Structural Basis for the Decarboxylation of Orotidine 5'-Monophosphate (OMP) by Plasmodium Falciparum OMP Decarboxylase

Tokuoka, K.; Kusakari, Yukiko; Krungkrai, Sudaratana R.; Matsumura, Hideki; Kai, Yasushi; Krungkrai, Jerapan; Horii, Toshihiro; Inoue, Tsuyoshi

doi:10.1093/jb/mvm193

Cited by 29 publications

(33 citation statements)

References 48 publications

(49 reference statements)

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“…6A) and in the crystal structure of the Pf ODCase-OMP complex. 55 Consequently, mutation of this lysine resulted in a 1,000-fold increase of K m and a 100-fold decrease of k cat . 12 …”

Section: Resultsmentioning

confidence: 99%

“…43,49,57–59 Various structures indicate that ligand binding leads to the closure of a loop (residues 182–190), which is disordered in the ligand-free enzyme. 6,10,19,54,55,60–62 When locked down, this loop forms five interactions, directly or through water molecules, with the phosphate part of the ligand. 1-(β-D-erythrofuranosyl)orotic acid (EO), an OMP derivative missing O5 of the ribose ring and the phosphate group (Supporting Fig.…”

Section: Resultsmentioning

confidence: 99%

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Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase

et al. 2013

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Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme’s short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl- and ethyl-ester of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. MD and QM/MM computations of the enzyme-substrate (ES) complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted with the distortion contributing a 10–15% decrease of the ΔΔG‡ value. These results are consistent with ODCase using both substrate distortion as well as transition state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.

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“…6A) and in the crystal structure of the Pf ODCase-OMP complex. 55 Consequently, mutation of this lysine resulted in a 1,000-fold increase of K m and a 100-fold decrease of k cat . 12 …”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase

et al. 2013

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“…the strong contribution of the 5Ј-phosphate group (30,37,38) or the vinyl carbanion nature of a reaction intermediate (6,7). It is also generally assumed that Lys-72, which is completely conserved in all known ODCase sequences (16), plays an important role in balancing the negative charge of the vinyl carbanion and thereby lowers the energy of the transition state. The amino head group of the residue closely approaches the C6 atom of the pyrimidine rings of ligands (2-5, 11, 29), and its mutation to an alanine decreases the decarboxylation rate by 5 orders of magnitude (30).…”

Section: Resultsmentioning

confidence: 99%

“…For 6-cyano-UMP, such a distortion receives strong support from Raman spectroscopy, which indicates bond bending of about 20° (15). The crystal structure of ODCase from Plasmodium falciparum in complex with OMP (16) implied that charge repulsion between the two carboxylates of Asp-70 and OMP is a prime candidate for causing such a distortion.…”

mentioning

confidence: 98%

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Fujihashi

Mito

Pai

et al. 2013

Journal of Biological Chemistry

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Background: Low binding affinity of product UMP is used to argue against substrate distortion contributing to orotidine-5Ј-monophosphate decarboxylase catalysis. Results: Atomic resolution structure and surface plasmon resonance analysis reveal strong repulsion between active site residue and UMP. Conclusion: Low UMP affinity does not disprove contribution of substrate distortion to catalysis. Significance: Substrate distortion can still be considered as a mechanistic feature of this most proficient enzyme.Orotidine 5-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of its substrate by 17 orders of magnitude. One argument brought forward against steric/electrostatic repulsion causing substrate distortion at the carboxylate substituent as part of the catalysis has been the weak binding affinity of the decarboxylated product (UMP). The crystal structure of the UMP complex of ODCase at atomic resolution (1.03 Å) shows steric competition between the product UMP and the side chain of a catalytic lysine residue. Surface plasmon resonance analysis indicates that UMP binds 5 orders of magnitude more tightly to a mutant in which the interfering side chain has been removed than to wild-type ODCase. These results explain the low affinity of UMP and counter a seemingly very strong argument against a contribution of substrate distortion to the catalytic reaction mechanism of ODCase.Orotidine 5Ј-monophosphate decarboxylase (ODCase) 3 is one of the most proficient enzymes known (1). It decarboxylates orotidine 5Ј-monophosphate (OMP) and produces uridine 5Ј-monophosphate (UMP) in the final step of the de novo pyrimidine biosynthesis pathway (Fig. 1A). It also accelerates the reaction by 17 orders of magnitude, as compared with the spontaneous reaction in water at neutral pH, without employing cofactors or metal ions (1-5).The reaction mechanism of this enzyme has been the subject of extensive investigations. More than 170 crystal structures have been determined, and numerous kinetic assays at various conditions have been performed. These experiments established that an electrostatic residue network composed of the charged side chains of two aspartate and two lysine residues, all completely conserved, plays a dominant role in catalysis (Fig. 1B) (2-5). As with all enzymes, the reaction acceleration provided by ODCase is explained in part by transition state stabilization (6). Lys-72 (the sequence numbers in this study correspond to those of the ODCase from Methanothermobacter thermautotrophicus (MtODCase)) is considered to be the key residue to stabilize the intermediate vinyl anion (6,7). However, there is still no general agreement on all the details of the reaction mechanism. In particular, the observation that ODCase also converts 6-cyano-UMP into 6-hydroxy-UMP at the same site where the decarboxylation reaction occurs (Fig. 1A) (8) complicates the scenario. The environment required to stabilize the vinyl anion does not seem suitable to support, at the same time, the intermediate of the side reaction b...

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“…It salvages the preformed purine bases/nucleosides from the human host and converts them to their mono-, di-and triphosphates. The parasite can only synthesize pyrimidines de novo from HCO 3 -, ATP, glutamine, aspartate, and 5-phosphoribosyl-1-pyrophosphate [43][44][45][46][47][48][49][50][51][52][53] . These unique properties on both purine and pyrimidine requirement of the parasite are key differences from the human host, in which both functional de novo and salvage pathways of the purine and pyrimidine synthesis exists [46,48,[54][55][56][57][58].…”

Section: Basic Life Cycle Genomics and Biochemistry Of Human Malariamentioning

confidence: 99%

Malaria parasite carbonic anhydrase: inhibition of aromatic/heterocyclic sulfonamides and its therapeutic potential

Krungkrai¹,

Krungkrai²

2011

Asian Pacific Journal of Tropical Biomedicine

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Structural Basis for the Decarboxylation of Orotidine 5'-Monophosphate (OMP) by Plasmodium Falciparum OMP Decarboxylase

Cited by 29 publications

References 48 publications

Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase

Substrate Distortion Contributes to the Catalysis of Orotidine 5′-Monophosphate Decarboxylase

Atomic Resolution Structure of the Orotidine 5′-Monophosphate Decarboxylase Product Complex Combined with Surface Plasmon Resonance Analysis

Malaria parasite carbonic anhydrase: inhibition of aromatic/heterocyclic sulfonamides and its therapeutic potential

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