1
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Smith MM, Moran GR. Building on a theme: The redox hierarchy of pyridine nucleotide-disulfide oxidoreductases. Arch Biochem Biophys 2024; 755:109966. [PMID: 38537870 DOI: 10.1016/j.abb.2024.109966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/24/2024]
Abstract
Flavin disulfide reductases (FDRs) are FAD-dependent enzymes that transmit electrons from NAD(P)H to reduce specific oxidant substrate disulfides. These enzymes have been studied extensively, most particularly the paradigm examples: glutathione reductase and thioredoxin reductase. The common, though not universal, traits of the family include a tyrosine- or phenylalanine-gated binding pocket for NAD(P) nicotinamides adjacent to the FAD isoalloxazine re-face, and a disulfide stacked against the si-face of the isoalloxazine whose dithiol form is activated for subsequent exchange reactions by a nearby histidine acting as a base. This arrangement promotes transduction of the reducing equivalents for disulfide exchange relay reactions. From an observational standpoint the proximal parallel stacking of three redox moieties induces up to three opportunities for unique charge transfer interactions (NAD(P)H FAD, NAD(P)+•FADH2, and FAD•thiolate). In transient state, the charge transfer transitions provide discrete signals to assign reaction sequences. This review summarizes the lineage of observations for the FDR enzymes that have been extensively studied. Where applicable and in order to chart a consistent interpretation of the record, only data derived from studies that used anaerobic methods are cited. These data reveal a recurring theme for catalysis that is elaborated with specific additional functionalities for each oxidant substrate.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, United States.
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2
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Smith CO, Moran GR. Elucidation of the Catalytic Sequence of Dihydroorotate Dehydrogenase B from Lactoccocus lactis: Evidence for Accumulation of a Flavin Bisemiquinone State in Catalysis. Biochemistry 2024. [PMID: 38691339 DOI: 10.1021/acs.biochem.4c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
The physiological role of dihydroorotate dehydrogenase (DHOD) enzymes is to catalyze the oxidation of dihydroorotate to orotate in pyrimidine biosynthesis. DHOD enzymes are structurally diverse existing as both soluble and membrane-associated forms. The Family 1 enzymes are soluble and act either as conventional single subunit flavin-dependent dehydrogenases known as Class 1A (DHODA) or as unusual heterodimeric enzymes known as Class 1B (DHODB). DHODBs possess two active sites separated by ∼20 Å, each with a noncovalently bound flavin cofactor. NAD is thought to interact at the FAD containing site, and the pyrimidine substrate is known to bind at the FMN containing site. At the approximate center of the protein is a single Fe2S2 center that is assumed to act as a conduit, facilitating one-electron transfers between the flavins. We present anaerobic transient state analysis of a DHODB enzyme from Lactoccocus lactis. The data presented primarily report the exothermic reaction that reduces orotate to dihydroorotate. The reductive half reaction reveals rapid two-electron reduction that is followed by the accumulation of a four-electron reduced state when NADH is added in excess, suggesting that the initial two electrons acquired reside on the FMN cofactor. Concomitant with the first reduction is the accumulation of a long-wavelength absorption feature consistent with the blue form of a flavin semiquinone. Spectral deconvolution and fitting to a model that includes reversibility for the second electron transfer reveals equilibrium accumulation of a flavin bisemiquinone state that has features of both red and blue semiquinones. Single turnover reactions with limiting NADH and excess orotate reveal that the flavin bisemiquinone accumulates with reduction of the enzyme by NADH and decays with reduction of the pyrimidine substrate, establishing the bisemiquinone as a fractional state of the two-electron reduced intermediate observed.
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Affiliation(s)
- Corine O Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Rd Chicago Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan Rd Chicago Illinois 60660, United States
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3
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Devitt AN, Vargas AL, Zhu W, Des Soye BJ, Butun FA, Alt T, Kaley N, Ferreira GM, Moran GR, Kelleher NL, Liu D, Silverman RB. Design, Synthesis, and Mechanistic Studies of ( R)-3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase. ACS Chem Biol 2024. [PMID: 38630468 DOI: 10.1021/acschembio.4c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Human ornithine aminotransferase (hOAT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme, has been shown to play an essential role in the metabolic reprogramming and progression of hepatocellular carcinoma (HCC). HCC accounts for approximately 75% of primary liver cancers and is within the top three causes of cancer death worldwide. As a result of treatment limitations, the overall 5-year survival rate for all patients with HCC is under 20%. The prevalence of HCC necessitates continued development of novel and effective treatment methods. In recent years, the therapeutic potential of selective inactivation of hOAT has been demonstrated for the treatment of HCC. Inspired by previous increased selectivity for hOAT by the expansion of the cyclopentene ring scaffold to a cyclohexene, we designed, synthesized, and evaluated a series of novel fluorinated cyclohexene analogues and identified (R)-3-amino-5,5-difluorocyclohex-1-ene-1-carboxylic acid as a time-dependent inhibitor of hOAT. Structural and mechanistic studies have elucidated the mechanism of inactivation of hOAT by 5, resulting in a PLP-inactivator adduct tightly bound to the active site of the enzyme. Intact protein mass spectrometry, 19F NMR spectroscopy, transient state kinetic studies, and X-ray crystallography were used to determine the structure of the final adduct and elucidate the mechanisms of inactivation. Interestingly, despite the highly electrophilic intermediate species conferred by fluorine and structural evidence of solvent accessibility in the hOAT active site, Lys292 and water did not participate in nucleophilic addition during the inactivation mechanism of hOAT by 5. Instead, rapid aromatization to yield the final adduct was favored.
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Affiliation(s)
- Allison N Devitt
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Abigail L Vargas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Benjamin James Des Soye
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatma Ayaloglu Butun
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Tyler Alt
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Nicholas Kaley
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Glaucio M Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard B Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Pharmacology, Northwestern University, Chicago, Illinois 60611, United States
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4
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Alt TB, Hoag MR, Moran GR. Dihydropyrmidine dehydrogenase from Escherichia coli: Transient state analysis reveals both reductive activation prior to turnover and diminished substrate effector roles relative to the mammalian form. Arch Biochem Biophys 2023; 748:109772. [PMID: 37820757 DOI: 10.1016/j.abb.2023.109772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is an enzyme that uses an elaborate architecture to catalyze a simple net reaction: the reduction of the vinylic bond of uracil and thymine. Known DPDs have two active sites separated by approximately 60 Å. One active site has an FAD cofactor and binds NAD(P) and the other has an FMN cofactor and binds pyrimidines. The intervening distance is spanned by four Fe4S4 centers that act as an electron conduit. Recent advancements with porcine DPD have revealed unexpected chemical sequences where the enzyme undergoes reductive activation by transferring two electrons from NADPH to the FMN via the FAD such that the active form has the cofactor set FAD•4(Fe4S4)•FMNH2. Here we describe the first comprehensive kinetic investigation of a bacterial form of DPD. Using primarily transient state methods, DPD from E. coli (EcDPD) was shown to have a similar mechanism to that observed with the mammalian form in that EcDPD is observed to undergo reductive activation before pyrimidine reduction and displays half-of-sites activity. However, two distinct aspects of the EcDPD reaction relative to the mammalian enzyme were observed that relate to the effector roles for substrates: (i) the enzyme will rapidly take up electrons from NADH, reducing a flavin in the absence of pyrimidine substrate, and (ii) the activated form of the enzyme can become fully oxidized by transferring electrons to pyrimidine substrates in the absence of NADH.
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Affiliation(s)
- Tyler B Alt
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660, USA.
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5
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Smith MM, Moran GR. Assigning function to active site residues of Schistosoma mansoni thioredoxin/glutathione reductase from analysis of transient state reductive half-reactions with variant forms of the enzyme. Front Mol Biosci 2023; 10:1258333. [PMID: 37780207 PMCID: PMC10535113 DOI: 10.3389/fmolb.2023.1258333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 10/03/2023] Open
Abstract
Thioredoxin/glutathione reductase (TGR) from the platyhelminthic parasitic worms has recently been identified as a drug target for the treatment of schistosomiasis. Schistosomes lack catalase, and so are heavily reliant on the regeneration of reduced thioredoxin (Trx) and glutathione (GSH) to reduce peroxiredoxins that ameliorate oxidative damage from hydrogen peroxide generated by the host immune response. This study focuses on the characterization of the catalytic mechanism of Schistosoma mansoni TGR (SmTGR). Variant forms of SmTGR were studied to assign the function of residues that participate in the electron distribution chain within the enzyme. Using anaerobic transient state spectrophotometric methods, redox changes for the FAD and NADPH were observed and the function of specific residues was defined from observation of charge transfer absorption transitions that are indicative of specific complexations and redox states. The C159S variant prevented distribution of electrons beyond the flavin and as such did not accumulate thiolate-FAD charge transfer absorption. The lack of this absorption facilitated observation of a new charge transfer absorption consistent with proximity of NADPH and FAD. The C159S variant was used to confine electrons from NADPH at the flavin, and it was shown that NADPH and FAD exchange hydride in both directions and come to an equilibrium that yields only fractional FAD reduction, suggesting that both have similar reduction potentials. Mutation of U597 to serine resulted in sustained thiolate-FAD charge transfer absorption and loss of the ability to reduce Trx, indicating that the C596-U597 disulfide functions in the catalytic sequence to receive electrons from the C154 C159 pair and distribute them to Trx. No kinetic evidence for a loss or change in function associated with the distal C28-C31 disulfide was observed when the C31S variant reductive half-reaction was observed. The Y296A variant was shown to slow the rate of but increase extent of reduction of the flavin, and the dissociation of NADP+. The H571 residue was confirmed to be the residue responsible for the deprotonation of the C159 thiol, increasing its reactivity and generating the prominent thiolate-FAD charge transfer absorption that accumulates with oxidation of the flavin.
