1
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Quaye JA, Wood KE, Snelgrove C, Ouedraogo D, Gadda G. An active site mutation induces oxygen reactivity in D-arginine dehydrogenase: A case of superoxide diverting protons. J Biol Chem 2024; 300:107381. [PMID: 38762175 PMCID: PMC11193025 DOI: 10.1016/j.jbc.2024.107381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
Enzymes are potent catalysts that increase biochemical reaction rates by several orders of magnitude. Flavoproteins are a class of enzymes whose classification relies on their ability to react with molecular oxygen (O2) during catalysis using ionizable active site residues. Pseudomonas aeruginosa D-arginine dehydrogenase (PaDADH) is a flavoprotein that oxidizes D-arginine for P. aeruginosa survival and biofilm formation. The crystal structure of PaDADH reveals the interaction of the glutamate 246 (E246) side chain with the substrate and at least three other active site residues, establishing a hydrogen bond network in the active site. Additionally, E246 likely ionizes to facilitate substrate binding during PaDADH catalysis. This study aimed to investigate how replacing the E246 residue with leucine affects PaDADH catalysis and its ability to react with O2 using steady-state kinetics coupled with pH profile studies. The data reveal a gain of O2 reactivity in the E246L variant, resulting in a reduced flavin semiquinone species and superoxide (O2•-) during substrate oxidation. The O2•- reacts with active site protons, resulting in an observed nonstoichiometric slope of 1.5 in the enzyme's log (kcat/Km) pH profile with D-arginine. Adding superoxide dismutase results in an observed correction of the slope to 1.0. This study demonstrates how O2•- can alter the slopes of limbs in the pH profiles of flavin-dependent enzymes and serves as a model for correcting nonstoichiometric slopes in elucidating reaction mechanisms of flavoproteins.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Kendall E Wood
- Biology Department, Morehouse College, Atlanta, Georgia, USA
| | - Claire Snelgrove
- The Gwinnett School of Mathematics, Science, and Technology, Lawrenceville, Georgia, USA
| | - Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA; Department of Biology, Georgia State University, Atlanta, Georgia, USA; Department of the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA.
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2
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Simpson M, Harding CJ, Czekster RM, Remmel L, Bode BE, Czekster CM. Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Biochemistry 2023; 62:3188-3205. [PMID: 37924287 PMCID: PMC10666288 DOI: 10.1021/acs.biochem.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
Intracellular leucine aminopeptidases (PepA) are metalloproteases from the family M17. These enzymes catalyze peptide bond cleavage, removing N-terminal residues from peptide and protein substrates, with consequences for protein homeostasis and quality control. While general mechanistic studies using model substrates have been conducted on PepA enzymes from various organisms, specific information about their substrate preferences and promiscuity, choice of metal, activation mechanisms, and the steps that limit steady-state turnover remain unexplored. Here, we dissected the catalytic and chemical mechanisms of PaPepA: a leucine aminopeptidase from Pseudomonas aeruginosa. Cleavage assays using peptides and small-molecule substrate mimics allowed us to propose a mechanism for catalysis. Steady-state and pre-steady-state kinetics, pH rate profiles, solvent kinetic isotope effects, and biophysical techniques were used to evaluate metal binding and activation. This revealed that metal binding to a tight affinity site is insufficient for enzyme activity; binding to a weaker affinity site is essential for catalysis. Progress curves for peptide hydrolysis and crystal structures of free and inhibitor-bound PaPepA revealed that PaPepA cleaves peptide substrates in a processive manner. We propose three distinct modes for activity regulation: tight packing of PaPepA in a hexameric assembly controls substrate length and reaction processivity; the product leucine acts as an inhibitor, and the high concentration of metal ions required for activation limits catalytic turnover. Our work uncovers catalysis by a metalloaminopeptidase, revealing the intricacies of metal activation and substrate selection. This will pave the way for a deeper understanding of metalloenzymes and processive peptidases/proteases.
