5LFD

Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR

Summary for 5LFD

• Entry DOI: 10.2210/pdb5lfd/pdb
• Descriptor: Allantoin racemase (2 entities in total)
• Functional Keywords: evolution of catalytic mechanisms, rate degradation, racemization intermediates, proton transfer, gene identification, isomerase
• Biological source: Pseudomonas fluorescens
• Total number of polymer chains: 2
• Total formula weight: 51685.22

Authors

Cendron, l.,Zanotti, G.,Percudani, R.,Ramazzina, I.,Puggioni, V.,Maccacaro, E.,Liuzzi, A.,Secchi, A. (deposition date: 2016-07-01, release date: 2017-05-10, Last modification date: 2024-01-10)

Primary citation

Cendron, L.,Ramazzina, I.,Puggioni, V.,Maccacaro, E.,Liuzzi, A.,Secchi, A.,Zanotti, G.,Percudani, R.
The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.
Biochemistry, 55:6421-6432, 2016

PubMed Abstract: The S enantiomer of allantoin is an intermediate of purine degradation in several organisms and the final product of uricolysis in nonhominoid mammals. Bioinformatics indicated that proteins of the Asp/Glu racemase superfamily could be responsible for the allantoin racemase (AllR) activity originally described in Pseudomonas species. In these proteins, a cysteine of the catalytic dyad is substituted with glycine, yet the recombinant enzyme displayed racemization activity with a similar efficiency (k/K ≈ 5 × 10 M s) for the R and S enantiomers of allantoin. The protein crystal structure identified a glutamate residue located three residues downstream (E78) that can functionally replace the missing cysteine; the catalytic role of E78 was confirmed by site-directed mutagenesis. Allantoin can undergo racemization through formation of a bicyclic intermediate (faster) or proton exchange at the chiral center (slower). By monitoring the two alternative mechanisms by C and H nuclear magnetic resonance, we found that the velocity of the faster reaction is unaffected by the enzyme, whereas the velocity of the slower reaction is increased by 7 orders of magnitude. Protein phylogenies trace the origin of the racemization mechanism in enzymes acting on glutamate, a substrate for which proton exchange is the only viable reaction mechanism. This mechanism was inherited by allantoin racemase through divergent evolution and conserved in spite of the substitution of catalytic residues.

PubMed: 27797489
DOI: 10.1021/acs.biochem.6b00881

Experimental method

X-RAY DIFFRACTION (2.15 Å)