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Affiliation(s)
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, Habeeb Mohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. Correction to "Rational Design, Synthesis, and Mechanism of (3 S,4 R)-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase". J Am Chem Soc 2023; 145:9895-9896. [PMID: 37075548 DOI: 10.1021/jacs.3c03364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
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7
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Smith MM, Moran GR. The unusual chemical sequences of mammalian dihydropyrimidine dehydrogenase revealed by transient-state analysis. Methods Enzymol 2023; 685:373-403. [PMID: 37245908 DOI: 10.1016/bs.mie.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Dihydropyrimidine dehydrogenase (DPD) catalyzes the reduction of the 5,6-vinylic bond of uracil and thymine with electrons from NADPH. The complexity of the enzyme belies the simplicity of the reaction catalyzed. To accomplish this chemistry DPD has two active sites that are ∼60Å apart, both of which house flavin cofactors, FAD and FMN. The FAD site interacts with NADPH, while the FMN site with pyrimidines. The distance between the flavins is spanned by four Fe4S4 centers. Though DPD has been studied for nearly 50years, it is only recently that the novel apects of its mechanism have been described. The primary reason for this is that the chemistry of DPD is not portrayed adequately by known descriptive steady-state mechanism categories. The highly chromophoric nature of the enzyme has recently been exploited in transient-state to document unexpected reaction sequences. Specifically, DPD undergoes reductive activation prior to catalytic turnover. Two electrons are taken up from NADPH and transmitted via the FAD and Fe4S4 centers to form the FAD•4(Fe4S4)•FMNH2 form of the enzyme. This form of the enzyme will only reduce pyrimidine substrates in the presence NADPH, establishing that hydride transfer to the pyrimidine precedes reductive reactivation that reinstates the active form of the enzyme. DPD is therefore the first flavoprotein dehydrogenase known to complete the oxidative half-reaction prior to the reductive half-reaction. Here we describe the methods and deduction that led to this mechanistic assignment.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States.
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8
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Smith MM, Alt TB, Williams DL, Moran GR. Descriptive Analysis of Transient-State Observations for Thioredoxin/Glutathione Reductase (Sec597Cys) from Schistosoma mansoni. Biochemistry 2023; 62:1497-1508. [PMID: 37071546 DOI: 10.1021/acs.biochem.3c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Thioredoxin/glutathione reductase from Schistosoma mansoni (SmTGR) catalyzes the reduction of both oxidized thioredoxin and glutathione with electrons from reduced nicotinamide adenine dinucleotide phosphate (NADPH). SmTGR is a drug target for the treatment of Schistosomiasis, an infection caused by Schistosoma platyhelminths residing in the blood vessels of the host. Schistosoma spp. are reliant on TGR enzymes as they lack catalase and so use reduced thioredoxin and glutathione to regenerate peroxiredoxins consumed in the detoxification of reactive oxygen species. SmTGR is a flavin adenine dinucleotide (FAD)-dependent enzyme, and we have used the flavin as a spectrophotometric reporter to observe the movement of electrons within the enzyme. The data show that NADPH fractionally reduces the active site flavin with an observed rate constant estimated in this study to be ∼3000 s-1. The flavin then reoxidizes by passing electrons at a similar rate to the proximal Cys159-Cys154 disulfide pair. The dissociation of NADP+ occurs with a rate of ∼180 s-1, which induces the deprotonation of Cys159, and this coincides with the accumulation of an intense FAD-thiolate charge transfer band. It is proposed that the electrons then pass to the Cys596-Cys597 disulfide pair of the associated subunit in the dimer with a net rate constant of ∼2 s-1. (Note: Cys597 is Sec597 in wild-type (WT) SmTGR.) From this position, the electrons can be passed to oxidized thioredoxin or further into the protein to reduce the Cys28-Cys31 disulfide pair of the originating subunit of the dimer. From the Cys28-Cys31 center, electrons can then pass to oxidized glutathione that has a binding site directly adjacent.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Tyler B Alt
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - David L Williams
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
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9
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Smith MM, Forouzesh DC, Kaley NE, Liu D, Moran GR. Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes. Arch Biochem Biophys 2023; 736:109517. [PMID: 36681231 DOI: 10.1016/j.abb.2023.109517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is a flavin dependent enzyme that catalyzes the reduction of the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons from NADPH. DPD has two active sites that are separated by ∼60 Å. At one site NADPH binds adjacent to an FAD cofactor and at the other pyrimidine binds proximal to an FMN. Four Fe4S4 centers span the distance between these active sites. It has recently been established that the enzyme undergoes reductive activation prior to reducing the pyrimidine. In this initial process NADPH is oxidized at the FAD site and electrons are transmitted to the FMN via the Fe4S4 centers to yield the active state with a cofactor set of FAD•4(Fe4S4)•FMNH2. The catalytic chemistry of DPD can be studied in transient-state by observation of either NADPH consumption or charge transfer absorption associated with complexation of NADPH adjacent to the FAD. Here we have utilized both sets of absorption transitions to find evidence for specific additional aspects of the DPD mechanism. Competition for binding with NADP+ indicates that the two charge transfer species observed in activation/single turnover reactions arise from NADPH populating the FAD site before and after reductive activation. An additional charge transfer species is observed to accumulate at longer times when high NADPH concentrations are mixed with the enzyme•pyrimidine complex and this data can be modelled based on asymmetry in the homodimer. It was also shown that, like pyrimidines, dihydropyrimidines induce rapid reductive activation indicating that the reduced pyrimidine formed in turnover can stimulate the reinstatement of the active state of the enzyme. Investigation of the reverse reaction revealed that dihydropyrimidines alone can reductively activate the enzyme, albeit inefficiently. In the presence of dihydropyrimidine and NADP+ DPD will form NADPH but apparently without measurable reductive activation. Pyrimidines that have 5-substituent halogens were utilized to probe both reductive activation and turnover. The linearity of the Hammett plot based on the rate of hydride transfer to the pyrimidine establishes that, at least to the radius of an iodo-group, the 5-substituent volume does not have influence on the observed kinetics of pyrimidine reduction.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Dariush C Forouzesh
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Nicholas E Kaley
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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10
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Shen S, Butrin A, Beaupre BA, Ferreira GM, Doubleday PF, Grass DH, Zhu W, Kelleher NL, Moran GR, Liu D, Silverman RB. Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S,4 S)-3-Amino-4-fluorocyclopentenecarboxylic Acid. Molecules 2023; 28:1133. [PMID: 36770800 PMCID: PMC9921285 DOI: 10.3390/molecules28031133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Ornithine aminotransferase (OAT) is overexpressed in hepatocellular carcinoma (HCC), and we previously showed that inactivation of OAT inhibits the growth of HCC. Recently, we found that (3S,4S)-3-amino-4-fluorocyclopentenecarboxylic acid (5) was a potent inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), proceeding by an enamine mechanism. Here we describe our investigations into the activity and mechanism of 5 as an inactivator of human OAT. We have found that 5 exhibits 10-fold less inactivation efficiency (kinact/KI) against hOAT than GABA-AT. A comprehensive mechanistic study was carried out to understand its inactivation mechanism with hOAT. pKa and electrostatic potential calculations were performed to further support the notion that the α,β-unsaturated alkene of 5 is critical for enhancing acidity and nucleophilicity of the corresponding intermediates and ultimately responsible for the improved inactivation efficiency of 5 over the corresponding saturated analogue (4). Intact protein mass spectrometry and the crystal structure complex with hOAT provide evidence to conclude that 5 mainly inactivates hOAT through noncovalent interactions, and that, unlike with GABA-AT, covalent binding with hOAT is a minor component of the total inhibition which is unique relative to other monofluoro-substituted derivatives. Furthermore, based on the results of transient-state measurements and free energy calculations, it is suggested that the α,β-unsaturated carboxylate group of PLP-bound 5 may be directly involved in the inactivation cascade by forming an enolate intermediate. Overall, compound 5 exhibits unusual structural conversions which are catalyzed by specific residues within hOAT, ultimately leading to an enamine mechanism-based inactivation of hOAT through noncovalent interactions and covalent modification.
