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Quintero-Jaime AF, Conzuelo F, Schuhmann W, Cazorla-Amorós D, Morallón E. Multi‐wall carbon nanotubes electrochemically modified with phosphorus and nitrogen functionalities as a basis for bioelectrodes with improved performance. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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2
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Gamella M, Guo Z, Alexandrov K, Katz E. Bioelectrocatalytic Electrodes Modified with PQQ‐Glucose Dehydrogenase‐Calmodulin Chimera Switchable by Peptide Signals: Pathway to Generic Bioelectronic Systems Controlled by Biomolecular Inputs. ChemElectroChem 2019. [DOI: 10.1002/celc.201801095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maria Gamella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699–5810 USA
| | - Zhong Guo
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Kirill Alexandrov
- Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699–5810 USA
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3
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Uchida W, Wakabayashi M, Ikemoto K, Nakano M, Ohtani H, Nakamura S. Mechanism of glycine oxidation catalyzed by pyrroloquinoline quinone in aqueous solution. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Khanna S, Kaur D, Kaur R. The saturated five-membered heterocyclic molecules as organic hydride donors: a computational study. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shweta Khanna
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
| | - Damanjit Kaur
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
| | - Rajinder Kaur
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
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Vajdič T, Ošlaj M, Kopitar G, Mrak P. Engineered, highly productive biosynthesis of artificial, lactonized statin side-chain building blocks: The hidden potential of Escherichia coli unleashed. Metab Eng 2014; 24:160-72. [DOI: 10.1016/j.ymben.2014.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/22/2014] [Accepted: 05/06/2014] [Indexed: 12/26/2022]
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6
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Myers AE, Teague MR, Messina M. Tunneling Dynamics in a Double-Well Model of an H Transfer Reaction. J Chem Theory Comput 2009; 5:468-81. [PMID: 26610214 DOI: 10.1021/ct800436u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study the role that tunneling can play in the reaction dynamics of H atom transfer. The small mass of the H atom offers it another, nonclassical route, from reactants to products, tunneling through an activation barrier. In this work, we carefully define the portion of a reaction rate constant that is caused by tunneling in such reactions. We do this by decomposing an initial H atom wavepacket into above and below the barrier components. We show that for a very particular decomposition, the quantum dynamics of the system can be separated into two events: tunneling and above-the-barrier product production. We show for such decomposition it is possible to determine a rate constant because of tunneling alone. Finally, we demonstrate that from a single experimental observable, the overall decay of reactant concentration, one can extract structural and dynamical information about the H atom transfer reaction.
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Affiliation(s)
- Ashley E Myers
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, North Carolina 28403
| | - Matt R Teague
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, North Carolina 28403
| | - Michael Messina
- Department of Chemistry and Biochemistry, University of North Carolina, Wilmington, North Carolina 28403
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7
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Campodónico PR, Aizman A, Contreras R. Electrophilicity of quinones and its relationship with hydride affinity. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Gadda G. Hydride transfer made easy in the reaction of alcohol oxidation catalyzed by flavin-dependent oxidases. Biochemistry 2009; 47:13745-53. [PMID: 19053234 DOI: 10.1021/bi801994c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Choline oxidase (E.C. 1.1.3.17; choline-oxygen 1-oxidoreductase) catalyzes the two-step, four-electron oxidation of choline to glycine betaine with betaine aldehyde as enzyme-associated intermediate and molecular oxygen as final electron acceptor. Biochemical, structural, and mechanistic studies on the wild-type and a number of mutant forms of choline oxidase from Arthrobacter globiformis have recently been carried out, allowing for the delineation at molecular and atomic levels of the mechanism of alcohol oxidation catalyzed by the enzyme. First, the alcohol substrate is activated to its alkoxide species by the removal of the hydroxyl proton in the enzyme-substrate complex. The resulting activated alkoxide is correctly positioned for catalysis through electrostatic and hydrogen bonding interactions with a number of active site residues. After substrate activation and correct positioning are attained, alcohol oxidation occurs in a highly preorganized enzyme-substrate complex through quantum mechanical transfer of a hydride ion from the alpha-carbon of the chelated, alkoxide species to the N(5) atom of the enzyme-bound flavin. This mechanism in its essence is shared by another class of alcohol oxidizing enzymes that utilize a catalytic zinc to stabilize an alkoxide intermediate and NAD(P)(+) as the organic cofactor that accepts the hydride ion, whose paradigm example is alcohol dehydrogenase. It will be interesting to experimentally evaluate the attractive hypothesis of whether the mechanism of choline oxidase can be extended to other flavin-dependent enzymes as well as enzymes that utilize cofactors other than flavins in the oxidation of alcohols.
