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Sieg J, Rarey M. Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Brief Bioinform 2023; 24:bbad357. [PMID: 37833838 DOI: 10.1093/bib/bbad357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
The available protein structure data are rapidly increasing. Within these structures, numerous local structural sites depict the details characterizing structure and function. However, searching and analyzing these sites extensively and at scale poses a challenge. We present a new method to search local sites in protein structure databases using residue-defined local 3D micro-environments. We implemented the method in a new tool called MicroMiner and demonstrate the capabilities of residue micro-environment search on the example of structural mutation analysis. Usually, experimental structures for both the wild-type and the mutant are unavailable for comparison. With MicroMiner, we extracted $>255 \times 10^{6}$ amino acid pairs in protein structures from the PDB, exemplifying single mutations' local structural changes for single chains and $>45 \times 10^{6}$ pairs for protein-protein interfaces. We further annotate existing data sets of experimentally measured mutation effects, like $\Delta \Delta G$ measurements, with the extracted structure pairs to combine the mutation effect measurement with the structural change upon mutation. In addition, we show how MicroMiner can bridge the gap between mutation analysis and structure-based drug design tools. MicroMiner is available as a command line tool and interactively on the https://proteins.plus/ webserver.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Bundesstraße 43, 20146 Hamburg, Germany
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2
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Chen Q, Yang X, Meng Q, Zhao L, Yuan Y, Chi W, He L, Shi K, Liu S. Integrative multiomics analysis of the acid stress response of Oenococcus oeni mutants at different growth stages. Food Microbiol 2021; 102:103905. [PMID: 34809937 DOI: 10.1016/j.fm.2021.103905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Acid stress is one of the most important environmental stresses that adversely affect the growth of lactic acid bacteria (LAB), such as Oenococcus oeni which was isolated from grape-berries and mainly used in wine fermentation. The aim of this paper is to comprehensively characterize the mechanisms of acid stress regulation in O. oeni and to provide a viable theoretical basis for breed and improvement of existing LAB. METHOD First, six O. oeni mutants with acid-sensitive (strains b2, a1, c2) and acid-tolerant (strains b1, a3, c1) phenotypes were screened from three wild-type O. oeni, and then their genome (sequencing), transcriptome and metabolome (LC-MS/MS) were examined. RESULTS A total of 459 genes were identified with one or more intragenic single nucleotide polymorphisms (SNPs) in these mutants, and were extensively involved in metabolism and cellular functions with a high mutation rates in purine (46%) and pyrimidine (48%) metabolic pathways. There were 210 mutated genes that cause significant changes in expression levels. In addition, 446 differentially accumulated metabolites were detected, and they were consistently detected at relatively high levels in the acid-tolerant O. oeni mutant. The levels of intracellular differentially expressed genes and differential metabolites changed with increasing culture time. CONCLUSION The integrative pathways analysis showed that the intracellular response associated with acid regulation differed significantly between acid-sensitive and acid-tolerant O. oeni mutants, and also changed at different growth stages.
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Affiliation(s)
- Qiling Chen
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Xiangke Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Henan University of Animal Husbandry and Economy, Zhenzhou, Henan, China
| | - Qiang Meng
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lili Zhao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Yuan
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wei Chi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ling He
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Kan Shi
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
| | - Shuwen Liu
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China; Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of, Northwest A&F University, Yongning, Ningxia, 750104, China.
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Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): Structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148321. [PMID: 32991846 DOI: 10.1016/j.bbabio.2020.148321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022]
Abstract
Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.
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Reis RAG, Calil FA, Feliciano PR, Pinheiro MP, Nonato MC. The dihydroorotate dehydrogenases: Past and present. Arch Biochem Biophys 2017; 632:175-191. [PMID: 28666740 DOI: 10.1016/j.abb.2017.06.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 01/24/2023]
Abstract
The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs. It also attempts to describe the latest advances in medicinal chemistry for therapeutic development based on the selective inhibition of DHODH, including an overview of the experimental techniques used for ligand screening during the process of drug discovery.
