1
|
Kreppel A, Ochsenfeld C. The Enzymatic Decarboxylation Mechanism of 5-Carboxy Uracil: A Comprehensive Quantum Chemical Study. J Chem Theory Comput 2021; 17:96-104. [PMID: 33356236 DOI: 10.1021/acs.jctc.0c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic regulation of DNA methylation is an important process for the control of gene expression in mammals. It is believed that in the demethylation pathway of 5-methyl cytosine, the intermediate 5-carboxy cytosine (5caC) can be actively decarboxylated alongside the substitution in the base excision repair. For the active decarboxylation of 5caC, a decarboxylase has not been identified so far. Due to the similar chemistry of the decarboxylation of 5-carboxy uracil (5caU) to uracil (U) in the pyrimidine salvage pathway catalyzed by the iso-orotate decarboxylase (IDCase), the study of this reaction might give valuable insights into the active 5caC decarboxylation process. In this work, we employ quantum chemical and molecular mechanic calculations and find that the catalytic mechanism of IDCase proceeds via a direct decarboxylation mechanism. Detailed investigations on the reaction coordinate reveal that it is a one-step mechanism with concerted proton transfer and C-C bond opening.
Collapse
Affiliation(s)
- Andrea Kreppel
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), D-81377 Munich, Germany.,Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
| |
Collapse
|
2
|
Králová M, Bergougnoux V, Frébort I. CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea. J Biotechnol 2020; 325:341-354. [PMID: 33053363 DOI: 10.1016/j.jbiotec.2020.09.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 02/09/2023]
Abstract
Claviceps purpurea is a filamentous fungus well known as a widespread plant pathogen, but it is also an important ergot alkaloid producer exploited by the pharmaceutic industry. In this work, we demonstrated that CRISPR/Cas9 can be a tool for directed mutagenesis in C. purpurea targeting pyr4 and TrpE genes encoding the orotidine 5'-phosphate decarboxylase involved in pyrimidine biosynthesis and the α-subunit of the anthranilate synthase involved in tryptophan biosynthesis, respectively. After protoplast transformation and single spore isolation, homokaryotic mutants showing uridine or tryptophan auxotrophy were selected. In all cases, insertions or insertions combined with deletions were found mostly 3 bp upstream of the PAM sequence. However, transformation efficiencies of CRISPR/Cas9 and CRISPR/Cas9 mediated homology-directed repair only slightly improved in comparison to homologous recombination-mediated knocking-out of the TrpE gene. Moreover, Trp auxotrophs were non-infectious towards rye plants likely due to a decreased production of the plant hormones auxins, which are synthesized by C. purpurea from indole-3-glycerolphosphate in Trp-dependent and Trp-independent biosynthetic pathways, and help the fungus to colonize the plant host. It was demonstrated that the CRISPR/Cas9 vector containing autonomous replicative sequence AMA1 can be fully removed by further culturing of C. purpurea on non-selective media. This method enables introducing multiple mutations in Claviceps and makes feasible metabolic engineering of industrial strains.
Collapse
Affiliation(s)
- Michaela Králová
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Véronique Bergougnoux
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| | - Ivo Frébort
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Šlechtitelů 27, Olomouc, 783 71, Czech Republic.
| |
Collapse
|
3
|
Decarboxylation of orotic acid analogues: Comparison of solution and gas-phase reactivity. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
4
|
Rao NS, Deshpande PA. A mechanistic model for uridine 5′-monophosphate nucleotide synthesis. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.05.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
5
|
Fujihashi M, Mnpotra JS, Mishra RK, Pai EF, Kotra LP. Orotidine Monophosphate Decarboxylase--A Fascinating Workhorse Enzyme with Therapeutic Potential. J Genet Genomics 2015; 42:221-34. [PMID: 26059770 DOI: 10.1016/j.jgg.2015.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/13/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) is known as one of the most proficient enzymes. The enzyme catalyzes the last reaction step of the de novo pyrimidine biosynthesis, the conversion from orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate. The enzyme is found in all three domains of life, Bacteria, Eukarya and Archaea. Multiple sequence alignment of 750 putative ODCase sequences resulted in five distinct groups. While the universally conserved DxKxxDx motif is present in all the groups, depending on the groups, several characteristic motifs and residues can be identified. Over 200 crystal structures of ODCases have been determined so far. The structures, together with biochemical assays and computational studies, elucidated that ODCase utilized both transition state stabilization and substrate distortion to accelerate the decarboxylation of its natural substrate. Stabilization of the vinyl anion intermediate by a conserved lysine residue at the catalytic site is considered the largest contributing factor to catalysis, while bending of the carboxyl group from the plane of the aromatic pyrimidine ring of OMP accounts for substrate distortion. A number of crystal structures of ODCases complexed with potential drug candidate molecules have also been determined, including with 6-iodo-uridine, a potential antimalarial agent.
Collapse
Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Jagjeet S Mnpotra
- Department of Chemistry & Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, 27412, USA
| | - Ram Kumar Mishra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Lakshmi P Kotra
- Center for Molecular Design and Preformulations, and Toronto General Research Institute, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, M5S 3M2, Canada.
| |
Collapse
|
6
|
Jamshidi S, Jalili S, Rafii-Tabar H. Study of orotidine 5'-monophosphate decarboxylase in complex with the top three OMP, BMP, and PMP ligands by molecular dynamics simulation. J Biomol Struct Dyn 2014; 33:404-17. [PMID: 24559040 DOI: 10.1080/07391102.2014.881303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in its free form as well as in complex with different ligands, namely 1-(5'-phospho-D-ribofuranosyl) barbituric acid (BMP), orotidine 5'-monophosphate (OMP), and 6-phosphonouridine 5'-monophosphate (PMP). The importance of this biological system is justified both by its high rate enhancement and its potential use as a target in chemotherapy. This work focuses on comparing two physicochemical states of the enzyme (protonated and deprotonated Asp91) and three ligands (substrate OMP, inhibitor, and transition state analog BMP and substrate analog PMP). Detailed analysis of the active site geometry and its interactions is properly put in context by extensive comparison with relevant experimental works. Our overall results show that in terms of hydrogen bond occupancy, electrostatic interactions, dihedral angles, active site configuration, and movement of loops, notable differences among different complexes are observed. Comparison of the results obtained from these simulations provides some detailed structural data for the complexes, the enzyme, and the ligands, as well as useful insights into the inhibition mechanism of the OMPDC enzyme. Furthermore, these simulations are applied to clarify the ambiguous mechanism of the OMPDC enzyme, and imply that the substrate destabilization and transition state stabilization contribute to the mechanism of action of the most proficient enzyme, OMPDC.
Collapse
Affiliation(s)
- Shirin Jamshidi
- a Faculty of Medicine, Department of Medical Physics and Biomedical Engineering , Shahid Beheshti University of Medical Sciences , Evin, Tehran , Iran
| | | | | |
Collapse
|
7
|
Abstract
ODCase is a highly proficient enzyme responsible for the decarboxylation of orotidine monophosphate to generate uridine monophosphate. ODCase has attracted early attention due to its interesting mechanism of catalysis. In order to exploit therapeutic advantages due to the inhibition of ODCase, one must have selective inhibitors of this enzyme from the pathogen, or a dysregulated molecular mechanism involving ODCase. ODCase inhibitors have potential applications as anticancer agents, antiviral agents, antimalarial agents and potentially act against other parasitic diseases. A variety of C6-substituted uridine monophosphate derivatives have shown excellent inhibition of ODCase. 6-iodouridine is a potent inhibitor of the malaria parasite, and its monophosphate form covalently inhibits ODCase. A variety of inhibitors of ODCase with potential applications as therapeutic agents are discussed in this review.
