMID 16446443. Bibcode: 2006PNAS..103.1705B.
- ↑ "Energetics and mechanism of proline racemase". Biochemistry 25 (9): 2572–7. May 1986. doi:10.1021/bi00357a043. PMID 3718964.
Further reading
- "Studies on the enzymic reduction of amino acids. II. Purification and properties of D-proline reductase and a proline racemase from Clostridium sticklandii". The Journal of Biological Chemistry 228 (2): 983–97. October 1957. doi:10.1016/S0021-9258(18)70675-3. PMID 13475375.
- "The catalytic activity of proline racemase: a quantum mechanical/molecular mechanical study". The Journal of Physical Chemistry B 112 (4): 1057–9. January 2008. doi:10.1021/jp7104105. PMID 18044876.
- "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity". Molecular Microbiology 58 (1): 46–60. October 2005. doi:10.1111/j.1365-2958.2005.04808.x. PMID 16164548.
- "Trypanosoma vivax infections: pushing ahead with mouse models for the study of Nagana. I. Parasitological, hematological and pathological parameters". PLOS Neglected Tropical Diseases 4 (8): e792. 2010. doi:10.1371/journal.pntd.0000792. PMID 20706595.
- "Trypanosoma vivax infections: pushing ahead with mouse models for the study of Nagana. II. Immunobiological dysfunctions". PLOS Neglected Tropical Diseases 4 (8): e793. 2010. doi:10.1371/journal.pntd.0000793. PMID 20711524.
- "Drug Discovery Targeting Amino Acid Racemases". Chemical Reviews 111 (11): 6919–46. September 2011. doi:10.1021/cr2000702. PMID 21913633. https://hal-pasteur.archives-ouvertes.fr/pasteur-02510858/file/Drug%20Discovery%20Targeting%20Amino%20Acid.pdf.
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