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Affiliation(s)
- Martha
Clementine Simpson
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
| | - Christopher John Harding
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
| | - Ricardo Melo Czekster
- School
of Computer Science and Digital Technologies, Department of Software
Engineering and Cybersecurity, Aston University, B4 7ET, Birmingham,United Kingdom
| | - Laura Remmel
- School
of Chemistry, University of St Andrews, North Haugh, Purdie Building, KY16 9ST, Saint Andrews , United Kingdom
| | - Bela E. Bode
- School
of Chemistry, University of St Andrews, North Haugh, Purdie Building, KY16 9ST, Saint Andrews , United Kingdom
| | - Clarissa Melo Czekster
- School
of Biology, University of St Andrews, North Haugh, Biomolecular Sciences
Building, KY16 9ST, Saint Andrews, United Kingdom
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3
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Yildiz I. Computational insights on the hydride and proton transfer mechanisms of L-proline dehydrogenase. PLoS One 2023; 18:e0290901. [PMID: 37967056 PMCID: PMC10651016 DOI: 10.1371/journal.pone.0290901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/18/2023] [Indexed: 11/17/2023] Open
Abstract
L-Proline dehydrogenase (ProDH) is a flavin-dependent oxidoreductase, which catalyzes the oxidation of L-proline to (S)-1-pyrroline-5-carboxylate. Based on the experimental studies, a stepwise proton and hydride transfer mechanism is supported. According to this mechanism, the amino group of L-proline is deprotonated by a nearby Lys residue, which is followed by the hydride transfer process from C5 position of L-proline to N5 position of isoalloxazine ring of FAD. It was concluded that the hydride transfer step is rate limiting in the reductive half-reaction, however, in the overall reaction, the oxidation of FAD is the rate limiting step. In this study, we performed a computational mechanistic investigation based on ONIOM method to elucidate the mechanism of the reductive half-reaction corresponding to the oxidation of L-proline into iminoproline. Our calculations support the stepwise mechanism in which the deprotonation occurs initially as a fast step as result of a proton transfer from L-proline to the Lys residue. Subsequently, a hydride ion transfers from L-proline to FAD with a higher activation barrier. The enzyme-product complex showed a strong interaction between reduced FAD and iminoproline, which might help to explain why a step in the oxidative half-reaction is rate-limiting.
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Affiliation(s)
- Ibrahim Yildiz
- Chemistry Department and Applied Material Chemistry Center (AMCC), Khalifa University, Abu Dhabi, UAE
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4
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Quaye J, Ouedraogo D, Gadda G. Targeted Mutation of a Non-catalytic Gating Residue Increases the Rate of Pseudomonas aeruginosa d-Arginine Dehydrogenase Catalytic Turnover. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71. [PMID: 37933126 PMCID: PMC10655190 DOI: 10.1021/acs.jafc.3c05328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
Commercial food and l-amino acid industries rely on bioengineered d-amino acid oxidizing enzymes to detect and remove d-amino acid contaminants. However, the bioengineering of enzymes to generate faster biological catalysts has proven difficult as a result of the failure to target specific kinetic steps that limit enzyme turnover, kcat, and the poor understanding of loop dynamics critical for catalysis. Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) oxidizes most d-amino acids and is a good candidate for application in the l-amino acid and food industries. The side chain of the loop L2 E246 residue located at the entrance of the PaDADH active site pocket potentially favors the closed active site conformation and secures the substrate upon binding. This study used site-directed mutagenesis, steady-state, and rapid reaction kinetics to generate the glutamine, glycine, and leucine variants and investigate whether increasing the rate of product release could translate to an increased enzyme turnover rate. Upon E246 mutation to glycine, there was an increased rate of d-arginine turnover kcat from 122 to 500 s-1. Likewise, the kcat values increased 2-fold for the glutamine or leucine variants. Thus, we have engineered a faster biocatalyst for industrial applications by selectively increasing the rate of the PaDADH product release.