Collapse
|
8
|
Goryanova B, Goldman LM, Amyes TL, Gerlt JA, Richard JP. Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions. Biochemistry 2013; 52:7500-11. [PMID: 24053466 DOI: 10.1021/bi401117y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The side chain cation of Arg235 provides a 5.6 and 2.6 kcal/mol stabilization of the transition states for orotidine 5'-monophosphate (OMP) decarboxylase (OMPDC) from Saccharomyces cerevisiae catalyzed reactions of OMP and 5-fluoroorotidine 5'-monophosphate (FOMP), respectively, a 7.2 kcal/mol stabilization of the vinyl carbanion-like transition state for enzyme-catalyzed exchange of the C-6 proton of 5-fluorouridine 5'-monophosphate (FUMP), but no stabilization of the transition states for enzyme-catalyzed decarboxylation of truncated substrates 1-(β-d-erythrofuranosyl)orotic acid and 1-(β-d-erythrofuranosyl) 5-fluorouracil. These observations show that the transition state stabilization results from formation of a protein cation-phosphodianion pair, and that there is no detectable stabilization from an interaction between the side chain and the pyrimidine ring of substrate. The 5.6 kcal/mol side chain interaction with the transition state for the decarboxylation reaction is 50% of the total 11.2 kcal/mol transition state stabilization by interactions with the phosphodianion of OMP, whereas the 7.2 kcal/mol side chain interaction with the transition state for the deuterium exchange reaction is a larger 78% of the total 9.2 kcal/mol transition state stabilization by interactions with the phosphodianion of FUMP. The effect of the R235A mutation on the enzyme-catalyzed deuterium exchange is expressed predominantly as a change in the turnover number kex, whereas the effect on the enzyme-catalyzed decarboxylation of OMP is expressed predominantly as a change in the Michaelis constant Km. These results are rationalized by a mechanism in which the binding of OMP, compared with that for FUMP, provides a larger driving force for conversion of OMPDC from an inactive open conformation to a productive, active, closed conformation.
Collapse
Affiliation(s)
- Bogdana Goryanova
- Department of Chemistry, University at Buffalo , Buffalo, New York 14260, United States
| | | | | | | | | |
Collapse
|
9
|
Senger NA, Bliss CE, Keeffe JR, Gronert S, Wu W. Stabilities of Uracil and Pyridone-Based Carbanions: A Systematic Study in the Gas Phase and Solution and Implications for the Mechanism of Orotidine-5'-Monophosphate Decarboxylase. Tetrahedron 2013; 69:5287-5292. [PMID: 24072938 DOI: 10.1016/j.tet.2013.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The stabilities of the C6-centered carbanions derived from 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were systematically investigated in the gas phase and in DMSO and water solutions. The stabilities of the carbanions in the gas phase and DMSO were directly measured through their reactions with carbon acids with known proton affinity or pKa values. The stabilities of the carbanions in DMSO were also probed through their kinetic isotope effects of protonation over deuteriation using acids with different acidity. The stabilities of the carbanions in water were determined through the rates of hydrogen-deuterium exchange reactions of the corresponding conjugate acids. The carbanions derived from the two pyridones were found to have the same stability, whereas the carbanion derived from 1,3-dimethyluracil was more stable. The order of the stability of the carbanions showed no correlation with the decarboxylation rates of their corresponding carboxylic acids. The implications of the results for the mechanism of orotidine-5'-monophosphate decarboxylase (ODCase) are discussed.
Collapse
Affiliation(s)
- Nicholas A Senger
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | | | | | | | | |
Collapse
|
10
|
Vardi-Kilshtain A, Doron D, Major DT. Quantum and classical simulations of orotidine monophosphate decarboxylase: support for a direct decarboxylation mechanism. Biochemistry 2013; 52:4382-90. [PMID: 23692207 DOI: 10.1021/bi400190v] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Orotidine 5'-monophosphate (OMP) decarboxylase (ODCase) catalyzes the decarboxylation of OMP to uridine 5'-monophosphate (UMP). Numerous studies of this reaction have suggested a plethora of mechanisms including covalent addition, ylide or carbene formation, and concerted or stepwise protonation. Recent experiments and simulations present strong evidence for a direct decarboxylation mechanism, although direct comparison between experiment and theory is still lacking. In the current work we present hybrid quantum mechanics-molecular mechanics simulations that address the detailed decarboxylation mechanisms for OMP and 5-fluoro-OMP by ODCase. Multidimensional potentials of mean force are computed as functions of structural progress coordinates for the Methanobacterium thermoautotrophicum ODCase reaction: the decarboxylation reaction coordinate, an orbital rehybridization coordinate, and the proton transfer coordinate between Lys72 and the substrate. The computed free energy profiles are in accord with the available experimental data. To facilitate further direct comparison with experiment, we compute the kinetic isotope effects (KIEs) for the enzyme-catalyzed reactions using a mass-perturbation-based path-integral method. The computed KIE provide further support for a direct decarboxylation mechanism. In agreement with experiment, the data suggest a role for Lys72 in stabilizing the transition state in the catalysis of OMP and, to a somewhat lesser extent, in 5-fluoro-OMP.
Collapse
Affiliation(s)
- Alexandra Vardi-Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | | |
Collapse
|
11
|
Avoiding CO2 in Catalysis of Decarboxylation. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2013. [DOI: 10.1016/b978-0-12-407754-6.00002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|
12
|
Nosrati GR, Houk KN. Using catalytic atom maps to predict the catalytic functions present in enzyme active sites. Biochemistry 2012; 51:7321-9. [PMID: 22909276 DOI: 10.1021/bi3008438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic atom maps (CAMs) are minimal models of enzyme active sites. The structures in the Protein Data Bank (PDB) were examined to determine if proteins with CAM-like geometries in their active sites all share the same catalytic function. We combined the CAM-based search protocol with a filter based on the weighted contact number (WCN) of the catalytic residues, a measure of the "crowdedness" of the microenvironment around a protein residue. Using this technique, a CAM based on the Ser-His-Asp catalytic triad of trypsin was able to correctly identify catalytic triads in other enzymes within 0.5 Å rmsd of the CAM with 96% accuracy. A CAM based on the Cys-Arg-(Asp/Glu) active site residues from the tyrosine phosphatase active site achieved 89% accuracy in identifying this type of catalytic functionality. Both of these CAMs were able to identify active sites across different fold types. Finally, the PDB was searched to locate proteins with catalytic functionality similar to that present in the active site of orotidine 5'-monophosphate decarboxylase (ODCase), whose mechanism is not known with certainty. A CAM, based on the conserved Lys-Asp-Lys-Asp tetrad in the ODCase active site, was used to search the PDB for enzymes with similar active sites. The ODCase active site has a geometry similar to that of Schiff base-forming Class I aldolases, with lowest aldolase rmsd to the ODCase CAM at 0.48 Å. The similarity between this CAM and the aldolase active site suggests that ODCase has the correct catalytic functionality present in its active site for the generation of a nucleophilic lysine.