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Affiliation(s)
- Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Felipe Antunes Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Patricia Rosa Feliciano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Matheus Pinto Pinheiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, 13083-970, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
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The mechanistic study of Leishmania major dihydro-orotate dehydrogenase based on steady- and pre-steady-state kinetic analysis. Biochem J 2016; 473:651-60. [DOI: 10.1042/bj20150921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/11/2015] [Indexed: 11/17/2022]
Abstract
Leishmania major dihydro-orotate dehydrogenase (DHODHLm) oxidizes dihydro-orotate to orotate (ORO) in the de novo pyrimidine biosynthetic pathway. The enzyme reaction mechanism was elucidated by steady- and pre-steady-state kinetics. ORO release was found to be the rate-limiting step in the overall catalysis.
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Kazazić S, Bertoša B, Luić M, Mikleušević G, Tarnowski K, Dadlez M, Narczyk M, Bzowska A. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:73-82. [PMID: 26337516 DOI: 10.1007/s13361-015-1239-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/24/2015] [Accepted: 07/26/2015] [Indexed: 06/05/2023]
Abstract
The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.
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Affiliation(s)
- Saša Kazazić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Branimir Bertoša
- Division of Physical Chemistry, Faculty of Science at University of Zagreb, Zagreb, Croatia.
| | - Marija Luić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Goran Mikleušević
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krzysztof Tarnowski
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
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Alves CN, Silva JRA, Roitberg AE. Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study. Phys Chem Chem Phys 2015; 17:17790-6. [PMID: 26087682 DOI: 10.1039/c5cp02016f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) enzyme catalyzes the unique redox reaction in the de novo pyrimidine biosynthesis pathway. In this reaction, the oxidation of dihydroorotate (DHO) to orotate (OA) and reduction of the flavin mononucleotide (FMN) cofactor is catalysed by DHOD. The class 2 DHOD, to which the human enzyme belongs, was experimentally shown to follow a stepwise mechanism but the data did not allow the determination of the order of bond-breaking in a stepwise oxidation of DHO. The goal of this study is to understand the reaction mechanism at the molecular level of class 2 DHOD, which may aid in the design of inhibitors that selectively impact the activity of only certain members of the enzyme family. In this paper, the catalytic mechanism of oxidation of DHO to OA in human DHOD was studied using a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) approach and Molecular Dynamics (MD) simulations. The free energy barriers calculated reveal that the mechanism in human DHOD occurs via a stepwise reaction pathway. In the first step, a proton is abstracted from the C5 of DHO to the deprotonated Ser215 side chain. Whereas, in the second step, the transfer of the hydride or hydride equivalent from the C6 of DHO to the N5 of FMN, where free energy barrier calculated by the DFT/MM level is 10.84 kcal mol(-1). Finally, a residual decomposition analysis was carried out in order to elucidate the influence of the catalytic region residues during DHO oxidation.
