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Catalytic Site Atlas

CSA LITERATURE entry for 1dbt

E.C. nameorotidine-5'-phosphate decarboxylase
SpeciesBacillus subtilis (Bacteria)
E.C. Number (IntEnz) 4.1.1.23
CSA Homologues of 1dbtThere are 115 Homologs
CSA Entries With UniProtID P25971
CSA Entries With EC Number 4.1.1.23
PDBe Entry 1dbt
PDBSum Entry 1dbt
MACiE Entry M0050

Literature Report

IntroductionOrotidine-5'-phosphate decarboxylase catalyses the decarboxylation of orotidine-5'-phosphate, the sixth and final step in the de novo pyrimidine biosynthesis of uridine monophosphate. It accelerates the reaction by 10^17 and hence is the most proficient enzyme discovered so far. In most prokaryotes the bioactive form is a homodimer. In higher organisms it is part of a bifunctional enzyme.
MechansimThe enzyme has a novel mechanism: the carbanion generated by carbon dioxide loss is localised in an sp2 orbital perpendicular to the pi system of the pyrimidine. In all other decarboxylases, the carbanion is delocalised either into an adjacent carbonyl or into a covalently bound thiamin, pyridoxal or pyruvoyl cofactor.
The currently proposed mechanism is a bimolecular electrophilic substitution SE2 in which decarboxylation and protonation are concerted. Firstly, the anionic carboxylate of the substrate is positioned in a negatively charged region close to the carboxylate of Asp60 and Asp65(B) and the carbon of the pyrimidine destined to become the carbanium is close to the positive protonated Lys62. This allows destabilisation of the ground state and the stabilisation of negative charge accumulation in the transition state.
Extensive hydrogen bonding interactions within the active site provide the binding energy required to force the carboxylate groups into close proximity. As the reaction proceeds, the weakly basic C-C bond linking the carboxy group to the pyrimidine becomes progressively more basic until proton transfer from the adjacent Lys62 occurs.
Reaction

Catalytic Sites for 1dbt

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA6262macie:sideChainThe residue acts as a general acid to the cleaving carboxy-pyrimidine C-C bond in concert with decarboxylation. The residue is then reprotonated by solvent to regenerate the active site. Its pKa is modified through electrostatic interactions with the neighbouring carboxyl groups of Asp60 and Asp65(B).
AspA6060macie:sideChainThe carboxylate side chains remain deprotonated and anionic within close proximity to the substrate carboxyl group. Although the groups repel one another, the strength of the surrounding hydrogen bonding network directs them towards one another. These repulsive interactions increase the energy of the groundstate so it resembles that of the transition state and therefore reduces the reaction activation barrier while also stabilising the polar transition state.
AspB6565macie:sideChain The carboxylate side chains remain deprotonated and anionic within close proximity to the substrate carboxyl group. Although the groups repel one another, the strength of the surrounding hydrogen bonding network directs them towards one another. These repulsive interactions increase the energy of the groundstate so it resembles that of the transition state and therefore reduces the reaction activation barrier while also stabilising the polar transition state.

Literature References

Notes:
Appleby TC
The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase.
Proc Natl Acad Sci U S A 2000 97 2005-2010
PubMed: 10681442
Begley TP
The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase.
Curr Opin Struct Biol 2000 10 711-718
PubMed: 11114509
Heinrich D
Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase.
Chemistry 2009 15 6619-6625
PubMed: 19472232
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