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Affiliation(s)
- Sida Shen
- Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Glaucio M. Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Daniel H. Grass
- Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Wei Zhu
- Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
| | - Neil L. Kelleher
- Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL 60208, USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660, USA
| | - Richard B. Silverman
- Department of Chemistry and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
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Richard JP, Moran GR. Preface. Methods Enzymol 2023; 685:xvii-xx. [PMID: 37245917 DOI: 10.1016/s0076-6879(23)00190-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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12
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Kenjić N, Meneely KM, Wherritt DJ, Denler MC, Jackson TA, Moran GR, Lamb AL. Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. J Am Chem Soc 2022; 144:12769-12780. [PMID: 35802469 PMCID: PMC9305975 DOI: 10.1021/jacs.2c03376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase)
is a magnesium-dependent
enzyme that excises the C4 of d-ribulose-5-phosphate (d-Ru5P) as formate. RibB generates the four-carbon substrate
for lumazine synthase that is incorporated into the xylene moiety
of lumazine and ultimately the riboflavin isoalloxazine. The reaction
was first identified by Bacher and co-workers in the 1990s, and their
chemical mechanism hypothesis became canonical despite minimal direct
evidence. X-ray crystal structures of RibB typically show two metal
ions when solved in the presence of non-native metals and/or liganding
non-substrate analogues, and the consensus hypothetical mechanism
has incorporated this cofactor set. We have used a variety of biochemical
approaches to further characterize the chemistry catalyzed by RibB
from Vibrio cholera (VcRibB). We show
that full activity is achieved at metal ion concentrations equal to
the enzyme concentration. This was confirmed by electron paramagnetic
resonance of the enzyme reconstituted with manganese and crystal structures
liganded with Mn2+ and a variety of sugar phosphates. Two
transient species prior to the formation of products were identified
using acid quench of single turnover reactions in combination with
NMR for singly and fully 13C-labeled d-Ru5P. These
data indicate that dehydration of C1 forms the first transient species,
which undergoes rearrangement by a 1,2 migration, fusing C5 to C3
and generating a hydrated C4 that is poised for elimination as formate.
Structures determined from time-dependent Mn2+ soaks of
VcRibB-d-Ru5P crystals show accumulation in crystallo of
the same intermediates. Collectively, these data reveal for the first
time crucial transient chemical states in the mechanism of RibB.
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Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Daniel J Wherritt
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Melissa C Denler
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Timothy A Jackson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Loyola, Chicago, Illinois 60660, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States.,Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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13
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Butrin A, Butrin A, Wawrzak Z, Moran GR, Liu D. Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase. J Biol Chem 2022; 298:101969. [PMID: 35460691 PMCID: PMC9136103 DOI: 10.1016/j.jbc.2022.101969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/17/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver and occurs predominantly in patients with underlying chronic liver diseases. Over the past decade, human ornithine aminotransferase (hOAT), which is an enzyme that catalyzes the metabolic conversion of ornithine into an intermediate for proline or glutamate synthesis, has been found to be overexpressed in HCC cells. hOAT has since emerged as a promising target for novel anticancer therapies, especially for the ongoing rational design effort to discover mechanism-based inactivators (MBIs). Despite the significance of hOAT in human metabolism and its clinical potential as a drug target against HCC, there are significant knowledge deficits with regard to its catalytic mechanism and structural characteristics. Ongoing MBI design efforts require in-depth knowledge of the enzyme active site, in particular, pKa values of potential nucleophiles and residues necessary for the molecular recognition of ligands. Here, we conducted a study detailing the fundamental active-site properties of hOAT using stopped-flow spectrophotometry and X-ray crystallography. Our results quantitatively revealed the pH dependence of the multistep reaction mechanism and illuminated the roles of ornithine α-amino and δ-amino groups in substrate recognition and in facilitating catalytic turnover. These findings provided insights of the catalytic mechanism that could benefit the rational design of MBIs against hOAT. In addition, substrate recognition and turnover of several fragment-sized alternative substrates of hOATs, which could serve as structural templates for MBI design, were also elucidated.
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Affiliation(s)
- Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Anastassiya Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
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14
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Zhu W, Butrin A, Melani RD, Doubleday PF, Ferreira GM, Tavares MT, Habeeb Mohammad TS, Beaupre BA, Kelleher NL, Moran GR, Liu D, Silverman RB. Rational Design, Synthesis, and Mechanism of (3 S,4 R)-3-Amino-4-(difluoromethyl)cyclopent-1-ene-1-carboxylic Acid: Employing a Second-Deprotonation Strategy for Selectivity of Human Ornithine Aminotransferase over GABA Aminotransferase. J Am Chem Soc 2022; 144:5629-5642. [PMID: 35293728 PMCID: PMC9181902 DOI: 10.1021/jacs.2c00924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that contains a similar active site to that of γ-aminobutyric acid aminotransferase (GABA-AT). Recently, pharmacological inhibition of hOAT was recognized as a potential therapeutic approach for hepatocellular carcinoma. In this work, we first studied the inactivation mechanisms of hOAT by two well-known GABA-AT inactivators (CPP-115 and OV329). Inspired by the inactivation mechanistic difference between these two aminotransferases, a series of analogues were designed and synthesized, leading to the discovery of analogue 10b as a highly selective and potent hOAT inhibitor. Intact protein mass spectrometry, protein crystallography, and dialysis experiments indicated that 10b was converted to an irreversible tight-binding adduct (34) in the active site of hOAT, as was the unsaturated analogue (11). The comparison of kinetic studies between 10b and 11 suggested that the active intermediate (17b) was only generated in hOAT and not in GABA-AT. Molecular docking studies and pKa computational calculations highlighted the importance of chirality and the endocyclic double bond for inhibitory activity. The turnover mechanism of 10b was supported by mass spectrometric analysis of dissociable products and fluoride ion release experiments. Notably, the stopped-flow experiments were highly consistent with the proposed mechanism, suggesting a relatively slow hydrolysis rate for hOAT. The novel second-deprotonation mechanism of 10b contributes to its high potency and significantly enhanced selectivity for hOAT inhibition.
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Affiliation(s)
- Wei Zhu
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Rafael D Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Peter F Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Mauricio T Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Thahani S Habeeb Mohammad
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Neil L Kelleher
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Richard B Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States.,Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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15
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Forouzesh DC, Moran GR. Mammalian dihydropyrimidine dehydrogenase. Arch Biochem Biophys 2021; 714:109066. [PMID: 34717904 DOI: 10.1016/j.abb.2021.109066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/26/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) catalyzes the two-electron reduction of pyrimidine bases uracil and thymine as the first step in pyrimidine catabolism. The enzyme achieves this simple chemistry using a complex cofactor set including two flavins and four Fe4S4 centers. The flavins, FAD and FMN, interact with respective NADPH and pyrimidine substrates and the iron-sulfur centers form an electron transfer wire that links the two active sites that are separated by 56 Å. DPD accepts the common antineoplastic agent 5-fluorouracil as a substrate and so undermines the establishment of efficacious toxicity. Though studied for multiple decades, a precise description of the behavior of the enzyme had remained elusive. It was recently shown that the active form of DPD has the cofactor set of FAD-4(Fe4S4)-FMNH2. This two-electron reduced state is consistent with fewer mechanistic possibilities and data suggests that the instigating and rate determining step in the catalytic cycle is reduction of the pyrimidine substrate that is followed by relatively rapid oxidation of NADPH at the FAD that, via the electron conduit of the 4(Fe4S4) centers, reinstates the FMNH2 cofactor for subsequent catalytic turnover.