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Affiliation(s)
- Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil. mail:
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Silva JRA, Roitberg AE, Alves CN. A QM/MM free energy study of the oxidation mechanism of dihydroorotate dehydrogenase (class 1A) from Lactococcus lactis. J Phys Chem B 2015; 119:1468-73. [PMID: 25564307 DOI: 10.1021/jp512860r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) class 1A enzyme catalyzes is the only redox enzyme in the biosynthetic pathway (de novo) of pyrimidines where dihydroorotate (DHO) is oxidized to orotate (OA) coupled to reduction of a flavin mononucleotide (FMN) cofactor. The rupture of two DHO C-H bonds can proceed in a concerted or stepwise way. Herein, the catalytic mechanism of DHOD from Lactococcus lactis involving DHO oxidation (first half-reaction) was described using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach and molecular dynamics simulations. The free energy profile obtained from self-consistent charge-density functional tight binding/molecular mechanics calculations (corrected by DFT/MM) reveals that this occurs with the proton abstraction from DHO C5 to Cys130 deprotonated and DHO H6 is transferred to FMN N5 in a concerted mechanism with a very low barrier of 5.64 kcal/mol. Finally, through a residual decomposition analysis, the residues that have the main influence on the redox reaction were identified.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , Belém, PA 66075-110, Brazil
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9
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Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
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Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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de Farias Silva N, Lameira J, Alves CN, Martí S. Computational study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi. Phys Chem Chem Phys 2013; 15:18863-71. [DOI: 10.1039/c3cp52692e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Couto SG, Cristina Nonato M, Costa-Filho AJ. Site directed spin labeling studies of Escherichia coli dihydroorotate dehydrogenase N-terminal extension. Biochem Biophys Res Commun 2011; 414:487-92. [PMID: 21986535 DOI: 10.1016/j.bbrc.2011.09.092] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenases (DHODHs) are enzymes that catalyze the fourth step of the de novo synthesis of pyrimidine nucleotides. In this reaction, DHODH converts dihydroorotate to orotate, using a flavine mononucleotide as a cofactor. Since the synthesis of nucleotides has different pathways in mammals as compared to parasites, DHODH has gained much attention as a promising target for drug design. Escherichia coli DHODH (EcDHODH) is a family 2 DHODH that interacts with cell membranes in order to promote catalysis. The membrane association is supposedly made via an extension found in the enzyme's N-terminal. In the present work, we used site directed spin labeling (SDSL) to specifically place a magnetic probe at positions 2, 5, 19, and 21 within the N-terminal and thus monitor, by using Electron Spin Resonance (ESR), dynamics and structural changes in this region in the presence of a membrane model system. Overall, our ESR spectra show that the N-terminal indeed binds to membranes and that it experiences a somewhat high flexibility that could be related to the role of this region as a molecular lid controlling the entrance of the enzyme's active site and thus allowing the enzyme to give access to quinones that are dispersed in the membrane and that are necessary for the catalysis.
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Affiliation(s)
- Sheila G Couto
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, C.P. 369, 13560-970, São Carlos, SP, Brazil
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McDonald CA, Palfey BA. Substrate binding and reactivity are not linked: grafting a proton-transfer network into a Class 1A dihydroorotate dehydrogenase. Biochemistry 2011; 50:2714-6. [PMID: 21401078 DOI: 10.1021/bi200258y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adding the two residues comprising the conserved proton-transfer network of Class 2 dihydroorotate dehydrogenase (DHOD) to the Cys130Ser Class 1A DHOD did not restore the function of the active site base or rapid flavin reduction. Studies of triple, double, and single mutant Class 1A enzymes showed that the network actually prevents cysteine from acting as a base and that the network residues act independently. Our data show that residue 71 is an important determinant of ligand binding specificity. The Leu71Phe mutation tightens dihydrooroate binding but weakens the binding of benzoate inhibitors of Class 1A enzymes.