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Affiliation(s)
- Joanna
Afokai Quaye
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Daniel Ouedraogo
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
| | - Giovanni Gadda
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Department
of Biology, Georgia State University, Atlanta, Georgia 30302-3965, United
States
- Center
for Diagnostics and Therapeutics, Georgia
State University, Atlanta, Georgia 30302-3965, United States
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5
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Yildiz I. Computational Insights on the Hydride and Proton Transfer Mechanisms of D-Arginine Dehydrogenase. Chemphyschem 2023; 24:e202300431. [PMID: 37540527 DOI: 10.1002/cphc.202300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
D-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is an amine oxidase which catalyzes the conversion of D-arginine into iminoarginine. It contains a non-covalent FAD cofactor that is involved in the oxidation mechanism. Based on substrate, solvent, and multiple kinetic isotope effects studies, a stepwise hydride transfer mechanism is proposed. It was shown that D-arginine binds to the active site of enzyme as α-amino group protonated, and it is deprotonated before a hydride ion is transferred from its α-C to FAD. Based on a mutagenesis study, it was concluded that a water molecule is the most likely catalytic base responsible from the deprotonation of α-amino group. In this study, we formulated computational models based on ONIOM method to elucidate the oxidation mechanism of D-arginine into iminoarginine using the crystal structure of enzyme complexed with iminoarginine. The calculations showed that Arg222, Arg305, Tyr249, Glu87, His 48, and two active site water molecules play key roles in binding and catalysis. Model systems showed that the deprotonation step occurs prior to hydride transfer step, and active site water molecule(s) may have participated in the deprotonation process.
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Affiliation(s)
- Ibrahim Yildiz
- Khalifa University, Chemistry Department and Applied Material Chemistry Center (AMCC), PO Box, 127788, Abu Dhabi, UAE
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6
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Ouedraogo D, Souffrant M, Yao XQ, Hamelberg D, Gadda G. Non-active Site Residue in Loop L4 Alters Substrate Capture and Product Release in d-Arginine Dehydrogenase. Biochemistry 2023; 62:1070-1081. [PMID: 36795942 PMCID: PMC9996824 DOI: 10.1021/acs.biochem.2c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Numerous studies demonstrate that enzymes undergo multiple conformational changes during catalysis. The malleability of enzymes forms the basis for allosteric regulation: residues located far from the active site can exert long-range dynamical effects on the active site residues to modulate catalysis. The structure of Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) shows four loops (L1, L2, L3, and L4) that span the substrate and the FAD-binding domains. Loop L4 comprises residues 329-336, spanning over the flavin cofactor. The I335 residue on loop L4 is ∼10 Å away from the active site and ∼3.8 Å from N(1)-C(2)═O atoms of the flavin. In this study, we used molecular dynamics and biochemical techniques to investigate the effect of the mutation of I335 to histidine on the catalytic function of PaDADH. Molecular dynamics showed that the conformational dynamics of PaDADH are shifted to a more closed conformation in the I335H variant. In agreement with an enzyme that samples more in a closed conformation, the kinetic data of the I335H variant showed a 40-fold decrease in the rate constant of substrate association (k1), a 340-fold reduction in the rate constant of substrate dissociation from the enzyme-substrate complex (k2), and a 24-fold decrease in the rate constant of product release (k5), compared to that of the wild-type. Surprisingly, the kinetic data are consistent with the mutation having a negligible effect on the reactivity of the flavin. Altogether, the data indicate that the residue at position 335 has a long-range dynamical effect on the catalytic function in PaDADH.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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7
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Quaye JA, Ball J, Gadda G. Kinetic solvent viscosity effects uncover an internal isomerization of the enzyme-substrate complex in Pseudomonas aeruginosa PAO1 NADH:Quinone oxidoreductase. Arch Biochem Biophys 2022; 727:109342. [PMID: 35777523 DOI: 10.1016/j.abb.2022.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 11/02/2022]
Abstract
NAD(P)H:quinone oxidoreductases (NQOs) play an essential protective role as antioxidants in the detoxification of quinones in both Prokaryotes and Eukaryotes. NQO from Pseudomonas aeruginosa PAO1 uses FMN to catalyze the two-electron reduction of various quinones with NADH. In this study, steady-state kinetics, kinetic solvent viscosity effects, and rapid reaction kinetics were used to determine which kinetic steps control the overall turnover of the enzyme with benzoquinone or juglone. The rate constant for flavin reduction (kred) at pH 6.0 was 12.9 ± 0.3 s-1, and the Kd for NADH was at least an order of magnitude lower than 90 μM. With benzoquinone, the kcat value was 11.7 ± 0.3 s-1, consistent with flavin reduction being almost entirely rate-limiting for overall turnover. With juglone, a kcat value of 10.0 ± 0.5 s-1 was recorded. The normalized plot of the relative solvent viscosity effects on the kcat values established that hydride transfer from NADH to the FMN and quinol product release, with a calculated rate constant (kP-rel) of 52 s-1, are partially rate-limiting for the overall turnover of NQO. Kinetic solvent viscosity effects with glucose or sucrose revealed a hyperbolic dependence on the kcat and kcat/Km values with benzoquinone or juglone, respectively, consistent with the presence of a solvent-sensitive internal isomerization of the enzyme-substrate complex (ES). The data demonstrate opposing effects of benzoquinone and juglone on the equilibrium of the NQO ES isomerization with glucose or sucrose. Thus, our study demonstrates how quinol substrate properties alter the equilibrium of NQO ES isomerization.