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Affiliation(s)
- Dariush C Forouzesh
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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16
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Smith MM, Beaupre BA, Fourozesh DC, Meneely KM, Lamb AL, Moran GR. Finding Ways to Relax: A Revisionistic Analysis of the Chemistry of E. coli GTP Cyclohydrolase II. Biochemistry 2021; 60:3027-3039. [PMID: 34569786 DOI: 10.1021/acs.biochem.1c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanosine triphosphate (GTP) cyclohydrolase II (RibA) is one of three enzymes that hydrolytically cleave the C8-N9 bond of the GTP guanine. RibA also catalyzes a subsequent hydrolytic attack at the base liberating formate and in addition cleaves the α-β phosphodiester bond of the triphosphate to form pyrophosphate (PPi). These hydrolytic reactions are promoted by tandem active-site metal ions, zinc and magnesium, that respectively function at the GTP guanine and triphosphate moieties. The RibA reaction is part of riboflavin biosynthesis and forms 2,5-diamino-6-β-pyrimidinone 5'-phosphate, an exocyclic pyrimidine nucleotide that ultimately forms the pyrimidine ring of the isoalloxazine of riboflavin. The stoichiometry of the RibA reaction was defined in the study that first identified this activity in Escherichia coli (Foor, F., Brown, G. M. J. Biol. Chem., 1975, 250, 9, 3545-3551) and has not been quantitatively evaluated in subsequent works. Using primarily transient state approaches we examined the interaction of RibA from E. coli with the GTP, inosine triphosphate, and PPi. Our data indicate that PPi is a slow substrate for RibA that is cleaved to form two phosphate ions (Pi). A combination of real-time enzymatically coupled Pi reporter assays and end-point 31P NMR revealed that Pi is formed at a catalytically relevant rate in the native reaction of RibA with GTP, redefining the reaction stoichiometry. Furthermore, our data indicate that both PPi and GTP stimulate conformational changes prior to hydrolytic chemistry, and we conclude that the cleavage of PPi bound as a substrate or an intermediate state results in conformational relaxation.
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Affiliation(s)
- Madison M Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Dariush C Fourozesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Kathleen M Meneely
- Department of Chemistry, University of Texas San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Audrey L Lamb
- Department of Chemistry, University of Texas San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
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17
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Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB. Turnover and Inactivation Mechanisms for ( S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase. J Am Chem Soc 2021; 143:8689-8703. [PMID: 34097381 PMCID: PMC8367020 DOI: 10.1021/jacs.1c02456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inhibition of human ornithine δ-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
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Affiliation(s)
- Sida Shen
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Peter F. Doubleday
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D. Melani
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Mauricio T. Tavares
- Department of Molecular Medicine, Scripps Research, Jupiter, Florida 33458, United States
| | - Glaucio M. Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, 05508-000, Brazil
| | - Neil L. Kelleher
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
| | - Richard B. Silverman
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States,Department of Pharmacology, Northwestern University, Chicago, Illinois, 60611, United States,Corresponding authors: (R.B.S.) . Phone: +1-847-491-5653; (D.L.) . Phone: +1-773-508-3093
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18
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Beaupre BA, Forouzesh DC, Butrin A, Liu D, Moran GR. Perturbing the Movement of Hydrogens to Delineate and Assign Events in the Reductive Activation and Turnover of Porcine Dihydropyrimidine Dehydrogenase. Biochemistry 2021; 60:1764-1775. [PMID: 34032117 DOI: 10.1021/acs.biochem.1c00243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The native function of dihydropyrimidine dehydrogenase (DPD) is to reduce the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons obtained from NADPH. NADPH and pyrimidines bind at separate active sites separated by ∼60 Å that are bridged by four Fe4S4 centers. We have shown that DPD undergoes reductive activation, taking up two electrons from NADPH [Beaupre, B. A., et al. (2020) Biochemistry 59, 2419-2431]. pH studies indicate that the rate of turnover is not controlled by the protonation state of the general acid, cysteine 671. The activation of the C671 variants is delineated into two phases particularly at low pH values. Spectral deconvolution of the delineated reductive activation reaction reveals that the initial phase results in the accumulation of charge transfer absorption added to the binding difference spectrum for NADPH. The second phase results in reduction of one of the two flavins. X-ray crystal structure analysis of the C671S variant soaked with NADPH and the slow substrate, thymine, in a low-oxygen atmosphere resolved the presumed activated form of the enzyme that has the FMN cofactor reduced. These data reveal that charge transfer arises from the proximity of the NADPH and FAD bases and that the ensuing flavin is a result of rapid transfer of electrons to the FMN without accumulation of reduced forms of the FAD or Fe4S4 centers. These data suggest that the slow rate of turnover of DPD is governed by the movement of a mobile structural feature that carries the C671 residue.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Dariush C Forouzesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
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19
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Forouzesh DC, Beaupre BA, Butrin A, Wawrzak Z, Liu D, Moran GR. The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry 2021; 60:1120-1132. [PMID: 33755421 DOI: 10.1021/acs.biochem.1c00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is a complex enzyme that reduces the 5,6-vinylic bond of pyrimidines, uracil, and thymine. 5-Fluorouracil (5FU) is also a substrate for DPD and a common chemotherapeutic agent used to treat numerous cancers. The reduction of 5FU to 5-fluoro-5,6-dihydrouracil negates its toxicity and efficacy. Patients with high DPD activity levels typically have poor outcomes when treated with 5FU. DPD is thus a central mitigating factor in the treatment of a variety of cancers. 5-Ethynyluracil (5EU) covalently inactivates DPD by cross-linking with the active-site general acid cysteine in the pyrimidine binding site. This reaction is dependent on the simultaneous binding of 5EU and nicotinamide adenine dinucleotide phosphate (NADPH). This ternary complex induces DPD to become activated by taking up two electrons from the NADPH. The covalent inactivation of DPD by 5EU occurs concomitantly with this reductive activation with a rate constant of ∼0.2 s-1. This kinact value is correlated with the rate of reduction of one of the two flavin cofactors and the localization of a mobile loop in the pyrimidine active site that places the cysteine that serves as the general acid in catalysis proximal to the 5EU ethynyl group. Efficient cross-linking is reliant on enzyme activation, but this process appears to also have a conformational aspect in that nonreductive NADPH analogues can also induce a partial inactivation. Cross-linking then renders DPD inactive by severing the proton-coupled electron transfer mechanism that transmits electrons 56 Å across the protein.
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Affiliation(s)
- Dariush C Forouzesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Arseniy Butrin
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States
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20
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Butrin A, Beaupre BA, Kadamandla N, Zhao P, Shen S, Silverman RB, Moran GR, Liu D. Structural and Kinetic Analyses Reveal the Dual Inhibition Modes of Ornithine Aminotransferase by (1 S,3 S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic Acid (BCF 3). ACS Chem Biol 2021; 16:67-75. [PMID: 33316155 PMCID: PMC8474141 DOI: 10.1021/acschembio.0c00728] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common form of liver cancer and the leading cause of death among people with cirrhosis. HCC is typically diagnosed in advanced stages when tumors are resistant to both radio- and chemotherapy. Human ornithine aminotransferase (hOAT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme involved in glutamine and proline metabolism. Because hOAT is overexpressed in HCC cells and a contributing factor for the uncontrolled cellular division that propagates malignant tumors (Ueno et al. J. Hepatol. 2014, 61, 1080-1087), it is a potential drug target for the treatment of HCC. (1S,3S)-3-Amino-4-(hexafluoropropan-2-ylidenyl)-cyclopentane-1-carboxylic acid (BCF3) has been shown in animal models to slow the progression of HCC by acting as a selective and potent mechanism-based inactivator of OAT (Zigmond et al. ACS Med. Chem. Lett. 2015, 6, 840-844). Previous studies have shown that the BCF3-hOAT reaction has a bifurcation in which only 8% of the inhibitor inactivates the enzyme while the remaining 92% ultimately acts as a substrate and undergoes hydrolysis to regenerate the active PLP form of the enzyme. In this manuscript, the rate-limiting step of the inactivation mechanism was determined by stopped-flow spectrophotometry and time-dependent 19F NMR experiments to be the decay of a long-lived external aldimine species. A crystal structure of this transient complex revealed both the structural basis for fractional irreversible inhibition and the principal mode of inhibition of hOAT by BCF3, which is to trap the enzyme in this transient but quasi-stable external aldimine form.
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Affiliation(s)
- Arseniy Butrin
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Brett A. Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Noel Kadamandla
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Peidong Zhao
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Sida Shen
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208
| | - Richard B. Silverman
- Department of Chemistry, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Rd, Evanston, IL 60208,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208; Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660
| | - Dali Liu
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL 60660.,Corresponding author; phone: (773)508-3093;
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21
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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22
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Roman JV, Melkonian TR, Silvaggi NR, Moran GR. Correction to “Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States”. Biochemistry 2020; 59:3284. [DOI: 10.1021/acs.biochem.0c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Beaupre BA, Reabe KR, Roman JV, Moran GR. Hydrogen movements in the oxidative half-reaction of kynurenine 3-monooxygenase from Pseudomonas fluorescens reveal the mechanism of hydroxylation. Arch Biochem Biophys 2020; 690:108474. [PMID: 32687799 DOI: 10.1016/j.abb.2020.108474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022]
Abstract
Kynurenine 3-monoxygenase (KMO) catalyzes the conversion of l-kynurenine (L-Kyn) to 3-hydroxykynurenine (3-OHKyn) in the pathway for tryptophan catabolism. We have investigated the effects of pH and deuterium substitution on the oxidative half-reaction of KMO from P. fluorescens (PfKMO). The three phases observed during the oxidative half reaction are formation of the hydroperoxyflavin, hydroxylation and product release. The measured rate constants for these phases proved largely unchanging with pH, suggesting that the KMO active site is insulated from exchange with solvent during catalysis. A solvent inventory study indicated that a solvent isotope effect of 2-3 is observed for the hydroxylation phase and that two or more protons are in flight during this step. An inverse isotope effect of 0.84 ± 0.01 on the rate constant for the hydroxylation step with ring perdeutero-L-Kyn as a substrate indicates a shift from sp2 to sp3 hybridization in the transition state leading to the formation of a non-aromatic intermediate. The pH dependence of transient state data collected for the substrate analog meta-nitrobenzoylalanine indicate that groups proximal to the hydroperoxyflavin are titrated in the range pH 5-8.5 and can be described by a pKa of 8.8. That higher pH values do not slow the rate of hydroxylation precludes that the pKa measured pertains to the proton of the hydroperoxflavin. Together, these observations indicate that the C4a-hydroperoxyflavin has a pKa ≫ 8.5, that a non-aromatic species is the immediate product of hydroxylation and that at least two solvent derived protons are in-flight during oxygen insertion to the substrate aromatic ring. A unifying mechanistic proposal for these observations is proposed.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Karen R Reabe
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI, 53211-3029, USA
| | - Joseph V Roman
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.