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Affiliation(s)
- Claudia A McDonald
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, United States
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13
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Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. Eur J Med Chem 2010; 45:5899-909. [DOI: 10.1016/j.ejmech.2010.09.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 11/22/2022]
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Nisimoto Y, Jackson HM, Ogawa H, Kawahara T, Lambeth JD. Constitutive NADPH-dependent electron transferase activity of the Nox4 dehydrogenase domain. Biochemistry 2010; 49:2433-42. [PMID: 20163138 PMCID: PMC2839512 DOI: 10.1021/bi9022285] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
NADPH oxidase 4 (Nox4) is constitutively active, while Nox2 requires the cytosolic regulatory subunits p47(phox) and p67(phox) and activated Rac with activation by phorbol 12-myristate 13-acetate (PMA). This study was undertaken to identify the domain on Nox4 that confers constitutive activity. Lysates from Nox4-expressing cells exhibited constitutive NADPH- but not NADH-dependent hydrogen peroxide production with a K(m) for NADPH of 55 +/- 10 microM. The concentration of Nox4 in cell lysates was estimated using Western blotting and allowed calculation of a turnover of approximately 200 mol of H(2)O(2) min(-1) (mol of Nox4)(-1). A chimeric protein (Nox2/4) consisting of the Nox2 transmembrane (TM) domain and the Nox4 dehydrogenase (DH) domain showed H(2)O(2) production in the absence of cytosolic regulatory subunits. In contrast, chimera Nox4/2, consisting of the Nox4 TM and Nox2 DH domains, exhibited PMA-dependent activation that required coexpression of regulatory subunits. Nox DH domains from several Nox isoforms were purified and evaluated for their electron transferase activities. Nox1 DH, Nox2 DH, and Nox5 DH domains exhibited barely detectable activities toward artificial electron acceptors, while the Nox4 DH domain exhibited significant rates of reduction of cytochrome c (160 min(-1), largely superoxide dismutase-independent), ferricyanide (470 min(-1)), and other electron acceptors (artificial dyes and cytochrome b(5)). Rates were similar to those observed for H(2)O(2) production by the Nox4 holoenzyme in cell lysates. The activity required added FAD and was seen with NADPH but not NADH. These results indicate that the Nox4 DH domain exists in an intrinsically activated state and that electron transfer from NADPH to FAD is likely to be rate-limiting in the NADPH-dependent reduction of oxygen by holo-Nox4.
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Affiliation(s)
- Yukio Nisimoto
- Department of Pathology and Laboratory Medicine, Emory University Medical School, Atlanta, Georgia 30322, USA
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15
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Fagan RL, Palfey BA. Roles in binding and chemistry for conserved active site residues in the class 2 dihydroorotate dehydrogenase from Escherichia coli. Biochemistry 2009; 48:7169-78. [PMID: 19530672 DOI: 10.1021/bi900370s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) catalyze the only redox step in de novo pyrimidine biosynthesis, the oxidation of dihydroorotate (DHO) to orotate (OA). During the reaction, the hydrogen at C6 of DHO is transferred to N5 of the isoalloxazine ring of an enzyme-bound FMN prosthetic group as a hydride, and an active site base (Ser175 in the class 2 DHOD from Escherichia coli) deprotonates C5 of DHO. Aside from the identity of the active site base, the pyrimidine binding site of all DHODs is nearly identical. Several strictly conserved residues (four asparagines and either a serine or threonine) make extensive hydrogen bonds to the pyrimidine). The roles these conserved residues play in DHO oxidation are unknown. Site-directed mutagenesis was used to investigate the role of each residue during DHO oxidation. The effects of each mutation on substrate and product binding, as well as the effect on the rate constant of the chemical step, were determined. The effects of the mutations ranged from negligible to severe. Some of the residues were very important for chemistry, while others were important for binding. Mutation of residues capable of stabilizing reaction intermediates resulted in large decreases in the rate constant of the chemical step, suggesting these residues are quite important for stabilizing charge buildup in the active site. This finding is consistent with previous results that class 2 DHODs use a stepwise mechanism for DHO oxidation.
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Affiliation(s)
- Rebecca L Fagan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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Kow RL, Whicher JR, McDonald CA, Palfey BA, Fagan RL. Disruption of the proton relay network in the class 2 dihydroorotate dehydrogenase from Escherichia coli. Biochemistry 2009; 48:9801-9. [PMID: 19694481 DOI: 10.1021/bi901024m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) are FMN-containing enzymes that catalyze the conversion of dihydroorotate (DHO) to orotate in the de novo synthesis of pyrimidines. During the reaction, a proton is transferred from C5 of DHO to an active site base and the hydrogen at C6 of DHO is transferred to N5 of the isoalloxazine ring of the flavin as a hydride. In class 2 DHODs, a hydrogen bond network observed in crystal structures has been proposed to deprotonate the C5 atom of DHO. The active site base (Ser175 in the Escherichia coli enzyme) hydrogen bonds to a crystallographic water molecule that sits on a phenylalanine (Phe115 in the E. coli enzyme) and hydrogen bonds to a threonine (Thr178 in the E. coli enzyme), residues that are conserved in class 2 enzymes. The importance of these residues in the oxidation of DHO was investigated using site-directed mutagenesis. Mutating Ser175 to alanine had severe effects on the rate of flavin reduction, slowing it by more than 3 orders of magnitude. Changing the size and/or hydrophobicity of the residues of the hydrogen bond network, Thr178 and Phe115, slowed flavin reduction as much as 2 orders of magnitude, indicating that the active site base and the hydrogen bond network work together for efficient deprotonation of DHO.