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Affiliation(s)
- Joanna A Quaye
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Jacob Ball
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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8
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Iyer A, Reis RAG, Agniswamy J, Weber IT, Gadda G. Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase. Arch Biochem Biophys 2022; 715:109100. [PMID: 34864048 DOI: 10.1016/j.abb.2021.109100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 Å resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA, 30302, USA; Department of Biology, Georgia State University, Atlanta, GA, 30302, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA.
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9
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Gadda G, Sobrado P. Kinetic Solvent Viscosity Effects as Probes for Studying the Mechanisms of Enzyme Action. Biochemistry 2018; 57:3445-3453. [DOI: 10.1021/acs.biochem.8b00232] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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10
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Gadda G, Yuan H. Substitutions of S101 decrease proton and hydride transfers in the oxidation of betaine aldehyde by choline oxidase. Arch Biochem Biophys 2017; 634:76-82. [PMID: 29029877 DOI: 10.1016/j.abb.2017.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/25/2022]
Abstract
Choline oxidase oxidizes choline to glycine betaine, with two flavin-mediated reactions to convert the alcohol substrate to the carbon acid product. Proton abstraction from choline or hydrated betaine aldehyde in the wild-type enzyme occurs in the mixing time of the stopped-flow spectrophotometer, thereby precluding a mechanistic investigation. Mutagenesis of S101 rendered the proton transfer reaction amenable to study. Here, we have investigated the aldehyde oxidation reaction catalyzed by the mutant enzymes using steady-state and rapid kinetics with betaine aldehyde. Stopped-flow traces for the reductive half-reaction of the S101T/V/C variants were biphasic, corresponding to the reactions of proton abstraction and hydride transfer. In contrast, the S101A enzyme yielded monophasic traces like wild-type choline oxidase. The rate constants for proton transfer in the S101T/C/V variants decreased logarithmically with increasing hydrophobicity of residue 101, indicating a behavior different from that seen previously with choline for which no correlation was determined. The rate constants for hydride transfer also showed a logarithmic decrease with increasing hydrophobicity at position 101, which was similar to previous results with choline as a substrate for the enzyme. Thus, the hydrophilic character of S101 is necessary not only for efficient hydride transfer but also for the proton abstraction reaction.
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Affiliation(s)
- Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States; Department of Biology, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States; Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States.
| | - Hongling Yuan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, United States
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11
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Hodge-Hanson KM, Downs DM. Members of the Rid protein family have broad imine deaminase activity and can accelerate the Pseudomonas aeruginosa D-arginine dehydrogenase (DauA) reaction in vitro. PLoS One 2017; 12:e0185544. [PMID: 28957411 PMCID: PMC5619798 DOI: 10.1371/journal.pone.0185544] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/14/2017] [Indexed: 11/18/2022] Open
Abstract
The Rid (YjgF/YER057c/UK114) protein family is a group of small, sequence diverse proteins that consists of eight subfamilies. The archetypal RidA subfamily is found in all domains, while the Rid1-7 subfamilies are present only in prokaryotes. Bacterial genomes often encode multiple members of the Rid superfamily. The best characterized member of this protein family, RidA from Salmonella enterica, is a deaminase that quenches the reactive metabolite 2-aminoacrylate generated by pyridoxal 5’-phosphate-dependent enzymes and ultimately spares certain enzymes from damage. The accumulation of 2-aminoacrylate can damage enzymes and lead to growth defects in bacteria, plants, and yeast. While all subfamily members have been annotated as imine deaminases based on the RidA characterization, experimental evidence to support this annotation exists for a single protein outside the RidA subfamily. Here we report that six proteins, spanning Rid subfamilies 1–3, deaminate a variety of imine/enamine substrates with differing specific activities. Proteins from the Rid2 and Rid3 subfamilies, but not from the RidA and Rid1 subfamilies deaminated iminoarginine, generated in situ by the Pseudomonas aeruginosa D-arginine dehydrogenase DauA. These data biochemically distinguished the subfamilies and showed Rid proteins have activity on a metabolite that is physiologically relevant in Pseudomonas and other bacteria.