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Beaupre BA, Roman JV, Moran GR. An improved method for the expression and purification of porcine dihydropyrimidine dehydrogenase. Protein Expr Purif 2020; 171:105610. [DOI: 10.1016/j.pep.2020.105610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/19/2019] [Accepted: 02/18/2020] [Indexed: 11/17/2022]
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Beaupre BA, Forouzesh DC, Moran GR. Transient-State Analysis of Porcine Dihydropyrimidine Dehydrogenase Reveals Reductive Activation by NADPH. Biochemistry 2020; 59:2419-2431. [PMID: 32516529 DOI: 10.1021/acs.biochem.0c00223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) catalyzes the initial step in the catabolism of the pyrimidines uracil and thymine. Crystal structures have revealed an elaborate subunit architecture consisting of two flavin cofactors, apparently linked by four Fe4S4 centers. Analysis of the DPD reaction(s) equilibrium position under anaerobic conditions revealed a reaction that favors dihydropyrimidine formation. Single-turnover analysis shows biphasic kinetics. The serine variant of the candidate general acid, cysteine 671, provided enhanced kinetic resolution for these phases. In the first event, one subunit of the DPD dimer takes up two electrons from NADPH in a reductive activation. Spectrophotometric deconvolution suggests that these electrons reside on one of the two flavins. The fact that oxidation of the enzyme by dioxygen can be suppressed by the addition of pyrimidine is consistent with these electrons residing on the FMN. The second phase involves further oxidation of NADPH and concomitant reduction of the pyrimidine substrate. During this phase no net reduction of DPD cofactors is observed, indicating that the entire cofactor set acts as a wire, transmitting electrons from NADPH to the pyrimidine rapidly. This indicates that the availability of the proton from the C671 general acid controls the transmittance of electrons from NADPH to the pyrimidine. Acid quench and high-performance liquid chromatography product analysis of single-turnover reactions with limiting NADPH confirmed a 2:1 NADPH:pyrimidine stoichiometry for the enzyme, accounting for successive activation and pyrimidine reduction. These data support an alternating subunit model in which one protomer is activated and turns over before the other subunit can be activated and enter catalysis.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Dariush C Forouzesh
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60660, United States
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McFarlane JS, Zhang J, Wang S, Lei X, Moran GR, Lamb AL. Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores. J Biol Chem 2019; 294:17988-18001. [PMID: 31615895 DOI: 10.1074/jbc.ra119.011059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Indexed: 11/06/2022] Open
Abstract
Pseudopaline and staphylopine are opine metallophores biosynthesized by Pseudomonas aeruginosa and Staphylococcus aureus, respectively. The final step in opine metallophore biosynthesis is the condensation of the product of a nicotianamine (NA) synthase reaction (i.e. l-HisNA for pseudopaline and d-HisNA for staphylopine) with an α-keto acid (α-ketoglutarate for pseudopaline and pyruvate for staphylopine), which is performed by an opine dehydrogenase. We hypothesized that the opine dehydrogenase reaction would be reversible only for the opine metallophore product with (R)-stereochemistry at carbon C2 of the α-keto acid (prochiral prior to catalysis). A kinetic analysis using stopped-flow spectrometry with (R)- or (S)-staphylopine and kinetic and structural analysis with (R)- and (S)-pseudopaline confirmed catalysis in the reverse direction for only (R)-staphylopine and (R)-pseudopaline, verifying the stereochemistry of these two opine metallophores. Structural analysis at 1.57-1.85 Å resolution captured the hydrolysis of (R)-pseudopaline and allowed identification of a binding pocket for the l-histidine moiety of pseudopaline formed through a repositioning of Phe-340 and Tyr-289 during the catalytic cycle. Transient-state kinetic analysis revealed an ordered release of NADP+ followed by staphylopine, with staphylopine release being the rate-limiting step in catalysis. Knowledge of the stereochemistry for opine metallophores has implications for future studies involving kinetic analysis, as well as opine metallophore transport, metal coordination, and the generation of chiral amines for pharmaceutical development.
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Affiliation(s)
- Jeffrey S McFarlane
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Jian Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Sanshan Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University, Chicago, Illinois 60660
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
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Roman JV, Melkonian TR, Silvaggi NR, Moran GR. Transient-State Analysis of Human Isocitrate Dehydrogenase I: Accounting for the Interconversion of Active and Non-Active Conformational States. Biochemistry 2019; 58:5366-5380. [PMID: 31478653 DOI: 10.1021/acs.biochem.9b00518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human isocitrate dehydrogenase 1 (HsICDH1) is a cytoplasmic homodimeric Mg(II)-dependent enzyme that converts d-isocitrate (D-ICT) and NADP+ to α-ketoglutarate (AKG), CO2, and NADPH. The active sites are formed at the subunit interface and incorporate residues from both protomers. The turnover number titrates hyperbolically from 17.5 s-1 to a minimum of 7 s-1 with an increasing enzyme concentration. As isolated, the enzyme adopts an inactive open conformation and binds NADPH tightly. The open conformation displaces three of the eight residues that bind D-ICT and Mg(II). Enzyme activation occurs with the addition of Mg(II) or D-ICT with a rate constant of 0.12 s-1. The addition of both Mg(II) and D-ICT activates the enzyme with a rate constant of 0.6 s-1 and displaces half of the bound NADPH. This indicates that HsICDH1 may have a half-site mechanism in which the active sites alternate in catalysis. The X-ray crystal structure of the half-site activated complex reveals asymmetry in the homodimer with a single NADPH bound. The structure also indicates a pseudotetramer interface that impedes the egress of NADPH consistent with the suppression of the turnover number at high enzyme concentrations. When the half-site activated form of the enzyme is reacted with NADP+, NADPH forms with a rate constant of 204 s-1 followed by a shift in the NADPH absorption spectrum with a rate constant of 28 s-1. These data indicate the accumulation of two intermediate states. Once D-ICT is exhausted, HsICDH1 relaxes to the inactive open state with a rate constant of ∼3 s-1.
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Affiliation(s)
- Joseph V Roman
- Department of Chemistry and Biochemistry , Loyola University Chicago , Flanner Hall, 1068 West Sheridan Road , Chicago , Illinois 60660 , United States
| | - Trevor R Melkonian
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211-3209 , United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211-3209 , United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry , Loyola University Chicago , Flanner Hall, 1068 West Sheridan Road , Chicago , Illinois 60660 , United States
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Kenjic N, Moran GR, Lamb AL. 3,4‐dihydroxy‐2‐butanone‐4‐phosphate synthase (RibB) of riboflavin biosynthesis has a mononuclear magnesium active site. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.633.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nikola Kenjic
- Department of Molecular BiosciencesUniversity of KansasLawrenceKS
| | - Graham R Moran
- Department of Chemistry and BiochemistryUniversity of LoyolaChicagoIL
| | - Audrey L Lamb
- Department of Molecular BiosciencesUniversity of KansasLawrenceKS
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McFarlane JS, Davis CL, Moran GR, Lamb AL. An Opine on Opines: Characterizing Opine Metallophore Biosynthesis in Bacterial Pathogens. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.781.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kenjić N, Hoag MR, Moraski GC, Caperelli CA, Moran GR, Lamb AL. PvdF of pyoverdin biosynthesis is a structurally unique N 10-formyltetrahydrofolate-dependent formyltransferase. Arch Biochem Biophys 2019; 664:40-50. [PMID: 30689984 DOI: 10.1016/j.abb.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 11/17/2022]
Abstract
The hydroxyornithine transformylase from Pseudomonas aeruginosa is known by the gene name pvdF, and has been hypothesized to use N10-formyltetrahydrofolate (N10-fTHF) as a co-substrate formyl donor to convert N5-hydroxyornithine (OHOrn) to N5-formyl- N5-hydroxyornithine (fOHOrn). PvdF is in the biosynthetic pathway for pyoverdin biosynthesis, a siderophore generated under iron-limiting conditions that has been linked to virulence, quorum sensing and biofilm formation. The structure of PvdF was determined by X-ray crystallography to 2.3 Å, revealing a formyltransferase fold consistent with N10-formyltetrahydrofolate dependent enzymes, such as the glycinamide ribonucleotide transformylases, N-sugar transformylases and methionyl-tRNA transformylases. Whereas the core structure, including the catalytic triad, is conserved, PvdF has three insertions of 18 or more amino acids, which we hypothesize are key to binding the OHOrn substrate. Steady state kinetics revealed a non-hyperbolic rate curve, promoting the hypothesis that PvdF uses a random-sequential mechanism, and favors folate binding over OHOrn.
