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==Crystal structure of allantoin racemase from Pseudomonas fluorescens AllR== | |||
<StructureSection load='5lfd' size='340' side='right' caption='[[5lfd]], [[Resolution|resolution]] 2.15Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5lfd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LFD FirstGlance]. <br> | |||
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allantoin_racemase Allantoin racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.99.3 5.1.99.3] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5lfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lfd OCA], [http://pdbe.org/5lfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lfd RCSB], [http://www.ebi.ac.uk/pdbsum/5lfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lfd ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 (kcat/KM approximately 5 x 104 M-1 s-1) 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 13C and 1H 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. | |||
The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.,Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R Biochemistry. 2016 Nov 22;55(46):6421-6432. Epub 2016 Nov 7. PMID:27797489<ref>PMID:27797489</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5lfd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Allantoin racemase]] | |||
[[Category: Cendron, l]] | |||
[[Category: Liuzzi, A]] | [[Category: Liuzzi, A]] | ||
[[Category: Maccacaro, E]] | |||
[[Category: Percudani, R]] | |||
[[Category: Puggioni, V]] | [[Category: Puggioni, V]] | ||
[[Category: Ramazzina, I]] | [[Category: Ramazzina, I]] | ||
[[Category: Secchi, A]] | [[Category: Secchi, A]] | ||
[[Category: Zanotti, G]] | |||
[[Category: Evolution of catalytic mechanism]] | |||
[[Category: Gene identification]] | |||
[[Category: Isomerase]] | |||
[[Category: Proton transfer]] | |||
[[Category: Racemization intermediate]] | |||
[[Category: Rate degradation]] | |||
Revision as of 15:50, 10 May 2017
Crystal structure of allantoin racemase from Pseudomonas fluorescens AllRCrystal structure of allantoin racemase from Pseudomonas fluorescens AllR
Structural highlights
Publication Abstract from PubMedThe 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 (kcat/KM approximately 5 x 104 M-1 s-1) 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 13C and 1H 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. The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.,Cendron L, Ramazzina I, Puggioni V, Maccacaro E, Liuzzi A, Secchi A, Zanotti G, Percudani R Biochemistry. 2016 Nov 22;55(46):6421-6432. Epub 2016 Nov 7. PMID:27797489[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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