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Riera-Ruiz C, Moriyama H. Enzyme kinetics of deoxyuridine triphosphatase from Western corn rootworm. BMC Res Notes 2023; 16:336. [PMID: 37974243 PMCID: PMC10652518 DOI: 10.1186/s13104-023-06618-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVE The Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5'-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, therefore, contributes to thymineless death. In this study, we investigated the enzymatic properties of dUTPase. RESULTS The WCR dUTPase gene (DUT) was synthesized with the addition of His-tag corresponding DNA sequence and then cloned and expressed in Escherichia coli, and the protein product was purified. The product of WCR DUT hydrolyzed dUTP and was designated as dUTPase. WCR dUTPase did not hydrolyze dATP, dTTP, dCTP, or dGTP. WCR dUTPase was analyzed via size-exclusion chromatography and exhibited a molecular weight corresponding to that of trimer. The present format can be interpreted as nuclear trimer type. Possible isomers will be examined once transcriptome analyses are conducted.
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Affiliation(s)
- Carlos Riera-Ruiz
- School of Biological Sciences, University of Nebraska-Lincoln, 243 Manter Hall, Lincoln, NE, 68588-0118, USA
- Escuela Superior Politécnica del Litoral, Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O Box 09-01-5863, Guayaquil, Ecuador
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, 243 Manter Hall, Lincoln, NE, 68588-0118, USA.
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Pozzi C, Lopresti L, Tassone G, Mangani S. Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules 2019; 24:molecules24081638. [PMID: 31027295 PMCID: PMC6514825 DOI: 10.3390/molecules24081638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023] Open
Abstract
In cells, thymidylate synthases provide the only de novo source of 2′-deoxythymidine-5′-monophosphate (dTMP), required for DNA synthesis. The activity of these enzymes is pivotal for cell survival and proliferation. Two main families of thymidylate synthases have been identified in bacteria, folate-dependent thymidylate synthase (TS) and flavin-dependent TS (FDTS). TS and FDTS are highly divergent enzymes, characterized by exclusive catalytic mechanisms, involving different sets of cofactors. TS and FDTS mechanisms of action have been recently revised, providing new perspectives for the development of antibacterial drugs targeting these enzymes. Nonetheless, some catalytic details still remain elusive. For bacterial TSs, half-site reactivity is still an open debate and the recent evidences are somehow controversial. Furthermore, different behaviors have been identified among bacterial TSs, compromising the definition of common mechanisms. Moreover, the redox reaction responsible for the regeneration of reduced flavin in FDTSs is not completely clarified. This review describes the recent advances in the structural and functional characterization of bacterial TSs and FDTSs and the current understanding of their mechanisms of action. Furthermore, the recent progresses in the development of inhibitors targeting TS and FDTS in human pathogenic bacteria are summarized.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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Gurevic I, Islam Z, Świderek K, Trepka K, Ghosh AK, Moliner V, Kohen A. Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase. ACS Catal 2018; 8:10241-10253. [PMID: 31275729 DOI: 10.1021/acscatal.8b02554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TSase), an enzyme responsible for the de novo biosynthesis of 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) necessary for DNA synthesis, has been a drug target for decades. TSase is a highly conserved enzyme across species ranging from very primitive organisms to mammals. Among the many conserved active site residues, an asparagine (N177, using Escherichia coli residues numbering) appears to make direct hydrogen bonds with both the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate and its pyrimidine ring's N3. Recent studies have reassessed the TSase catalytic mechanism, focusing on the degree of negative charge accumulation at the O4 carbonyl of the substrate during two critical H-transfers - a proton abstraction and a hydride transfer. To obtain insights into the role of this conserved N177 on the hydride transfer, we examined its aspartic acid (D) and serine (S) mutants - each of which is expected to alter hydrogen bonding and charge stabilization around the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate. Steady-state kinetics, substrate binding order studies and temperature-dependency analysis of intrinsic KIEs for the hydride transfer step of the TSase catalytic cycle suggest the active site of N177D is not precisely organized for that step. A smaller disruption was observed for N177S, which could be rationalized by partial compensation by water molecules and rearrangement of other residues toward preparation of the system for the hydride transfer under study. These experimental findings are qualitatively mirrored by QM/MM computational simulations, thereby shedding light on the sequence and synchronicity of steps in the TSase-catalyzed reaction. This information could potentially inform the design of mechanism-based drugs targeting this enzyme.