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Affiliation(s)
- Nikola Kenjić
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - Garrett C Moraski
- Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA
| | - Carol A Caperelli
- Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA
| | - Graham R Moran
- Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Audrey L Lamb
- Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.
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Moran GR. Anaerobic methods for the transient-state study of flavoproteins: The use of specialized glassware to define the concentration of dioxygen. Methods Enzymol 2019; 620:27-49. [DOI: 10.1016/bs.mie.2019.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
Within the last two years catalytic substrates for renalase have been identified, some 10 years after its initial discovery. 2- and 6-dihydronicotinamide (2- and 6-DHNAD) isomers of β-NAD(P)H (4-dihydroNAD(P)) are rapidly oxidized by renalase to form β-NAD(P)+. The two electrons liberated are then passed to molecular oxygen by the renalase FAD cofactor forming hydrogen peroxide. This activity would appear to serve an intracellular detoxification/metabolite repair function that alleviates inhibition of primary metabolism dehydrogenases by 2- and 6-DHNAD molecules. This activity is supported by the complete structural assignment of the substrates, comprehensive kinetic analyses, defined species specific substrate specificity profiles and X-ray crystal structures that reveal ligand complexation consistent with this activity. This apparently intracellular function for the renalase enzyme is not allied with the majority of the renalase research that holds renalase to be a secreted mammalian protein that functions in blood to elicit a broad array of profound physiological changes. In this review a description of renalase as an enzyme is presented and an argument is offered that its enzymatic function can now reasonably be assumed to be uncoupled from whole organism physiological influences.
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Affiliation(s)
- Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, WI 53211-3209, United States.
| | - Matthew R Hoag
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, WI 53211-3209, United States
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Beaupre BA, Roman JV, Hoag MR, Meneely KM, Silvaggi NR, Lamb AL, Moran GR. Ligand binding phenomena that pertain to the metabolic function of renalase. Arch Biochem Biophys 2016; 612:46-56. [PMID: 27769837 PMCID: PMC5522708 DOI: 10.1016/j.abb.2016.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/07/2023]
Abstract
Renalase catalyzes the oxidation of isomers of β-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form β-NAD(P)+. This activity is thought to alleviate inhibition of multiple β-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (kred/Kd) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only β-NADH and β-NADPH compete with dinucleotide substrates for access to the active site.
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Affiliation(s)
- Brett A. Beaupre
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, Wisconsin 53211-3209
| | - Joseph V. Roman
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, Wisconsin 53211-3209
| | - Matthew R. Hoag
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, Wisconsin 53211-3209
| | - Kathleen M. Meneely
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66049
| | - Nicholas R. Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, Wisconsin 53211-3209
| | - Audrey L. Lamb
- Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave, Lawrence, KS 66049
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St, Milwaukee, Wisconsin 53211-3209.,To whom correspondence should be addressed: Ph: (414) 940 0059, Fax: (414) 229 5530,
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Peek J, Roman J, Moran GR, Christendat D. Structurally diverse dehydroshikimate dehydratase variants participate in microbial quinate catabolism. Mol Microbiol 2016; 103:39-54. [DOI: 10.1111/mmi.13542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2016] [Indexed: 11/30/2022]
Affiliation(s)
- James Peek
- Department of Cell and Systems BiologyUniversity of Toronto25 Willcocks StreetToronto, Ontario CanadaM5S 3B2
| | - Joseph Roman
- Department of Chemistry and BiochemistryUniversity of Wisconsin‐Milwaukee3210 North Cramer StreetMilwaukee WI53211‐3209 USA
| | - Graham R. Moran
- Department of Chemistry and BiochemistryUniversity of Wisconsin‐Milwaukee3210 North Cramer StreetMilwaukee WI53211‐3209 USA
| | - Dinesh Christendat
- Department of Cell and Systems BiologyUniversity of Toronto25 Willcocks StreetToronto, Ontario CanadaM5S 3B2
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoToronto, Ontario CanadaM5S 3B2
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Jeitner TM, Kalogiannis M, Krasnikov BF, Gomolin I, Peltier MR, Moran GR. Linking Inflammation and Parkinson Disease: Hypochlorous Acid Generates Parkinsonian Poisons. Toxicol Sci 2016; 153:410. [PMID: 27672164 DOI: 10.1093/toxsci/kfw149] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
![]()
The shikimate pathway of bacteria,
fungi, and plants generates
chorismate, which is drawn into biosynthetic pathways that form aromatic
amino acids and other important metabolites, including folates, menaquinone,
and siderophores. Many of the pathways initiated at this branch point
transform chorismate using an MST enzyme. The MST enzymes (menaquinone, siderophore, and tryptophan biosynthetic enzymes) are structurally homologous and magnesium-dependent,
and all perform similar chemical permutations to chorismate by nucleophilic
addition (hydroxyl or amine) at the 2-position of the ring, inducing
displacement of the 4-hydroxyl. The isomerase enzymes release isochorismate
or aminodeoxychorismate as the product, while the synthase enzymes
also have lyase activity that displaces pyruvate to form either salicylate
or anthranilate. This has led to the hypothesis that the isomerase
and lyase activities performed by the MST enzymes are functionally
conserved. Here we have developed tailored pre-steady-state approaches
to establish the kinetic mechanisms of the isochorismate and salicylate
synthase enzymes of siderophore biosynthesis. Our data are centered
on the role of magnesium ions, which inhibit the isochorismate synthase
enzymes but not the salicylate synthase enzymes. Prior structural
data have suggested that binding of the metal ion occludes access
or egress of substrates. Our kinetic data indicate that for the production
of isochorismate, a high magnesium ion concentration suppresses the
rate of release of product, accounting for the observed inhibition
and establishing the basis of the ordered-addition kinetic mechanism.
Moreover, we show that isochorismate is channeled through the synthase
reaction as an intermediate that is retained in the active site by
the magnesium ion. Indeed, the lyase-active enzyme has 3 orders of
magnitude higher affinity for the isochorismate complex relative to
the chorismate complex. Apparent negative-feedback inhibition by ferrous
ions is documented at nanomolar concentrations, which is a potentially
physiologically relevant mode of regulation for siderophore biosynthesis
in vivo.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
| | - Jesse A Sundlov
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Andrew M Gulick
- Hauptman-Woodward Medical Research Institute , 700 Ellicott Street, Buffalo, New York 14203, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53201, United States
| | - Audrey L Lamb
- Department of Molecular Biosciences, University of Kansas , Lawrence, Kansas 66045, United States
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Jeitner TM, Kalogiannis M, Krasnikov BF, Gomolin I, Peltier MR, Moran GR. Linking Inflammation and Parkinson Disease: Hypochlorous Acid Generates Parkinsonian Poisons. Toxicol Sci 2016; 151:388-402. [PMID: 27026709 DOI: 10.1093/toxsci/kfw052] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Inflammation is a common feature of Parkinson Disease and other neurodegenerative disorders. Hypochlorous acid (HOCl) is a reactive oxygen species formed by neutrophils and other myeloperoxidase-containing cells during inflammation. HOCl chlorinates the amine and catechol moieties of dopamine to produce chlorinated derivatives collectively termed chlorodopamine. Here, we report that chlorodopamine is toxic to dopaminergic neurons both in vivo and in vitro Intrastriatal administration of 90 nmol chlorodopamine to mice resulted in loss of dopaminergic neurons from the substantia nigra and decreased ambulation-results that were comparable to those produced by the same dose of the parkinsonian poison, 1-methyl-4-phenylpyridinium (MPP+). Chlorodopamine was also more toxic to differentiated SH SY5Y cells than HOCl. The basis of this selective toxicity is likely mediated by chlorodopamine uptake through the dopamine transporter, as expression of this transporter in COS-7 cells conferred sensitivity to chlorodopamine toxicity. Pharmacological blockade of the dopamine transporter also mitigated the deleterious effects of chlorodopamine in vivo The cellular actions of chlorodopamine included inactivation of the α-ketoglutarate dehydrogenase complex, as well as inhibition of mitochondrial respiration. The latter effect is consistent with inhibition of cytochrome c oxidase. Illumination at 670 nm, which stimulates cytochrome c oxidase, reversed the effects of chlorodopamine. The observed changes in mitochondrial biochemistry were also accompanied by the swelling of these organelles. Overall, our findings suggest that chlorination of dopamine by HOCl generates toxins that selectively kill dopaminergic neurons in the substantia nigra in a manner comparable to MPP+.