Collapse
Affiliation(s)
- Geoffrey R Nosrati
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | | |
Collapse
|
13
|
Wu YJ, Liao CC, Jen CH, Shih YC, Chien TC. Chemical models and their mechanistic implications for the transformation of 6-cyanouridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase. Chem Commun (Camb) 2010; 46:4821-3. [PMID: 20498911 DOI: 10.1039/c001865a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of 6-cyano-1,3-dimethyluracil have been studied as chemical models to illustrate the mechanism for the transformation of 6-cyanouridine 5'-monophosphate (6-CN-UMP) to barbiturate ribonucleoside 5'-monophosphate (BMP) catalyzed by orotidine 5'-monophosphate decarboxylase (ODCase). The results suggest that the Asp residue in the ODCase active site plays the role of a general base in the transformation.
Collapse
Affiliation(s)
- Yuen-Jen Wu
- Department of Chemistry, National Taiwan Normal University, No.88, Sec.4, Ting-Zhou Road, Taipei, 11677, Taiwan
| | | | | | | | | |
Collapse
|
14
|
Toth K, Amyes TL, Wood BM, Chan KK, Gerlt JA, Richard JP. An examination of the relationship between active site loop size and thermodynamic activation parameters for orotidine 5'-monophosphate decarboxylase from mesophilic and thermophilic organisms. Biochemistry 2009; 48:8006-13. [PMID: 19618917 DOI: 10.1021/bi901064k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Closure of the active site phosphate gripper loop of orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae (ScOMPDC) over the bound substrate orotidine 5'-monophosphate (OMP) activates the bound substrate for decarboxylation by at least 10(4)-fold [Amyes, T. L., Richard, J. P., and Tait, J. J. (2005) J. Am. Chem. Soc. 127, 15708-15709]. The 19-residue phosphate gripper loop of the mesophilic ScOMPDC is much larger than the nine-residue loop at the ortholog from the thermophile Methanothermobacter thermautotrophicus (MtOMPDC). This difference in loop size results in a small decrease in the total intrinsic phosphate binding energy of the phosphodianion group of OMP from 11.9 to 11.6 kcal/mol, along with a modest decrease in the extent of activation by phosphite dianion of decarboxylation of the truncated substrate 1-(beta-D-erythrofuranosyl)orotic acid. The activation parameters DeltaH(double dagger) and DeltaS(double dagger) for k(cat) for decarboxylation of OMP are 3.6 kcal/mol and 10 cal K(-1) mol(-1) more positive, respectively, for MtOMPDC than for ScOMPDC. We suggest that these differences are related to the difference in the size of the active site loops at the mesophilic ScOMPDC and the thermophilic MtOMPDC. The greater enthalpic transition state stabilization available from the more extensive loop-substrate interactions for the ScOMPDC-catalyzed reaction is largely balanced by a larger entropic requirement for immobilization of the larger loop at this enzyme.
Collapse
Affiliation(s)
- Krisztina Toth
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA
| | | | | | | | | | | |
Collapse
|
15
|
Wood BM, Chan KK, Amyes TL, Richard JP, Gerlt JA. Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: effect of solvent viscosity on kinetic constants. Biochemistry 2009; 48:5510-7. [PMID: 19435313 DOI: 10.1021/bi9006226] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (OMPDC) is an exceptionally proficient catalyst: the rate acceleration (k(cat)/k(non)) is 7.1 x 10(16), and the proficiency [(k(cat)/K(M))/k(non)] is 4.8 x 10(22) M(-1). The structural basis for the large rate acceleration and proficiency is unknown, although the mechanism has been established to involve a stabilized carbanion intermediate. To provide reaction coordinate context for interpretation of the values of k(cat), k(cat)/K(M), and kinetic isotope effects, we investigated the effect of solvent viscosity on k(cat) and k(cat)/K(M) for the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC). For MtOMPDC, we used not only the natural OMP substrate but also a catalytically impaired mutant (D70N) and a more reactive substrate (FOMP); for ScOMPDC, we used OMP and FOMP. With MtOMPDC and OMP, k(cat) is independent of solvent viscosity, indicating that decarboxylation is fully rate-determining; k(cat)/K(M) displays a fractional dependence of solvent viscosity, suggesting that both substrate binding and decarboxylation determine this kinetic constant. For ScOMPDC with OMP, we observed that both k(cat) and k(cat)/K(M) are fractionally dependent on solvent viscosity, suggesting that the rates of substrate binding, decarboxylation, and product dissociation are similar. Consistent with these interpretations, for both enzymes with FOMP, the increases in the values of k(cat) and k(cat)/K(M) are much less than expected based on the ability of the 5-fluoro substituent to stabilize the anionic intermediate; i.e., substrate binding and product dissociation mask the kinetic effects of stabilization of the intermediate by the substituent.
Collapse
Affiliation(s)
- B McKay Wood
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | | | |
Collapse
|
16
|
Heinrich D, Diederichsen U, Rudolph MG. Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase. Chemistry 2009; 15:6619-25. [PMID: 19472232 DOI: 10.1002/chem.200900397] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Orotidine-5'-monophosphate decarboxylase (OMPD) catalyzes the decarboxylation of orotidine-5'-monophosphate (OMP) to uridine-5'-monophosphate (UMP) in an extremely proficient manner. The reaction does not require any cofactors and proceeds by an unknown mechanism. In addition to decarboxylation, OMPD is able to catalyze other reactions. We show that several C6-substituted UMP derivatives undergo hydrolysis or substitution reactions that depend on a lysine residue (Lys314) in the OMPD active site. 6-Cyano-UMP is converted to UMP, and UMP derivatives with good leaving groups inhibit OMPD by a suicide mechanism in which Lys314 covalently binds to the substrate. These non-classical reactivities of human OMPD were characterized by cocrystallization and freeze-trapping experiments with wild-type OMPD and two active-site mutants by using substrate and inhibitor nucleotides. The structures show that the C6-substituents are not coplanar with the pyrimidine ring. The extent of this substrate distortion is a function of the substituent geometry. Structure-based mechanisms for the reaction of 6-substituted UMP derivatives are extracted in accordance with results from mutagenesis, mass spectrometry, and OMPD enzyme activity. The Lys314-based mechanisms explain the chemodiversity of OMPD, and offer a strategy to design mechanism-based inhibitors that could be used for antineoplastic purposes for example.