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Affiliation(s)
- Rebecca L Kow
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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Liu WY, Wang MM, Huang J, Tang HJ, Lan HX, Zhang HS. The OsDHODH1 gene is involved in salt and drought tolerance in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:825-833. [PMID: 19723241 DOI: 10.1111/j.1744-7909.2009.00853.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In the present paper, we identified and cloned OsDHODH1 encoding a putative cytosolic dihydroorotate dehydrogenase (DHODH) in rice. Expression analysis indicated that OsDHODH1 is upregulated by salt, drought and exogenous abscisic acid (ABA), but not by cold. By prokaryotic expression, we determined the enzymatic activity of OsDHODH1 and found that overproduction of OsDHODH1 significantly improved the tolerance of Escherichia coli cells to salt and osmotic stresses. Overexpression of the OsDHODH1 gene in rice increased the DHODH activity and enhanced plant tolerance to salt and drought stresses as compared with wild type and OsDHODH1-antisense transgenic plants. Our findings reveal, for the first time, that cytosolic dihydroorotate dehydrogenase is involved in plant stress response and that OsDHODH1 could be used in engineering crop plants with enhanced tolerance to salt and drought.
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Affiliation(s)
- Wen-Ying Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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18
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Inaoka DK, Sakamoto K, Shimizu H, Shiba T, Kurisu G, Nara T, Aoki T, Kita K, Harada S. Structures of Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexed with Substrates and Products: Atomic Resolution Insights into Mechanisms of Dihydroorotate Oxidation and Fumarate Reduction. Biochemistry 2008; 47:10881-91. [DOI: 10.1021/bi800413r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Kimitoshi Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Hironari Shimizu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Tomoo Shiba
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Genji Kurisu
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Takeshi Nara
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Takashi Aoki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Shigeharu Harada
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan, Department of Molecular and Cellular Parasitology, Juntendo University, Tokyo 113-8421, Japan, and Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
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19
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Arakaki TL, Buckner FS, Gillespie JR, Malmquist NA, Phillips MA, Kalyuzhniy O, Luft JR, Detitta GT, Verlinde CLMJ, Van Voorhis WC, Hol WGJ, Merritt EA. Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies. Mol Microbiol 2008; 68:37-50. [PMID: 18312275 DOI: 10.1111/j.1365-2958.2008.06131.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nucleotide biosynthesis pathways have been reported to be essential in some protozoan pathogens. Hence, we evaluated the essentiality of one enzyme in the pyrimidine biosynthetic pathway, dihydroorotate dehydrogenase (DHODH) from the eukaryotic parasite Trypanosoma brucei through gene knockdown studies. RNAi knockdown of DHODH expression in bloodstream form T. brucei did not inhibit growth in normal medium, but profoundly retarded growth in pyrimidine-depleted media or in the presence of the known pyrimidine uptake antagonist 5-fluorouracil (5-FU). These results have significant implications for the development of therapeutics to combat T. brucei infection. Specifically, a combination therapy including a T. brucei-specific DHODH inhibitor plus 5-FU may prove to be an effective therapeutic strategy. We also show that this trypanosomal enzyme is inhibited by known inhibitors of bacterial Class 1A DHODH, in distinction to the sensitivity of DHODH from human and other higher eukaryotes. This selectivity is supported by the crystal structure of the T. brucei enzyme, which is reported here at a resolution of 1.95 A. Additional research, guided by the crystal structure described herein, is needed to identify potent inhibitors of T. brucei DHODH.