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Affiliation(s)
- Thomas M Jeitner
- *Department of Biochemistry and Molecular Biology, New York Medical College, Basic Science, Valhalla, NY 10595; Department of Biomedical Research
| | | | | | - Irving Gomolin
- Department of Geriatrics, Winthrop University Hospital, Mineola, NY 11501
| | | | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin - Milwaukee, Milwaukee, WI 53211
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Han L, Schwabacher AW, Moran GR, Silvaggi NR. Streptomyces wadayamensis MppP Is a Pyridoxal 5′-Phosphate-Dependent l-Arginine α-Deaminase, γ-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry 2015; 54:7029-40. [DOI: 10.1021/acs.biochem.5b01016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lanlan Han
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Alan W. Schwabacher
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Graham R. Moran
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
| | - Nicholas R. Silvaggi
- Department of Chemistry and
Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211, United States
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Hoag MR, Roman J, Beaupre BA, Silvaggi NR, Moran GR. Bacterial Renalase: Structure and Kinetics of an Enzyme with 2- and 6-Dihydro-β-NAD(P) Oxidase Activity from Pseudomonas phaseolicola. Biochemistry 2015; 54:3791-802. [PMID: 26016690 DOI: 10.1021/acs.biochem.5b00451] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Despite a lack of convincing in vitro evidence and a number of sound refutations, it is widely accepted that renalase is an enzyme unique to animals that catalyzes the oxidative degradation of catecholamines in blood in order to lower vascular tone. Very recently, we identified isomers of β-NAD(P)H as substrates for renalase (Beaupre, B. A. et al. (2015) Biochemistry, 54, 795-806). These molecules carry the hydride equivalent on the 2 or 6 position of the nicotinamide base and presumably arise in nonspecific redox reactions of nicotinamide dinucleotides. Renalase serves to rapidly oxidize these isomers to form β-NAD(P)⁺ and then pass the electrons to dioxygen, forming H₂O₂. We have also shown that these substrate molecules are highly inhibitory to dehydrogenase enzymes and thus have proposed an intracellular metabolic role for this enzyme. Here, we identify a renalase from an organism without a circulatory system. This bacterial form of renalase has the same substrate specificity profile as that of human renalase but, in terms of binding constant (K(d)), shows a marked preference for substrates derived from β-NAD⁺. 2-dihydroNAD(P) substrates reduce the enzyme with rate constants (k(red)) that greatly exceed those for 6-dihydroNAD(P) substrates. Taken together, k(red)/K(d) values indicate a minimum 20-fold preference for 2DHNAD. We also offer the first structures of a renalase in complex with catalytically relevant ligands β-NAD⁺ and β-NADH (the latter being an analogue of the substrate(s)). These structures show potential electrostatic repulsion interactions with the product and a unique binding orientation for the substrate nicotinamide base that is consistent with the identified activity.
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Affiliation(s)
- Matthew R Hoag
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Joseph Roman
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Brett A Beaupre
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Nicholas R Silvaggi
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
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Shah DD, Moran GR. 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase: 2-Oxo Acid-Dependent Oxygenases of Importance to Agriculture and Medicine. 2-Oxoglutarate-Dependent Oxygenases 2015. [DOI: 10.1039/9781782621959-00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Despite a separate evolutionary lineage, 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate synthase (HMS) are appropriately grouped with the 2-oxo acid-dependent oxygenase (2OADO) family of enzymes. HPPD and HMS accomplish highly similar overall chemistry to that observed in the majority of 2OADOs but require only two substrates rather than three. 2OADOs typically use the 2-oxo acid of 2-oxoglutarate (2OG) as a source of electrons to reduce and activate dioxygen in order to oxidize a third specific substrate. HPPD and HMS use instead the pyruvate substituent of 4-hydroxyphenylpyruvate to activate dioxygen and then proceed to also hydroxylate this substrate, each yielding a distinctly different aromatic product. HPPD catalyses the second and committed step of tyrosine catabolism, a pathway common to nearly all aerobes. Plants require the HPPD reaction to biosynthesize plastoquinones and therefore HPPD inhibitors can have potent herbicidal activity. The ubiquity of the HPPD reaction, however, has meant that HPPD-specific molecules developed as herbicides have other uses in different forms of life. In humans herbicidal HPPD inhibitors can be used therapeutically to alleviate specific inborn defects and also to retard the progress of certain bacterial and fungal infections. This review is intended as a concise overview of the contextual and catalytic chemistries of HPPD and HMS.
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Affiliation(s)
- Dhara D. Shah
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee 3210 N. Cramer St Milwaukee WI 53211-3209 USA
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Beaupre BA, Hoag MR, Roman J, Försterling FH, Moran GR. Metabolic function for human renalase: oxidation of isomeric forms of β-NAD(P)H that are inhibitory to primary metabolism. Biochemistry 2015; 54:795-806. [PMID: 25531177 DOI: 10.1021/bi5013436] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Renalase is a recently identified flavoprotein that has been associated with numerous physiological maladies. There remains a prevailing belief that renalase functions as a hormone, imparting an influence on vascular tone and heart rate by oxidizing circulating catecholamines, chiefly epinephrine. This activity, however, has not been convincingly demonstrated in vitro, nor has the stoichiometry of this transformation been shown. In prior work we demonstrated that renalase induced rapid oxidation of low-level contaminants of β-NAD(P)H solutions ( Beaupre, B. A. et al. (2013) Biochemistry 52 , 8929 - 8937 ; Beaupre, B. A. et al. (2013) J. Am. Chem. Soc . 135 , 13980 - 13987 ). Slow aqueous speciation of β-NAD(P)H resulted in the production of renalase substrate molecules whose spectrophotometric characteristics and equilibrium fractional accumulation closely matched those reported for α-anomers of NAD(P)H. The fleeting nature of these substrates precluded structural assignment. Here we structurally assign and identify two substrates for renalase. These molecules are 2- and 6-dihydroNAD(P), isomeric forms of β-NAD(P)H that arise either by nonspecific reduction of β-NAD(P)(+) or by tautomerization of β-NAD(P)H (4-dihydroNAD(P)). The pure preparations of these molecules induce rapid reduction of the renalase flavin cofactor (230 s(-1) for 6-dihydroNAD, 850 s(-1) for 2-dihydroNAD) but bind only a few fold more tightly than β-NADH. We also show that 2- and 6-dihydroNAD(P) are potent inhibitors of primary metabolism dehydrogenases and therefore conclude that the metabolic function of renalase is to oxidize these isomeric NAD(P)H molecules to β-NAD(P)(+), eliminating the threat they pose to normal respiratory activity.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
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Youngblut M, Pauly DJ, Stein N, Walters D, Conrad JA, Moran GR, Bennett B, Pacheco AA. Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) does not disproportionate hydroxylamine to ammonia and nitrite, despite a strongly favorable driving force. Biochemistry 2014; 53:2136-44. [PMID: 24645742 DOI: 10.1021/bi401705d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c nitrite reductase (ccNiR) from Shewanella oneidensis, which catalyzes the six-electron reduction of nitrite to ammonia in vivo, was shown to oxidize hydroxylamine in the presence of large quantities of this substrate, yielding nitrite as the sole free nitrogenous product. UV-visible stopped-flow and rapid-freeze-quench electron paramagnetic resonance data, along with product analysis, showed that the equilibrium between hydroxylamine and nitrite is fairly rapidly established in the presence of high initial concentrations of hydroxylamine, despite said equilibrium lying far to the left. By contrast, reduction of hydroxylamine to ammonia did not occur, even though disproportionation of hydroxylamine to yield both nitrite and ammonia is strongly thermodynamically favored. This suggests a kinetic barrier to the ccNiR-catalyzed reduction of hydroxylamine to ammonia. A mechanism for hydroxylamine reduction is proposed in which the hydroxide group is first protonated and released as water, leaving what is formally an NH2(+) moiety bound at the heme active site. This species could be a metastable intermediate or a transition state but in either case would exist only if it were stabilized by the donation of electrons from the ccNiR heme pool into the empty nitrogen p orbital. In this scenario, ccNiR does not catalyze disproportionation because the electron-donating hydroxylamine does not poise the enzyme at a sufficiently low potential to stabilize the putative dehydrated hydroxylamine; presumably, a stronger reductant is required for this.