Collapse
Affiliation(s)
- Daniel Heinrich
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | | | | |
Collapse
|
17
|
Fujihashi M, Bello AM, Kotra LP, Pai EF. Structural characterization of the molecular events during a slow substrate-product transition in orotidine 5'-monophosphate decarboxylase. J Mol Biol 2009; 387:1199-210. [PMID: 19236876 PMCID: PMC3125131 DOI: 10.1016/j.jmb.2009.02.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2008] [Revised: 02/05/2009] [Accepted: 02/06/2009] [Indexed: 01/07/2023]
Abstract
Crystal structures of substrate-product complexes of Methanobacterium thermoautotrophicum orotidine 5'-monophosphate decarboxylase, obtained at various steps in its catalysis of the unusual transformation of 6-cyano-uridine 5'-monophosphate (UMP) into barbituric acid ribosyl monophosphate, show that the cyano substituent of the substrate, when bound to the active site, is first bent significantly from the plane of the pyrimidine ring and then replaced by an oxygen atom. Although the K72A and D70A/K72A mutants are either catalytically impaired or even completely inactive, they still display bending of the C6 substituent. Interestingly, high-resolution structures of the D70A and D75N mutants revealed a covalent bond between C6 of UMP and the Lys72 side chain after the -CN moiety's release. The same covalent bond was observed when the native enzyme was incubated with 6-azido-UMP and 6-iodo-UMP; in contrast, the K72A mutant transformed 6-iodo-UMP to barbituric acid ribosyl 5'-monophosphate. These results demonstrate that, given a suitable environment, native orotidine 5'-monophosphate decarboxylase and several of its mutants are not restricted to the physiologically relevant decarboxylation; they are able to catalyze even nucleophilic substitution reactions but consistently maintain distortion on the C6 substituent as an important feature of catalysis.
Collapse
Affiliation(s)
- Masahiro Fujihashi
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan 606-8502, Division of Cancer Genomics & Proteomics, Ontario Cancer Institute/Princess Margaret Hospital, MaRS Centre/Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, M5G 1L7, Canada,Corresponding authors: and
| | - Angelica M. Bello
- Center for Molecular Design and Preformulations and Division of Cell and Molecular Biology, Toronto General Research Institute, MaRS Centre/Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Lakshmi P. Kotra
- Center for Molecular Design and Preformulations and Division of Cell and Molecular Biology, Toronto General Research Institute, MaRS Centre/Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, M5G 1L7, Canada, Departments of Pharmaceutical Sciences and Chemistry, University of Toronto, Toronto, Ontario, Canada, Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Emil F. Pai
- Division of Cancer Genomics & Proteomics, Ontario Cancer Institute/Princess Margaret Hospital, MaRS Centre/Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, M5G 1L7, Canada, Departments of Biochemistry, Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada,Corresponding authors: and
| |
Collapse
|
18
|
Hu H, Yang W. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. ACTA ACUST UNITED AC 2009; 898:17-30. [PMID: 24146439 DOI: 10.1016/j.theochem.2008.12.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes.
Collapse
Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | | |
Collapse
|
19
|
Hu H, Boone A, Yang W. Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2008; 130:14493-503. [PMID: 18839943 PMCID: PMC3651880 DOI: 10.1021/ja801202j] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite extensive experimental and theoretical studies, the detailed catalytic mechanism of orotidine 5'-monophosphate decarboxylase (ODCase) remains controversial. In particular simulation studies using high level quantum mechanics have failed to reproduce experimental activation free energy. One common feature of many previous simulations is that there is a water molecule in the vicinity of the leaving CO2 group whose presence was only observed in the inhibitor bound complex of ODCase/BMP. Various roles have even been proposed for this water molecule from the perspective of stabilizing the transition state and/or intermediate state. We hypothesize that this water molecule is not present in the active ODCase/OMP complex. Based on QM/MM minimum free energy path simulations with accurate density functional methods, we show here that in the absence of this water molecule the enzyme functions through a simple direct decarboxylation mechanism. Analysis of the interactions in the active site indicates multiple factors contributing to the catalysis, including the fine-tuned electrostatic environment of the active site and multiple hydrogen-bonding interactions. To understand better the interactions between the enzyme and the inhibitor BMP molecule, simulations were also carried out to determine the binding free energy of this special water molecule in the ODCase/BMP complex. The results indicate that the water molecule in the active site plays a significant role in the binding of BMP by contributing approximately -3 kcal/mol to the binding free energy of the complex. Therefore, the complex of BMP plus a water molecule, instead of the BMP molecule alone, better represents the tight binding transition state analogue of ODCase. Our simulation results support the direct decarboxylation mechanism and highlight the importance of proper recognition of protein bound water molecules in the protein-ligand binding and the enzyme catalysis.
Collapse
Affiliation(s)
- Hao Hu
- Department of Chemistry, Duke University, Durham, NC 27708
| | - Amy Boone
- Department of Chemistry, Duke University, Durham, NC 27708
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, NC 27708
| |
Collapse
|
20
|
Wong FM, Capule CC, Chen DX, Gronert S, Wu W. Surprisingly Low Aqueous Acidity at the α-Positions of Pyridiniums and Pyrimidinium: The Role of Solvation. Org Lett 2008; 10:2757-60. [DOI: 10.1021/ol800892d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Freeman M. Wong
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Christina C. Capule
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - David X. Chen
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Scott Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Weiming Wu
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, and Department of Chrmistry, Virginia Commonwealth University, Richmond, Virginia 23284
| |
Collapse
|
21
|
Wittmann JG, Heinrich D, Gasow K, Frey A, Diederichsen U, Rudolph MG. Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design. Structure 2008; 16:82-92. [PMID: 18184586 DOI: 10.1016/j.str.2007.10.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 10/26/2007] [Accepted: 10/26/2007] [Indexed: 02/05/2023]
Abstract
UMP synthase (UMPS) catalyzes the last two steps of de novo pyrimidine nucleotide synthesis and is a potential cancer drug target. The C-terminal domain of UMPS is orotidine-5'-monophosphate decarboxylase (OMPD), a cofactor-less yet extremely efficient enzyme. Studies of OMPDs from micro-organisms led to the proposal of several noncovalent decarboxylation mechanisms via high-energy intermediates. We describe nine crystal structures of human OMPD in complex with substrate, product, and nucleotide inhibitors. Unexpectedly, simple compounds can replace the natural nucleotides and induce a closed conformation of OMPD, defining a tripartite catalytic site. The structures outline the requirements drugs must meet to maximize therapeutic effects and minimize cross-species activity. Chemical mimicry by iodide identified a CO(2) product binding site. Plasticity of catalytic residues and a covalent OMPD-UMP complex prompt a reevaluation of the prevailing decarboxylation mechanism in favor of covalent intermediates. This mechanism can also explain the observed catalytic promiscuity of OMPD.
Collapse
Affiliation(s)
- Julia G Wittmann
- Department of Molecular Structural Biology, University of Göttingen, Göttingen, Germany
| | | | | | | | | | | |
Collapse
|
22
|
Stanton CL, Kuo IFW, Mundy CJ, Laino T, Houk KN. QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis. J Phys Chem B 2007; 111:12573-81. [PMID: 17927240 DOI: 10.1021/jp074858n] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite decades of study, the mechanism by which orotidine-5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine monophosphate remains unresolved. A computational investigation of the direct decarboxylation mechanism has been performed using mixed quantum mechanical/molecular mechanical (QM/MM) dynamics simulations. The study was performed with the program CP2K that integrates classical dynamics and ab initio dynamics based on the Born-Oppenheimer approach. Two different QM regions were explored. The free energy barriers for direct decarboxylation of orotidine-5'-monophosphate (OMP) in solution and in the enzyme (using the larger QM region) were determined with the metadynamics method to be 40 and 33 kcal/mol, respectively. The calculated change in activation free energy (DeltaDeltaG++) on going from solution to the enzyme is therefore -7 kcal/mol, far less than the experimental change of -23 kcal/ mol (for k(cat.)/k(uncat.): Radzicka, A.; Wolfenden, R., Science 1995, 267, 90-92). These results do not support the direct decarboxylation mechanism that has been proposed for the enzyme. However, in the context of QM/MM calculations, it was found that the size of the QM region has a dramatic effect on the calculated reaction barrier.