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Affiliation(s)
- Tracy L Arakaki
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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20
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Martin W, Russell MJ. On the origin of biochemistry at an alkaline hydrothermal vent. Philos Trans R Soc Lond B Biol Sci 2007; 362:1887-925. [PMID: 17255002 PMCID: PMC2442388 DOI: 10.1098/rstb.2006.1881] [Citation(s) in RCA: 381] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A model for the origin of biochemistry at an alkaline hydrothermal vent has been developed that focuses on the acetyl-CoA (Wood-Ljungdahl) pathway of CO2 fixation and central intermediary metabolism leading to the synthesis of the constituents of purines and pyrimidines. The idea that acetogenesis and methanogenesis were the ancestral forms of energy metabolism among the first free-living eubacteria and archaebacteria, respectively, stands in the foreground. The synthesis of formyl pterins, which are essential intermediates of the Wood-Ljungdahl pathway and purine biosynthesis, is found to confront early metabolic systems with steep bioenergetic demands that would appear to link some, but not all, steps of CO2 reduction to geochemical processes in or on the Earth's crust. Inorganically catalysed prebiotic analogues of the core biochemical reactions involved in pterin-dependent methyl synthesis of the modern acetyl-CoA pathway are considered. The following compounds appear as probable candidates for central involvement in prebiotic chemistry: metal sulphides, formate, carbon monoxide, methyl sulphide, acetate, formyl phosphate, carboxy phosphate, carbamate, carbamoyl phosphate, acetyl thioesters, acetyl phosphate, possibly carbonyl sulphide and eventually pterins. Carbon might have entered early metabolism via reactions hardly different from those in the modern Wood-Ljungdahl pathway, the pyruvate synthase reaction and the incomplete reverse citric acid cycle. The key energy-rich intermediates were perhaps acetyl thioesters, with acetyl phosphate possibly serving as the universal metabolic energy currency prior to the origin of genes. Nitrogen might have entered metabolism as geochemical NH3 via two routes: the synthesis of carbamoyl phosphate and reductive transaminations of alpha-keto acids. Together with intermediates of methyl synthesis, these two routes of nitrogen assimilation would directly supply all intermediates of modern purine and pyrimidine biosynthesis. Thermodynamic considerations related to formyl pterin synthesis suggest that the ability to harness a naturally pre-existing proton gradient at the vent-ocean interface via an ATPase is older than the ability to generate a proton gradient with chemistry that is specified by genes.
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Affiliation(s)
- William Martin
- Institute of Botany, University of Düsseldorf, 40225 Düsseldorf, Germany.
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21
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Wolfe AE, Thymark M, Gattis SG, Fagan RL, Hu YC, Johansson E, Arent S, Larsen S, Palfey BA. Interaction of Benzoate Pyrimidine Analogues with Class 1A Dihydroorotate Dehydrogenase from Lactococcus lactis,. Biochemistry 2007; 46:5741-53. [PMID: 17444658 DOI: 10.1021/bi7001554] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) catalyze the oxidation of dihydroorotate to orotate in the only redox reaction in pyrimidine biosynthesis. The pyrimidine binding sites are very similar in all structurally characterized DHODs, suggesting that the prospects for identifying a class-specific inhibitor directed against this site are poor. Nonetheless, two compounds that bind specifically to the Class 1A DHOD from Lactococcus lactis, 3,4-dihydroxybenzoate (3,4-diOHB) and 3,5-dihydroxybenzoate (3,5-diOHB), have been identified [Palfey et al. (2001) J. Med. Chem. 44, 2861-2864]. The mechanism of inhibitor binding to the Class 1A DHOD from L. lactis has now been studied in detail and is reported here. Titrations showed that 3,4-diOHB binds more tightly at higher pH, whereas the opposite is true for 3,5-diOHB. Isothermal titration calorimetry and absorbance spectroscopy showed that 3,4-diOHB ionizes to the phenolate upon binding to the enzyme, but 3,5-diOHB does not. The charge-transfer band that forms in the 3,4-diOHB complex allowed the kinetics of binding to be observed in stopped-flow experiments. Binding was slow enough to observe from pH 6 to pH 8 and was (minimally) a two-step process consisting of the rapid formation of a complex that isomerized to the final charge-transfer complex. Orotate and 3,5-diOHB bind too quickly to follow directly, but their dissociation kinetics were studied by competition and described adequately with a single step. Crystal structures of both inhibitor complexes were determined, showing that 3,5-diOHB binds in the same orientation as orotate. In contrast, 3,4-diOHB binds in a twisted orientation, enabling one of its phenolic oxygens to form a very strong hydrogen bond to an asparagine, thus stabilizing the phenolate and causing charge-transfer interactions with the pi-system of the flavin, resulting in a green color.