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Affiliation(s)
- Giovanni Gadda
- Departments of Chemistry and Biology, and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA.
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Lau C, Borgmann S, Maciejewska M, Ngounou B, Gründler P, Schuhmann W. Improved specificity of reagentless amperometric PQQ-sGDH glucose biosensors by using indirectly heated electrodes. Biosens Bioelectron 2007; 22:3014-20. [PMID: 17291745 DOI: 10.1016/j.bios.2006.12.033] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2006] [Revised: 12/21/2006] [Accepted: 12/21/2006] [Indexed: 11/18/2022]
Abstract
Indirectly heated electrodes operating in a non-isothermal mode have been used as transducers for reagentless glucose biosensors. Pyrroloquinoline quinone-dependent soluble glucose dehydrogenase (PQQ-sGDH) was entrapped on the electrode surface within a redox hydrogel layer. Localized polymer film precipitation was invoked by electrochemically modulating the pH-value in the diffusion zone in front of the electrode. The resulting decrease in solubility of an anodic electrodeposition paint (EDP) functionalized with Osmium complexes leads to precipitation of the redox hydrogel concomitantly entrapping the enzyme. The resulting sensor architecture enables a fast electron transfer between enzyme and electrode surface. The glucose sensor was operated at pre-defined temperatures using a multiple current-pulse mode allowing reproducible indirect heating of the sensor. The sensor characteristics such as the apparent Michaelis constants K(M)(app) and maximum currents I(max)(app) were determined at different temperatures for the main substrate glucose as well as a potential interfering co-substrate maltose. The limit of detection increased with higher temperatures for both substrates (0.020 mM for glucose, and 0.023 mM for maltose at 48 degrees C). The substrate specificity of PQQ-sGDH is highly temperature dependent. Therefore, a mathematical model based on a multiple linear regression approach could be applied to discriminate between the current response for glucose and maltose. This allowed accurate determination of glucose in a concentration range of 0-0.1mM in the presence of unknown maltose concentrations ranging from 0 to 0.04 mM.