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Affiliation(s)
- Kelsey M. Hodge-Hanson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Diana M. Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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12
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Ouedraogo D, Ball J, Iyer A, Reis RAG, Vodovoz M, Gadda G. Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa. Arch Biochem Biophys 2017. [PMID: 28625766 DOI: 10.1016/j.abb.2017.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme. The enzyme is a true dehydrogenase because it displays no reactivity towards molecular oxygen. As established through solvent and multiple kinetic isotope studies, PaDADH catalyzes an asynchronous CH and NH bond cleavage via a hydride transfer mechanism. Steady-state kinetic studies with d-arginine and d-histidine are consistent with the enzyme following a ping-pong bi-bi mechanism. As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Jacob Ball
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Maria Vodovoz
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States; Department of Biology, Georgia State University, Atlanta, GA 30302, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, United States; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302, United States.
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13
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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14
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Ball J, Bui QV, Gannavaram S, Gadda G. Importance of glutamate 87 and the substrate α-amine for the reaction catalyzed by d-arginine dehydrogenase. Arch Biochem Biophys 2015; 568:56-63. [DOI: 10.1016/j.abb.2015.01.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
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Fitzpatrick PF. Combining solvent isotope effects with substrate isotope effects in mechanistic studies of alcohol and amine oxidation by enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:1746-55. [PMID: 25448013 DOI: 10.1016/j.bbapap.2014.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 10/24/2022]
Abstract
Oxidation of alcohols and amines is catalyzed by multiple families of flavin- and pyridine nucleotide-dependent enzymes. Measurement of solvent isotope effects provides a unique mechanistic probe of the timing of the cleavage of the OH and NH bonds, necessary information for a complete description of the catalytic mechanism. The inherent ambiguities in interpretation of solvent isotope effects can be significantly decreased if isotope effects arising from isotopically labeled substrates are measured in combination with solvent isotope effects. The application of combined solvent and substrate (mainly deuterium) isotope effects to multiple enzymes is described here to illustrate the range of mechanistic insights that such an approach can provide. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78212, USA.
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Gannavaram S, Sirin S, Sherman W, Gadda G. Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase. Biochemistry 2014; 53:6574-83. [PMID: 25243743 DOI: 10.1021/bi500917q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sarah Sirin
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
| | - Woody Sherman
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
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Serrano H, Blanchard JS. Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry 2013; 52:5009-15. [PMID: 23834473 DOI: 10.1021/bi400338f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The monofunctional proline dehydrogenase (ProDH) from Mycobacterium tuberculosis performs the flavin-dependent oxidation of l-proline to Δ(1)-pyrroline-5-carboxylate in the proline catabolic pathway. The ProDH gene, prub, was cloned into the pYUB1062 vector, and the C-terminal His-tagged 37 kDa protein was expressed and purified by nickel affinity chromatography. A steady-state kinetic analysis revealed a ping-pong mechanism with an overall kcat of 33 ± 2 s(-1) and Km values of 5.7 ± 0.8 mM and 3.4 ± 0.3 μM for l-proline and 2,6-dichlorophenolindophenol (DCPIP), respectively. The pH dependence of kcat revealed that one enzyme group exhibiting a pK value of 6.8 must be deprotonated for optimal catalytic activity. Site-directed mutagenesis suggests that this group is Lys110. The primary kinetic isotope effects on V/KPro and V of 5.5 and 1.1, respectively, suggest that the transfer of hydride from l-proline to FAD is rate-limiting for the reductive half-reaction, but that FAD reoxidation is the rate-limiting step in the overall reaction. Solvent and multiple kinetic isotope effects suggest that l-proline oxidation occurs in a stepwise rather than concerted mechanism. Pre-steady-state kinetics reveal an overall kred of 88.5 ± 0.7 s(-1), and this rate is subject to a primary kinetic isotope effect of 5.2. These data confirm that the overall reaction is limited by reduced flavin reoxidation in the second half-reaction.