Collapse
Affiliation(s)
- Courtney L Stanton
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA
| | | | | | | | | |
Collapse
|
23
|
Wong FM, Capule C, Wu W. Stability of the 6-carbanion of uracil analogues: mechanistic implications for model reactions of orotidine-5'-monophosphate decarboxylase. Org Lett 2007; 8:6019-22. [PMID: 17165919 PMCID: PMC2743169 DOI: 10.1021/ol0624981] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[Structure: see text] The pKa's of the 6-CH groups of N-methyl-2-pyridone and N-methyl-4-pyridone in aqueous solution were determined. No correlation between the stability of the carbanions and the rate of decarboxylation of the corresponding carboxylic acids was found.
Collapse
|
24
|
Yeoh FY, Cuasito RR, Capule CC, Wong FM, Wu W. Carbanions from decarboxylation of orotate analogs: stability and mechanistic implications. Bioorg Chem 2007; 35:338-43. [PMID: 17400276 PMCID: PMC2757000 DOI: 10.1016/j.bioorg.2007.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 02/09/2007] [Accepted: 02/10/2007] [Indexed: 11/15/2022]
Abstract
The pKa's of the 6-CH groups of 1,3-dimethyluracil, N-methyl-2-pyridone, and N-methyl-4-pyridone were determined through their reactions with bases derived from carbon acids with known pKa and the reactions of their corresponding carbanions with the carbon acids. No correlation between the stability of the carbanions and the rate of decarboxylation of corresponding carboxylic acids was found.
Collapse
Affiliation(s)
| | | | | | | | - Weiming Wu
- To whom correspondence should be addressed: Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132. Telephone: (415) 338-1436. Fax: (415) 338-2384.
| |
Collapse
|
25
|
Phillips LM, Lee JK. Theoretical Studies of the Effect of Thio Substitution on Orotidine Monophosphate Decarboxylase Substrates. J Org Chem 2005; 70:1211-21. [PMID: 15704953 DOI: 10.1021/jo040279s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[reaction: see text] The effect of replacing carbonyl oxygens with sulfur in a series of orotidine 5'-monophosphate decarboxylase (ODCase) substrates was studied computationally. Previous experimental results indicate that while 2-thio-orotidine 5'-monophosphate (2-thio-OMP) is a poor substrate for ODCase, 4-thio-orotidine 5'-monophosphate (4-thio-OMP) binds to ODCase, and the resultant k(cat) is measurable. Energetics calculations on 2-thio-1-methyl-orotate and 4-thio-1-methyl-orotate (as models for the 2- and 4-thio-OMPs) indicate that mechanisms involving proton transfer to the 2- or 4-site, regardless of substrate and regardless of whether the 2- or 4-position is a carbonyl or thiocarbonyl, are energetically favorable, as compared to direct decarboxylation without proton transfer. Proton transfer to the 4-site during decarboxylation is found to be energetically more favorable than 2-protonation. Each thiocarbonyl is also found to be more basic than its carbonyl counterpart. Therefore, if 2- or 4-proton transfer is the operative catalytic pathway, energetics alone would not explain why 2-thio-orotidine 5'-monophosphate is a poor ODCase substrate. Conformational preferences for a series of ODCase substrates were also examined computationally. Specifically, the energies and Boltzmann probabilities of the conformers resulting from rotation about the C1'-N1 bond (O4'-C1'-N1-C2 rotation from 0 degrees to 360 degrees ) were calculated. It was found that a calculated preference for the syn versus the anti nucleoside conformation correlates to an experimentally better substrate: the OMP and 4-thio-OMP models show a preference for syn conformations, whereas the 2-thio-OMP (the only substrate of the three OMPs that is experimentally found to bind poorly) model shows a preference for an anti conformation. The same rough correlation was found for a series of ODCase inhibitors; that is, a preference for the syn conformation correlates to a better inhibitor. This result is of interest and points to the possibility that the ability for a substrate to bind well to ODCase may be related to its tendency to favor the syn conformation.
Collapse
Affiliation(s)
- Linda M Phillips
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
| | | |
Collapse
|
26
|
Shem DL, Gronert S, Wu W. Modest catalysis of the decarboxylation of orotate by hydrogen bonding: a theoretical model for orotidine- 5' -monophosphate decarboxylase. Bioorg Chem 2004; 32:76-81. [PMID: 14990306 DOI: 10.1016/j.bioorg.2003.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Indexed: 11/27/2022]
Abstract
As a model for interactions present in the active site of orotidine-5'-monophosphate decarboxylase (ODCase), the effect of hydrogen bonds to the carbonyl groups (O-2 and O-4) of orotic acid and its decarboxylation product was probed with ab initio calculations. We have found that the transition state/carbanion intermediate is a better proton receptor and therefore, the hydrogen bonds can be a modest source of catalysis. Comparison of the calculated data with results from site-directed mutagenesis provides some insights into the polarity of the active site.
Collapse
Affiliation(s)
- Diana L Shem
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132, USA
| | | | | |
Collapse
|
27
|
Catalysis by Enzyme Conformational Change. OROTIDINE MONOPHOSPHATE DECARBOXYLASE 2004. [DOI: 10.1007/b94541] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
28
|
Houk KN, Tantillo DJ, Stanton C, Hu Y. What Has Theory and Crystallography Revealed About the Mechanism of Catalysis by Orotidine Monophosphate Decarboxylase? OROTIDINE MONOPHOSPHATE DECARBOXYLASE 2004. [DOI: 10.1007/b94536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
29
|
Lee JK, Tantillo DJ. Computational Studies on the Mechanism of Orotidine Monophosphate Decarboxylase. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2003. [DOI: 10.1016/s0065-3160(03)38006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
30
|
Abstract
Enzymes are called upon to differ greatly in the difficulty of the tasks that they perform. The catalytic proficiency of an enzyme can be evaluated by comparing the second-order rate constant (kcat/Km) with the rate of the spontaneous reaction in neutral solution in the absence of a catalyst. The proficiencies of enzymes, measured in this way, are matched by their affinity constants for the altered substrate in the transition state. These values vary from approximately approximately 10(9) M(-1) for carbonic anhydrase to approximately 10(23) M(-1) for yeast orotidine 5'-phosphate decarboxylase (ODCase). ODCase turns its substrate over with a half-time of 18 ms, in a reaction that proceeds in its absence with a half-time of 78 million years in neutral solution. ODCase differs from other decarboxylases in that its catalytic activity does not depend on the presence of metals or other cofactors, or on the formation of a covalent bond to the substrate. Several mechanisms of transition state stabilization are considered in terms of ODCase crystal structures observed in the presence and absence of bound analogs of the substrate, transition state, and product. Very large connectivity effects are indicated by the results of experiments testing how transition state stabilization is affected by the truncation of binding determinants of the substrate and the active site.