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Affiliation(s)
- Ilya Gurevic
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Zahidul Islam
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Kai Trepka
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Ananda K. Ghosh
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
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Fusaro M, Jurkiewicz A, Jarmuła A, Leś A, Rode W. Hypothesis of a proton switch in QM/MM modelling of interaction of dUMP analogues with thymidylate synthase. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.502938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Newby Z, Lee TT, Morse RJ, Liu Y, Liu L, Venkatraman P, Santi DV, Finer-Moore JS, Stroud RM. The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261. Biochemistry 2006; 45:7415-28. [PMID: 16768437 PMCID: PMC2556892 DOI: 10.1021/bi060152s] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme thymidylate synthase (TS) catalyzes the reductive methylation of 2'-deoxyuridine 5'-monophosphate (dUMP) to 2'-deoxythymidine 5'-monophosphate. Using kinetic and X-ray crystallography experiments, we have examined the role of the highly conserved Tyr-261 in the catalytic mechanism of TS. While Tyr-261 is distant from the site of methyl transfer, mutants at this position show a marked decrease in enzymatic activity. Given that Tyr-261 forms a hydrogen bond with the dUMP 3'-O, we hypothesized that this interaction would be important for substrate binding, orientation, and specificity. Our results, surprisingly, show that Tyr-261 contributes little to these features of the mechanism of TS. However, the residue is part of the structural core of closed ternary complexes of TS, and conservation of the size and shape of the Tyr side chain is essential for maintaining wild-type values of kcat/Km. Moderate increases in Km values for both the substrate and cofactor upon mutation of Tyr-261 arise mainly from destabilization of the active conformation of a loop containing a dUMP-binding arginine. Besides binding dUMP, this loop has a key role in stabilizing the closed conformation of the enzyme and in shielding the active site from the bulk solvent during catalysis. Changes to atomic vibrations in crystals of a ternary complex of Escherichia coli Tyr261Trp are associated with a greater than 2000-fold drop in kcat/Km. These results underline the important contribution of dynamics to catalysis in TS.
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Affiliation(s)
- Zachary Newby
- University of California at San Francisco, San Francisco, California 94143-0448, USA
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Finer-Moore JS, Santi DV, Stroud RM. Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure. Biochemistry 2003; 42:248-56. [PMID: 12525151 DOI: 10.1021/bi020599a] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet S Finer-Moore
- S-960 Department of Biochemistry and Biophysics, University of California in San Francisco, San Francisco, California 94143-0448, USA
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Contestabile R, Angelaccio S, Bossa F, Wright HT, Scarsdale N, Kazanina G, Schirch V. Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase. Biochemistry 2000; 39:7492-500. [PMID: 10858298 DOI: 10.1021/bi000032z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Crystal structures of human and rabbit cytosolic serine hydroxymethyltransferase have shown that Tyr65 is likely to be a key residue in the mechanism of the enzyme. In the ternary complex of Escherichia coli serine hydroxymethyltransferase with glycine and 5-formyltetrahydrofolate, the hydroxyl of Tyr65 is one of four enzyme side chains within hydrogen-bonding distance of the carboxylate group of the substrate glycine. To probe the role of Tyr65 it was changed by site-directed mutagenesis to Phe65. The three-dimensional structure of the Y65F site mutant was determined and shown to be isomorphous with the wild-type enzyme except for the missing Tyr hydroxyl group. The kinetic properties of this mutant enzyme in catalyzing reactions with serine, glycine, allothreonine, D- and L-alanine, and 5,10-methenyltetrahydrofolate substrates were determined. The properties of the enzyme with D- and L-alanine, glycine in the absence of tetrahydrofolate, and 5, 10-methenyltetrahydrofolate were not significantly changed. However, catalytic activity was greatly decreased for serine and allothreonine cleavage and for the solvent alpha-proton exchange of glycine in the presence of tetrahydrofolate. The decreased catalytic activity for these reactions could be explained by a greater than 2 orders of magnitude increase in affinity of Y65F mutant serine hydroxymethyltransferase for these amino acids bound as the external aldimine. These data are consistent with a role for the Tyr65 hydroxyl group in the conversion of a closed active site to an open structure.
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Affiliation(s)
- R Contestabile
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Centro di Biologia Molecolare del Consiglio Nazionale delle Ricerche, Università La Sapienza, Roma, Italy
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Petsko GA, Ringe D. Observation of unstable species in enzyme-catalyzed transformations using protein crystallography. Curr Opin Chem Biol 2000; 4:89-94. [PMID: 10679381 DOI: 10.1016/s1367-5931(99)00057-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent advances in rapid X-ray diffraction data collection methods, cryocrystallography, and other techniques have made it possible to visualize short-lived species in enzyme-catalyzed reactions directly at atomic resolution for a significant number of crystalline enzymes. The wide range of reaction types, intermediate lifetimes, and crystal characteristics means that different methods must be employed in each case, but there are enough examples now of successful structure determinations of normally unstable species to suggest guidelines for future investigations.
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Affiliation(s)
- G A Petsko
- Departments of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454-9110, USA.
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