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Affiliation(s)
- Abigail E Wolfe
- Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109-0606, USA
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22
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Fagan RL, Jensen KF, Björnberg O, Palfey BA. Mechanism of flavin reduction in the class 1A dihydroorotate dehydrogenase from Lactococcus lactis. Biochemistry 2007; 46:4028-36. [PMID: 17341096 DOI: 10.1021/bi602460n] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) oxidize dihydroorotate (DHO) to orotate (OA) using the FMN prosthetic group to abstract a hydride equivalent from C6 and a protein residue (cysteine for class 1A DHODs) to deprotonate C5. The fundamental question of whether the scission of the two DHO C-H bonds is concerted or stepwise was addressed for the class 1A enzyme from Lactococcus lactis by determining kinetic isotope effects (KIEs) on flavin reduction in anaerobic stopped-flow experiments. Isotope effects were determined at two pH values. At pH 7.0, KIEs were approximately 2-fold for DHO labeled singly at the 5-position or the 6-position and approximately 4-fold for DHO labeled at both the 5- and 6-positions. At pH 8.5, the KIEs observed for DHO labeled at the 5-position, the 6-position, and the 5- and 6-positions were approximately 2-, approximately 3-, and approximately 6-fold, respectively. These isotope effects are consistent with a concerted oxidation of DHO. The pH dependence of reduction was also determined, and a pKa of 8.3 was found. This pKa can be attributed to the ionization of the active site cysteine which deprotonates C5 of DHO during the reaction. To further investigate the importance of the active site base, two site-directed mutants were also studied: Cys130Ala (removal of the active site base) and Cys130Ser (replacement with the active site base used by class 2 DHODs). Both mutant enzymes exhibited binding affinities for DHO similar to that of the wild-type enzyme. Reduction of both mutants was extremely slow compared to that of the wild type; the rate of reduction increased with pH, showing no sign of a plateau. Interestingly, double-deuterium isotope effects on the Cys130Ser mutant also showed a concerted mechanism for flavin reduction.
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Affiliation(s)
- Rebecca L Fagan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA
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23
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Small YA, Guallar V, Soudackov AV, Hammes-Schiffer S. Hydrogen Bonding Pathways in Human Dihydroorotate Dehydrogenase. J Phys Chem B 2006; 110:19704-10. [PMID: 17004840 DOI: 10.1021/jp065034t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.