Collapse
Affiliation(s)
- Brian G Miller
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, 53706-1544, USA.
| | | |
Collapse
|
31
|
Kurinovich MA, Lee JK. The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2002; 13:985-995. [PMID: 12216739 DOI: 10.1016/s1044-0305(02)00410-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.
Collapse
Affiliation(s)
- Mary Ann Kurinovich
- Department of Chemistry, Rutgers University, The State University of New Jersey, Piscataway 08854, USA
| | | |
Collapse
|
32
|
Harris P, Poulsen JCN, Jensen KF, Larsen S. Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase. J Mol Biol 2002; 318:1019-29. [PMID: 12054799 DOI: 10.1016/s0022-2836(02)00200-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate (UMP). We have earlier determined the structure of ODCase from Escherichia coli complexed with the inhibitor 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid (BMP); here we present the 2.5 A structure of the uncomplexed apo enzyme, determined from twinned crystals. A structural analysis and comparison of the two structures of the E. coli enzyme show that binding of the inhibitor is accompanied by significant domain movements of approximately 12 degrees around a hinge that crosses the active site. Hence, the ODCase dimer, which contains two active sites, may be divided in three domains: a central domain that is fixed, and two lids which independently move 12 degrees upon binding. Corresponding analyses, presented herein, of the two Saccharomyces cerevisiae ODCase structures (with and without BMP) and the Methanobacterium thermoautotrophicum ODCase structures (with and without 6-aza UMP) show very similar, but somewhat smaller domain movements. The domain movements seem to be initiated by the phosphoryl binding to the enzyme and can explain why the binding of the phosphoryl group is essential for the catalytic function.
Collapse
Affiliation(s)
- Pernille Harris
- Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, Denmark
| | | | | | | |
Collapse
|
33
|
Lee TS, Chong LT, Chodera JD, Kollman PA. An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. J Am Chem Soc 2001; 123:12837-48. [PMID: 11749542 DOI: 10.1021/ja011096f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Orotidine 5'-phosphate decarboxylase (ODCase) is the most proficient enzyme known, enhancing the rate of decarboxylation of orotidine 5'-phosphate (OMP) by a factor of 10(17), which corresponds to a DeltaDeltaG++ of approximately 24 kcal/mol. Ground-state destabilization through local electrostatic stress has been recently proposed as the basis of catalytic rate enhancement for a mechanism that is the same as in solution. We have carried out gas-phase ab initio quantum mechanical calculations combined with a free energy method, a continuum solvent model, and molecular dynamics simulations to assess an alternative mechanism. Although we are not able to reproduce the experimentally observed DeltaDeltaG++ quantitatively, we present evidence that this DeltaDeltaG++ is very large, in the range found experimentally. We thus conclude that the preferred mechanism may well be different from that in solution, involving an equilibrium pre-protonation of OMP C5 by a catalytic lysine residue that greatly reduces the barrier to subsequent decarboxylation.
Collapse
Affiliation(s)
- T S Lee
- Accelrys, Inc., 9685 Scranton Road, San Diego, California 92121-3752, USA
| | | | | | | |
Collapse
|
34
|
Phillips LM, Lee JK. Theoretical studies of mechanisms and kinetic isotope effects on the decarboxylation of orotic acid and derivatives. J Am Chem Soc 2001; 123:12067-73. [PMID: 11724615 DOI: 10.1021/ja0117332] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of orotidine 5'-monophosphate decarboxylase was studied computationally by using the decarboxylation of orotic acid analogues as model systems. These calculations indicate that mechanisms involving proton transfer to the 2-oxygen or the 4-oxygen are energetically favorable, as compared to direct decarboxylation without proton transfer, for a series of model compounds where N1 is substituted with respectively H, CH(3), and a tetrahydrofuran moiety. Proton transfer to the 4-oxygen during decarboxylation is found to be energetically more favorable than 2-protonation, which is attributable to both the 4-oxygen site being more basic and an apparent intrinsic preference for the 4-protonation pathway. (15)N isotope effect calculations were also conducted, and compared to experimental (15)N isotope effects previously measured at N1 by Rishavy and Cleland (Biochemistry 2000, 39, 4569-4574). The theoretical isotope effects establish, for the first time, that the experimental (15)N isotope effect is consistent with decarboxylation without protonation, as well as with decarboxylation with protonation, at either O2 or at O4. Furthermore, we propose herein an isotope measurement that could potentially distinguish among mechanisms involving protonation from those that do not involve proton transfer.
Collapse
Affiliation(s)
- L M Phillips
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | | |
Collapse
|
35
|
Houk KN, Lee JK, Tantillo DJ, Bahmanyar S, Hietbrink BN. Crystal structures of orotidine monophosphate decarboxylase: does the structure reveal the mechanism of nature's most proficient enzyme? Chembiochem 2001; 2:113-8. [PMID: 11828434 DOI: 10.1002/1439-7633(20010202)2:2<113::aid-cbic113>3.0.co;2-t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 405 Hilgard Avenue, Los Angeles, CA 90095-1569, USA.
| | | | | | | | | |
Collapse
|
36
|
Begley TP, Appleby TC, Ealick SE. The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase. Curr Opin Struct Biol 2000; 10:711-8. [PMID: 11114509 DOI: 10.1016/s0959-440x(00)00148-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The three-dimensional structures of orotidine 5'-monophosphate decarboxylases from four different organisms have been determined by X-ray crystallography. The structures reveal an active site in which the pyrimidine base and phosphate groups are rigidly held in place. Surprisingly, both pyrimidine carbonyl groups are hydrogen bonded to amide groups, rather than to strong active site acids, as was previously predicted. The positioning of a conserved aspartate sidechain close to the substrate carboxylate and a conserved lysine ammonium group close to the C6 of the pyrimidine suggests a novel mechanism to explain the extreme catalytic proficiency of this enzyme.
Collapse
Affiliation(s)
- T P Begley
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.
| | | | | |
Collapse
|
37
|
Harris P, Navarro Poulsen JC, Jensen KF, Larsen S. Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase. Biochemistry 2000; 39:4217-24. [PMID: 10757968 DOI: 10.1021/bi992952r] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.
Collapse
Affiliation(s)
- P Harris
- Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | | | | | |
Collapse
|
38
|
Appleby TC, Kinsland C, Begley TP, Ealick SE. The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase. Proc Natl Acad Sci U S A 2000; 97:2005-10. [PMID: 10681442 PMCID: PMC15744 DOI: 10.1073/pnas.259441296] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure of Bacillus subtilis orotidine 5'-monophosphate (OMP) decarboxylase with bound uridine 5'-monophosphate has been determined by multiple wavelength anomalous diffraction phasing techniques and refined to an R-factor of 19.3% at 2.4 A resolution. OMP decarboxylase is a dimer of two identical subunits. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. For each active site, most of the residues are contributed by one monomer with a few residues contributed from the adjacent monomer. The most highly conserved residues are located in the active site and suggest a novel catalytic mechanism for decarboxylation that is different from any previously proposed OMP decarboxylase mechanism. The uridine 5'-monophosphate molecule is bound to the active site such that the phosphate group is most exposed and the C5-C6 edge of the pyrimidine base is most buried. In the proposed catalytic mechanism, the ground state of the substrate is destabilized by electrostatic repulsion between the carboxylate of the substrate and the carboxylate of Asp60. This repulsion is reduced in the transition state by shifting negative charge from the carboxylate to C6 of the pyrimidine, which is close to the protonated amine of Lys62. We propose that the decarboxylation of OMP proceeds by an electrophilic substitution mechanism in which decarboxylation and carbon-carbon bond protonation by Lys62 occur in a concerted reaction.