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Affiliation(s)
- Hector Serrano
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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Gannavaram S, Gadda G. Relative Timing of Hydrogen and Proton Transfers in the Reaction of Flavin Oxidation Catalyzed by Choline Oxidase. Biochemistry 2013; 52:1221-6. [DOI: 10.1021/bi3016235] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Swathi Gannavaram
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, and §The Center for
Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, United States
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Tormos JR, Pozzi MH, Fitzpatrick PF. Mechanistic studies of the role of a conserved histidine in a mammalian polyamine oxidase. Arch Biochem Biophys 2012; 528:45-9. [PMID: 22959971 PMCID: PMC3483376 DOI: 10.1016/j.abb.2012.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 11/21/2022]
Abstract
Polyamine oxidases are peroxisomal flavoproteins that catalyze the oxidation of an endo carbon nitrogen bond of N1-acetylspermine in the catabolism of polyamines. While no structure has been reported for a mammalian polyamine oxidase, sequence alignments of polyamine oxidizing flavoproteins identify a conserved histidine residue. Based on the structure of a yeast polyamine oxidase, Saccharomyces cerevisiae Fms1, this residue has been proposed to hydrogen bond to the reactive nitrogen in the polyamine substrate. The corresponding histidine in mouse polyamine oxidase, His64, has been mutated to glutamine, asparagine, and alanine to determine if this residue plays a similar role in the mammalian enzymes. The kinetics of the mutant enzymes were examined with N1-acetylspermine and the slow substrates spermine and N,N'-dibenzyl-1,4-diaminobutane. On average the mutations result in a decrease of ~15-fold in the rate constant for amine oxidation. Rapid-reaction kinetic analyses established that amine oxidation is rate-limiting with spermine as substrate for the wild-type and mutant enzymes and for the H64N enzyme with N1-acetylspermine as substrate. The k(cat)/K(O(2)) value was unaffected by the mutations with N1-acetylspermine as substrate, but decreased ~55-fold with the two slower substrates. The results are consistent with this residue assisting in properly positioning the amine substrate for oxidation.
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Affiliation(s)
- José R. Tormos
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
| | | | - Paul F. Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio TX 78229
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Abstract
WT lactose permease of Escherichia coli (LacY) reconstituted into proteoliposomes loaded with a pH-sensitive fluorophore exhibits robust uphill H(+) translocation coupled with downhill lactose transport. However, galactoside binding by mutants defective in lactose-induced H(+) translocation is not accompanied by release of an H(+) on the interior of the proteoliposomes. Because the pK(a) value for galactoside binding is ∼10.5, protonation of LacY likely precedes sugar binding at physiological pH. Consistently, purified WT LacY, as well as the mutants, binds substrate at pH 7.5-8.5 in detergent, but no change in ambient pH is observed, demonstrating directly that LacY already is protonated when sugar binds. However, a kinetic isotope effect (KIE) on the rate of binding is observed, indicating that deuterium substitution for protium affects an H(+) transfer reaction within LacY that is associated with sugar binding. At neutral pH or pD, both the rate of sugar dissociation (k(off)) and the forward rate (k(on)) are slower in D(2)O than in H(2)O (KIE is ∼2), and, as a result, no change in affinity (K(d)) is observed. Alkaline conditions enhance the effect of D(2)O on k(off), the KIE increases to 3.6-4.0, and affinity for sugar increases compared with H(2)O. In contrast, LacY mutants that exhibit pH-independent high-affinity binding up to pH 11.0 (e.g., Glu325 → Gln) exhibit the same KIE (1.5-1.8) at neutral or alkaline pH (pD). Proton inventory studies exhibit a linear relationship between k(off) and D(2)O concentration at neutral and alkaline pH, indicating that internal transfer of a single H(+) is involved in the KIE.
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