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Affiliation(s)
- Yolanda A Small
- Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, 16802, USA
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24
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Combe JP, Basran J, Hothi P, Leys D, Rigby SEJ, Munro AW, Scrutton NS. Lys-D48 is required for charge stabilization, rapid flavin reduction, and internal electron transfer in the catalytic cycle of dihydroorotate dehydrogenase B of Lactococcus lactis. J Biol Chem 2006; 281:17977-88. [PMID: 16624811 DOI: 10.1074/jbc.m601417200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroorotate dehydrogenase B (DHODB) catalyzes the oxidation of dihydroorotate (DHO) to orotate and is found in the pyrimidine biosynthetic pathway. The Lactococcus lactis enzyme is a dimer of heterodimers containing FMN, FAD, and a 2Fe-2S center. Lys-D48 is found in the catalytic subunit and its side-chain adopts different positions, influenced by ligand binding. Based on crystal structures of DHODB in the presence and absence of orotate, we hypothesized that Lys-D48 has a role in facilitating electron transfer in DHODB, specifically in stabilizing negative charge in the reduced FMN isoalloxazine ring. We show that mutagenesis of Lys-D48 to an alanine, arginine, glutamine, or glutamate residue (mutants K38A, K48R, K48Q, and K48E) impairs catalytic turnover substantially (approximately 50-500-fold reduction in turnover number). Stopped-flow studies demonstrate that loss of catalytic activity is attributed to poor rates of FMN reduction by substrate. Mutation also impairs electron transfer from the 2Fe-2S center to FMN. Addition of methylamine leads to partial rescue of flavin reduction activity. Nicotinamide coenzyme oxidation and reduction at the distal FAD site is unaffected by the mutations. Formation of the spin-interacting state between the FMN semiquinone-reduced 2Fe-2S centers observed in wild-type enzyme is retained in the mutant proteins, consistent with there being little perturbation of the superexchange paths that contribute to the efficiency of electron transfer between these cofactors. Our data suggest a key charge-stabilizing role for Lys-D48 during reduction of FMN by dihydroorotate, or by electron transfer from the 2Fe-2S center, and establish a common mechanism of FMN reduction in the single FMN-containing A-type and the complex multicenter B-type DHOD enzymes.
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Affiliation(s)
- Jonathan P Combe
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Sackville Street, Manchester M60 1QD, United Kingdom
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Shi J, Dertouzos J, Gafni A, Steel D, Palfey BA. Single-molecule kinetics reveals signatures of half-sites reactivity in dihydroorotate dehydrogenase A catalysis. Proc Natl Acad Sci U S A 2006; 103:5775-80. [PMID: 16585513 PMCID: PMC1458649 DOI: 10.1073/pnas.0510482103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Subunit activity and cooperativity of a homodimeric flavoenzyme, dihydroorotate dehydrogenase A (DHODA) from Lactococcus lactis, were characterized by employing single-molecule spectroscopy to follow the turnover kinetics of individual DHODA molecules, eliminating ensemble averaging. Because the enzyme-bound FMN is fluorescent in its oxidized state but not when reduced, a single DHODA molecule exhibits stepwise fluorescence changes during turnover, providing a signal to determine reaction kinetics and study cooperativity. Our results showed significant heterogeneity in the catalytic behaviors of individual dimer molecules, with only 40% interconverting between the three possible redox states: the fully fluorescent (both subunits oxidized), the half-fluorescent (one subunit oxidized and the other reduced), and the nonfluorescent (both subunits reduced). Forty percent of the single dimer traces showed turnovers between only the fully fluorescent and half-fluorescent states. The remaining 20% of the molecules interconverted only between the half-fluorescent state and the nonfluorescent state. Kinetic analysis revealed very similar reaction rates in both the reductive and oxidative half-reactions for different DHODA dimers. Our single-molecule data provide strong evidence for half-sites reactivity, in which only one subunit reacts at a time. The present study presents an effective way to explore the subunit catalytic activity and cooperativity of oligomeric enzymes by virtue of single-molecule fluorescence.
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Affiliation(s)
- Jue Shi
- Biophysics Research Division and
| | - Joe Dertouzos
- Departments of Physics
- Electrical Engineering and Computer Science, and
| | - Ari Gafni
- Biophysics Research Division and
- Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Duncan Steel
- Biophysics Research Division and
- Departments of Physics
- Electrical Engineering and Computer Science, and
| | - Bruce A. Palfey
- Biophysics Research Division and
- Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
- To whom correspondence should be addressed. E-mail:
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Kilstrup M, Hammer K, Ruhdal Jensen P, Martinussen J. Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol Rev 2005. [DOI: 10.1016/j.fmrre.2005.04.006] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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