Collapse
Affiliation(s)
- T C Appleby
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | | | | | | |
Collapse
|
39
|
Feng WY, Austin TJ, Chew F, Gronert S, Wu W. The mechanism of orotidine 5'-monophosphate decarboxylase: catalysis by destabilization of the substrate. Biochemistry 2000; 39:1778-83. [PMID: 10677227 DOI: 10.1021/bi992553w] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of orotidine 5'-monophosphate decarboxylase (OMP decarboxylase, ODCase) was studied using the decarboxylation of orotic acid analogues as a model system. The rate of decarboxylation of 1,3-dimethylorotic acid and its analogues as well as the stability of their corresponding carbanion intermediates was determined. The results have shown that the stability of the carbanion intermediate is not a critical factor in the rate of decarboxylation. On the other hand, the reaction rate is largely dependent on the equilibrium constant for the formation of a zwitterion. Based on these results, we have proposed a new mechanism in which ODCase catalyzes the decarboxylation of OMP by binding the substrate in a zwitterionic form and providing a destabilizing environment for the carboxylate group of OMP.
Collapse
Affiliation(s)
- W Y Feng
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California 94132, USA
| | | | | | | | | |
Collapse
|
40
|
Cui W, DeWitt JG, Miller SM, Wu W. No metal cofactor in orotidine 5'-monophosphate decarboxylase. Biochem Biophys Res Commun 1999; 259:133-5. [PMID: 10334928 DOI: 10.1006/bbrc.1999.0737] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (OMP decarboxylase, ODCase) is an important enzyme that catalyzes the final step of de novo pyrimidine nucleotide biosynthesis. The mechanism of this unique enzyme and whether metal ions play any role in catalysis have been topics of intense research interest. In this report, the role of Zn in ODCase was reexamined. Atomic absorption (AA) and X-ray absorption (XAS) spectroscopic studies did not detect zinc in active enzyme samples at high concentration. The XAS results also indicated the absence of other transition metal ions in ODCase.
Collapse
Affiliation(s)
- W Cui
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, 94132, USA
| | | | | | | |
Collapse
|
41
|
Wu W, Ley-han A, Wong FM, Austin TJ, Miller SM. Decarboxylation of 1,3-dimethylorotic acid revisited: Determining the role of N-1. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)10028-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
42
|
Traut TW, Jones ME. Uracil metabolism--UMP synthesis from orotic acid or uridine and conversion of uracil to beta-alanine: enzymes and cDNAs. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:1-78. [PMID: 8650301 DOI: 10.1016/s0079-6603(08)60142-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- T W Traut
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599, USA
| | | |
Collapse
|
43
|
Zhuo JC, Wyler H. Hetero-Diels-Alder cycloadditions of ?,?-unsaturated acyl cyanides. Part 2. Reactions withN,N-dimethyluracils, a new route to 5-substituted uracil derivatives. Helv Chim Acta 1993. [DOI: 10.1002/hlca.19930760510] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
44
|
Smiley JA, Jones ME. A unique catalytic and inhibitor-binding role for Lys93 of yeast orotidylate decarboxylase. Biochemistry 1992; 31:12162-8. [PMID: 1457412 DOI: 10.1021/bi00163a027] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The presence of a proton-donating catalytic amino acid side chain in orotidylate decarboxylase (ODCase) was sought by site-directed mutagenesis. Replacement of yeast ODCase Lys93 with a cysteine resulted in a mutant protein (K93C) with no measurable activity, representing a decrease in activity by a factor of, at most, 2 x 10(-8) times the activity of the wild-type enzyme. Treatment of this mutant protein with 2-bromoethylamine, designed to append Cys93 to yield S-(2-aminoethyl)cysteine, restored activity by a factor of at least 5 x 10(5) over the untreated mutant protein. Activity could not be restored by treatment with other brominated reagents designed to replace the epsilon-amino of S-(2-aminoethyl)Cys93 with a different functional group. The overall architecture of the K93C protein was not significantly changed, as judged by the similar dimerization properties (in the absence of ligands) of the mutant enzyme compared to the wild-type enzyme. The binding affinity of the substrate orotidylate was not measurably changed by the mutation, indicating that Lys93 has an essential role in catalysis which is mechanistically distinguishable from substrate binding. Apparently the mutation removes an integral portion of the active site and does not drastically affect the structural or substrate binding properties. However, the affinities of the mutant protein for the competitive inhibitors 6-azauridylate (6-azaUMP) and UMP are significantly altered from the pattern seen with the wild-type enzyme. The K93C protein has an affinity for the neutral ligand UMP which is greater than that for the anionic 6-azaUMP, in clear contrast to the preference for 6-azaUMP displayed by the wild-type enzyme. Lys93 is apparently critical for catalysis of the substrate to product and for the binding of anionic inhibitors; the data are discussed in terms of previously existing models for transition-state analogue inhibitor binding and catalysis.
Collapse
Affiliation(s)
- J A Smiley
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599-7260
| | | |
Collapse
|
45
|
Shostak K, Jones ME. Orotidylate decarboxylase: insights into the catalytic mechanism from substrate specificity studies. Biochemistry 1992; 31:12155-61. [PMID: 1457411 DOI: 10.1021/bi00163a026] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pyrimidine nucleotides were tested as substrates for pure yeast orotidylate decarboxylase in an attempt to gain insight into the nature of the catalytic mechanism of the enzyme. Substitutions of the 5-position in the pyrimidine ring of the orotidylate substrate resulted in compounds that are either excellent inhibitors or substrates of the enzyme. The 5-bromo- and 5-chloroorotidylates are potent inhibitors while the 5-fluoro derivative is a good substrate with a turnover number 30 times that observed with orotidylate. When carbon 5 of the pyrimidine ring is replaced by nitrogen in 5-azaorotidylate, the resulting compound is unstable in solution with a half-life of 25 min at pH 6. However, studies with freshly generated 5-azaorotidylate show that an enzyme-dependent reaction occurs, presumably decarboxylation. This enzyme reaction follows simple Michaelis-Menten kinetics. Because the 5-aza group is not electrophilic, an enzyme mechanism utilizing a nucleophilic addition of the enzyme at the 5-position is ruled out. We also present studies that are not compatible with a mechanism requiring the formation of a Schiff's base prior to decarboxylation. The enzyme is tolerant of modest substitution at the 4-position, for the 4-keto group can be replaced with a thioketone. However, no catalysis is observed when the same substitution is made at the 2-position. Similarities in the substrate specificity of orotate phosphoribosyltransferase and orotidylate decarboxylase led us to compare the amino acid sequences of the two enzymes; significant (20%) sequence homology was observed.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- K Shostak
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599
| | | |
Collapse
|
46
|
Abstract
The mechanism for ODCase appears to involve the formation of a zwitterion of OMP and a ylid on decarboxylation. Thiamin pyrophosphate catalyzes various decarboxylation and transfer reactions involving ketone groups because the thiazolium ring with its positively charged N atom can, on the loss of a proton from the adjacent C-2, generate a ylid which adds to carbonyl groups to produce a substrate ylid. The unusual aspect, then, of the ODCase reaction is that the substrate itself becomes the ylid, presumably by gaining a proton from ODCase, which results in a positive charge on the N-1 atom of the pyrimidine ring. It is a zwitterion in the transition state which momentarily becomes a ylid on decarboxylation of OMP which then yields the product, UMP. There is no known cofactor for the ODCase reaction. It will be of interest to discover the groups on the enzyme that aid in formation of the zwitterion and the ylid. Further work on the crystal structure and on the production of altered enzymes (where specific amino acids suspected to be important for the reaction are changed) should reveal more details about this important and novel reaction.