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53211, United States
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Beaupre BA, Hoag MR, Carmichael BR, Moran GR. Kinetics and equilibria of the reductive and oxidative half-reactions of human renalase with α-NADPH. Biochemistry 2013; 52:8929-37. [PMID: 24266457 DOI: 10.1021/bi401185m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Renalase is a recently discovered flavoprotein that has been reported to be a hormone produced by the kidney to down-modulate blood pressure and heart rate. The consensus belief has been that renalase oxidizes circulating catecholamine neurotransmitters thereby attenuating vascular tone. However, a convincing in vitro demonstration of this activity has not been made. We have recently discovered that renalase has α-NAD(P)H oxidase/anomerase activity. Unlike most naturally occurring nucleotides, NAD(P)H can accumulate small amounts of the α-anomers that once oxidized are configurationally stable and unable to participate in cellular activity. Thus, anomerization of NAD(P)H would result in a continual loss of cellular redox currency. As such, it appears that the root purpose of renalase is to return α-anomers of nicotinamide dinucleotides to the β-anomer pool. In this article, we measure the kinetics and equilibria of renalase in turnover with α-NADPH. Renalase is selective for the α-anomer, which binds with a dissociation constant of ∼20±3 μM. This association precedes monophasic two-electron reduction of the FAD cofactor with a rate constant of 40.2±1.3 s(-1). The reduced enzyme then delivers both electrons to dioxygen in a second-order reaction with a rate constant of ∼2900 M(-1) s(-1). Renalase has modest affinity for its β-NADP+ product (Kd=2.2 mM), and the FAD cofactor has a reduction potential of -155 mV that is unaltered by saturating β-NADP+. Together these data suggest that the products are formed and released in a kinetically ordered sequence (β-NADP+ then H2O2), however, the reoxidation of renalase is not contingent on the dissociation of β-NADP+. Neither the oxidized nor the reduced form of renalase is able to catalyze anomerization, implying that the redox and anomerization chemistries are inextricably linked through a common intermediate.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 N. Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
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Abstract
Renalase is a protein hormone secreted into the blood by the kidney that is reported to lower blood pressure and slow heart rate. Since its discovery in 2005, renalase has been the subject of conjecture pertaining to its catalytic function. While it has been widely reported that renalase is the third monoamine oxidase (monoamine oxidase C) that oxidizes circulating catecholamines such as epinephrine, there has been no convincing demonstration of this catalysis in vitro. Renalase is a flavoprotein whose structural topology is similar to known oxidases, lysine demethylases, and monooxygenases, but its active site bears no resemblance to that of any known flavoprotein. We have identified the catalytic activity of renalase as an α-NAD(P)H oxidase/anomerase, whereby low equilibrium concentrations of the α-anomer of NADPH and NADH initiate rapid reduction of the renalase flavin cofactor. The reduced cofactor then reacts with dioxygen to form hydrogen peroxide and releases nicotinamide dinucleotide product in the β-form. These processes yield an apparent turnover number (0.5 s(-1) in atmospheric dioxygen) that is at least 2 orders of magnitude more rapid than any reported activity with catechol neurotransmitters. This highly novel activity is the first demonstration of a role for naturally occurring α-NAD(P)H anomers in mammalian physiology and the first report of a flavoprotein catalyzing an epimerization reaction.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , 3210 N. Cramer Street, Milwaukee, Wisconsin 53211-3209, United States
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Shah DD, Conrad JA, Moran GR. Intermediate Partitioning Kinetic Isotope Effects for the NIH Shift of 4-Hydroxyphenylpyruvate Dioxygenase and the Hydroxylation Reaction of Hydroxymandelate Synthase Reveal Mechanistic Complexity. Biochemistry 2013; 52:6097-107. [DOI: 10.1021/bi400534q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Dhara D. Shah
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
| | - John A. Conrad
- Department
of Chemistry, University of Nebraska—Omaha,
6001 Dodge Street, Omaha, Nebraska 68182-0109, United States
| | - Graham R. Moran
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 North Cramer Street, Milwaukee, Wisconsin 53211-3209, United
States
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Sergeant MJ, Harrison PJ, Jenkins R, Moran GR, Bugg TDH, Thompson AJ. Phytotoxic effects of selected N-benzyl-benzoylhydroxamic acid metallo-oxygenase inhibitors: investigation into mechanism of action. NEW J CHEM 2013. [DOI: 10.1039/c3nj00491k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Diebold AR, Brown-Marshall CD, Neidig ML, Brownlee JM, Moran GR, Solomon EI. Activation of α-keto acid-dependent dioxygenases: application of an {FeNO}7/{FeO2}8 methodology for characterizing the initial steps of O2 activation. J Am Chem Soc 2011; 133:18148-60. [PMID: 21981763 PMCID: PMC3212634 DOI: 10.1021/ja202549q] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The α-keto acid-dependent dioxygenases are a major subgroup within the O(2)-activating mononuclear nonheme iron enzymes. For these enzymes, the resting ferrous, the substrate plus cofactor-bound ferrous, and the Fe(IV)═O states of the reaction have been well studied. The initial O(2)-binding and activation steps are experimentally inaccessible and thus are not well understood. In this study, NO is used as an O(2) analogue to probe the effects of α-keto acid binding in 4-hydroxyphenylpyruvate dioxygenase (HPPD). A combination of EPR, UV-vis absorption, magnetic circular dichroism (MCD), and variable-temperature, variable-field (VTVH) MCD spectroscopies in conjunction with computational models is used to explore the HPPD-NO and HPPD-HPP-NO complexes. New spectroscopic features are present in the α-keto acid bound {FeNO}(7) site that reflect the strong donor interaction of the α-keto acid with the Fe. This promotes the transfer of charge from the Fe to NO. The calculations are extended to the O(2) reaction coordinate where the strong donation associated with the bound α-keto acid promotes formation of a new, S = 1 bridged Fe(IV)-peroxy species. These studies provide insight into the effects of a strong donor ligand on O(2) binding and activation by Fe(II) in the α-keto acid-dependent dioxygenases and are likely relevant to other subgroups of the O(2) activating nonheme ferrous enzymes.
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Affiliation(s)
- Adrienne R. Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Michael L. Neidig
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - June M. Brownlee
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Graham R. Moran
- Department of Chemistry and Biochemistry, University of Wisconsin-Madison, Milwaukee, Wisconsin 53211, USA
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford, CA 94309
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He P, Moran GR. Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily. J Inorg Biochem 2011; 105:1259-72. [DOI: 10.1016/j.jinorgbio.2011.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 06/21/2011] [Accepted: 06/24/2011] [Indexed: 11/30/2022]
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Shah DD, Conrad JA, Heinz B, Brownlee JM, Moran GR. Evidence for the Mechanism of Hydroxylation by 4-Hydroxyphenylpyruvate Dioxygenase and Hydroxymandelate Synthase from Intermediate Partitioning in Active Site Variants. Biochemistry 2011; 50:7694-704. [DOI: 10.1021/bi2009344] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dhara D. Shah
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - John A. Conrad
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - Brian Heinz
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - June M. Brownlee
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
| | - Graham R. Moran
- Department of Chemistry
and Biochemistry, University of Wisconsin—Milwaukee, 3210 N. Cramer
St., Milwaukee, Wisconsin 53211-3029, United States
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Abstract
The oxygen activating mononuclear non-heme ferrous enzymes catalyze a diverse range of chemistry yet typically maintain a common structural motif: two histidines and a carboxylate coordinating the iron center in a facial triad. A new Fe(II) coordinating triad has been observed in two enzymes, diketone-cleaving dioxygenase, Dke1, and cysteine dioxygenase (CDO), and is composed of three histidine residues. The effect of this three-His motif in Dke1 on the geometric and electronic structure of the Fe(II) center is explored via a combination of absorption, CD, MCD, and VTVH MCD spectroscopies and DFT calculations. This geometric and electronic structure of the three-His triad is compared to that of the classical (2-His-1-carboxylate) facial triad in the alpha-ketoglutarate (alphaKG)-dependent dioxygenases clavaminate synthase 2 (CS2) and hydroxyphenylpyruvate dioxygenase (HPPD). Comparison of the ligand fields at the Fe(II) shows little difference between the three-His and 2-His-1-carboxylate facial triad sites. Acetylacetone, the substrate for Dke1, will also bind to HPPD and is identified as a strong donor, similar to alphaKG. The major difference between the three-His and 2-His-1-carboxylate facial triad sites is in MLCT transitions observed for both types of triads and reflects their difference in charge. These studies provide insight into the effects of perturbation of the facial triad ligation of the non-heme ferrous enzymes on their geometric and electronic structure and their possible contributions to reactivity.
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Affiliation(s)
- Adrienne R Diebold
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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