Collapse
Affiliation(s)
- M E Jones
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599
| |
Collapse
|
47
|
Smiley JA, Paneth P, O'Leary MH, Bell JB, Jones ME. Investigation of the enzymatic mechanism of yeast orotidine-5'-monophosphate decarboxylase using 13C kinetic isotope effects. Biochemistry 1991; 30:6216-23. [PMID: 2059628 DOI: 10.1021/bi00239a020] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Orotidine-5'-monophosphate decarboxylase (ODCase) from Saccharomyces cerevisiae displays an observed 13C kinetic isotope effect of 1.0247 +/- 0.0008 at 25 degrees C, pH 6.8. The observed isotope effect is sensitive to changes in the reaction medium, such as pH, temperature, or glycerol content. The value of 1.0494 +/- 0.0006 measured at pH 4.0, 25 degrees C, is not altered significantly by temperature or glycerol, and thus the intrinsic isotope effect for the reaction is apparently being observed under these conditions and decarboxylation is almost entirely rate-determining. These data require a catalytic mechanism with freely reversible binding and one in which a very limited contribution to the overall rate is made by chemical steps preceding decarboxylation; the zwitterion mechanism of Beak and Siegel [Beak, P. & Siegel, B. (1976) J. Am. Chem. Soc. 98, 3601-3606], which involves only protonation of the pyrimidine ring, is such a mechanism. With use of an intrinsic isotope effect of 1.05, a partitioning factor of less than unity is calculated for ODCase at pH 6.0, 25 degrees C. A quantitative kinetic analysis using this result excludes the possibility of an enzymatic mechanism involving covalent attachment of an enzyme nucleophile to C-5 of the pyrimidine ring. The observed isotope effect does not rise to the intrinsic value above pH 8.5; instead, the observed isotope effects at 25 degrees C plotted against pH yield an asymmetric curve that at high pH plateaus at about 1.035. These data, in conjunction with the pH profile of Vmax/km, fit a kinetic model in which an enzyme proton necessary for catalysis is titrated at high pH, thus providing evidence for the catalytic mechanism of Beak and Siegel (1976).
Collapse
Affiliation(s)
- J A Smiley
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill 27599-7260
| | | | | | | | | |
Collapse
|
48
|
Bell JB, Jones ME, Carter CW. Crystallization of yeast orotidine 5'-monophosphate decarboxylase complexed with 1-(5'-phospho-beta-D-ribofuranosyl) barbituric acid. Proteins 1991; 9:143-51. [PMID: 2008434 DOI: 10.1002/prot.340090208] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Using an incomplete factorial experimental design, we have identified conditions for crystallization of yeast orotidine 5'-monophosphate decarboxylase (ODCase) in an unliganded state and complexed separately to two inhibitors: 6-azauridine 5'-monophosphate (aza-UMP) and 1-(5'-phospho-beta-D-ribofuranosyl) barbituric acid (BMP). Crystals of X-ray diffraction quality have been obtained of yeast ODCase complexed with BMP, a putative transition state analog inhibitor (Ki = 8.8 x 10(-12) M). ODCase:BMP complex crystals with a hexagonal rod habit were grown from a solution initially containing 12 mg/ml ODCase (205 microM dimer) plus 450 microM BMP by microdialysis at 4 degrees C against a mother liquor which consisted of 0.1 M Na-PIPES-acetate (pH 6.4), 37.5 microM BMP, 5 mM mercaptoethanol, 1% polyethylene glycol 400, and 2.3 M ammonium sulfate. Crystals were analyzed using precession photography and were assigned to trigonal space group R32 with unit cell dimensions a = b = 115 A, c = 385 A. The crystal density is 1.245 g/cm3 indicating the presence of two ODCase: BMP complex dimers (118 kDa each) per asymmetric unit with a packing density of 2.08 A3/Da and 41% solvent content. The morphological habit of crystals of the ODCase:BMP complex changed when the initial ammonium sulfate concentration was increased in 0.05 M steps from 2.3 to 2.45 M. All of these crystals diffracted to at least 3.0 A resolution over a period of several weeks at room temperature and are isomorphous.
Collapse
Affiliation(s)
- J B Bell
- Department of Biochemistry and Biophysics, School of Medicine University of North Carolina, Chapel Hill 27599
| | | | | |
Collapse
|
49
|
Jones ME. Pyrimidine pathways: news concerning the mechanism of orotidine-5'-monophosphate decarboxylase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1991; 309B:305-10. [PMID: 1781386 DOI: 10.1007/978-1-4615-7703-4_68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- M E Jones
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599-7260
| |
Collapse
|
50
|
Acheson SA, Bell JB, Jones ME, Wolfenden R. Orotidine-5'-monophosphate decarboxylase catalysis: kinetic isotope effects and the state of hybridization of a bound transition-state analogue. Biochemistry 1990; 29:3198-202. [PMID: 2334689 DOI: 10.1021/bi00465a007] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The enzymatic decarboxylation of orotidine 5'-monophosphate may proceed by an addition-elimination mechanism involving a covalently bound intermediate or by elimination of CO2 to generate a nitrogen ylide. In an attempt to distinguish between these two alternatives, 1-(phosphoribosyl)barbituric acid was synthesized with 13C at the 5-position. Interaction of this potential transition-state analogue inhibitor with yeast orotidine-5'-monophosphate decarboxylase resulted in a small (0.6 ppm) downfield displacement of the C-5 resonance, indicating no rehybridization of the kind that might have been expected to accompany 5,6-addition of an enzyme nucleophile. When the substrate orotidine 5'-monophosphate was synthesized with deuterium at C-5, no significant change in kcat (H/D = 0.99 +/- 0.06) or kcat/KM (H/D = 1.00 +/- 0.06) was found to result, suggesting that C-5 does not undergo significant changes in geometry before or during the step that determines the rate of the catalytic process. These results are consistent with a nitrogen ylide mechanism and offer no support for the intervention of covalently bound intermediates in the catalytic process.
Collapse
Affiliation(s)
- S A Acheson
- Department of Biochemistry, University of North Carolina School of Medicine, Chapel Hill 27599
| | | | | | | |
Collapse
|