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Affiliation(s)
- Carolin Lau
- Universität Rostock, Albert-Einsteinstrasse 3a, D-18051 Rostock, Germany
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Zhang X, Reddy SY, Bruice TC. Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase. Proc Natl Acad Sci U S A 2007; 104:745-9. [PMID: 17215371 PMCID: PMC3020142 DOI: 10.1073/pnas.0610126104] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
At neutral pH, oxidation of CH(3)OH --> CH(2)O by an o-quinone requires general-base catalysis and the reaction is endothermic. The active-site -CO(2)(-) groups of Glu-171 and Asp-297 (Glu-171-CO(2)(-) and Asp-297-CO(2)(-)) have been considered as the required general base catalysts in the bacterial o-quinoprotein methanol dehydrogenase (MDH) reaction. Based on quantum mechanics/molecular mechanics (QM/MM) calculations, the free energy for MeOH reduction of o-PQQ when MeOH is hydrogen bonded to Glu-171-CO(2)(-) and the crystal water (Wat1) is hydrogen bonded to Asp-297-CO(2)(-) is DeltaG++ = 11.7 kcal/mol, which is comparable with the experimental value of 8.5 kcal/mol. The calculated DeltaG++ when MeOH is hydrogen bonded to Asp-297-CO(2)(-) is >50 kcal/mol. The Asp-297-CO(2)(-)...Wat1 complex is very stable. Molecular dynamics (MD) simulations on MDH.PQQ.Wat1 complex in TIP3P water for 5 ns does not result in interchange of Asp-297-CO(2)(-) bound Wat1 for a solvent water. Starting with Wat1 removed and MeOH hydrogen bonded to Asp-297-CO(2)(-), we find that MeOH returns to be hydrogen bonded to Glu-171-CO(2)(-) and Asp-297-CO(2)(-) coordinates to Ca(2+) during 3 ns simulation. The Asp-297-CO(2)(-)...Wat1 of reactant complex does play a crucial role in catalysis. By QM/MM calculation DeltaG++ = 1.1 kcal/mol for Asp-297-CO(2)(-) general-base catalysis of Wat1 hydration of the immediate CH(2)==O product --> CH(2)(OH)(2). By this means, the endothermic oxidation-reduction reaction is pulled such that the overall conversion of MeOH to CH(2)(OH)(2) is exothermic.
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Affiliation(s)
- Xiaodong Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Swarnalatha Y. Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
| | - Thomas C. Bruice
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106
- *To whom correspondence should be addressed. E-mail:
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Hamamatsu N, Suzumura A, Nomiya Y, Sato M, Aita T, Nakajima M, Husimi Y, Shibanaka Y. Modified substrate specificity of pyrroloquinoline quinone glucose dehydrogenase by biased mutation assembling with optimized amino acid substitution. Appl Microbiol Biotechnol 2006; 73:607-17. [PMID: 16944137 DOI: 10.1007/s00253-006-0521-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2006] [Revised: 05/27/2006] [Accepted: 05/29/2006] [Indexed: 11/26/2022]
Abstract
A biased mutation-assembling method-that is, a directed evolution strategy to facilitate an optimal accumulation of multiple mutations on the basis of additivity principles, was applied to the directed evolution of water-soluble PQQ glucose dehydrogenase (PQQGDH-B) to reduce its maltose oxidation activity, which can lead to errors in blood glucose determination. Mutations appropriate for the reduction without fatal deterioration of its glucose oxidation activity were developed by an error-prone PCR method coupled with a saturation mutagenesis method. Moreover, two types of incorporation frequency based on their contribution were assigned to the mutations: high (80%) and evens (50%), in constructing a multiple mutant library. The best mutant created showed a marked reduction in maltose oxidation activity, corresponding to 4% of that of the wild-type enzyme, with 35% retention of glucose oxidation activity. In addition, this mutant showed a reduction in galactose oxidation activity corresponding to 5% of that of the wild-type enzyme. In conclusion, we succeeded in developing the PQQGDH-B mutants with improved substrate specificity and validated our method coupled with optimized mutations and their contribution-based incorporation frequencies by applying it to the development.
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Affiliation(s)
- Norio Hamamatsu
- Novartis Pharma K.K., Tsukuba Research Institute, Ohkubo 8, Tsukuba 300-2611, Japan
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Hiroya K, Matsumoto S, Ashikawa M, Kida H, Sakamoto T. The optimization for cyclization reaction of 2-(2-carbomethoxyethynyl)aniline derivatives and formal synthesis of pyrroloquinoline quinone and its analogue utilizing a sequential coupling-cyclization reaction. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.09.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Reddy SY, Bruice TC. Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase. Protein Sci 2005; 13:1965-78. [PMID: 15273299 PMCID: PMC2279812 DOI: 10.1110/ps.04673404] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base-catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH- [-HC5(O-)-C4(=O)-] and PQQH [-HC5(OH)-C4(=O)-] converts to the hydroquinone PQQH2 [-C5(OH)=C4(OH)-]. The main focus is on MD structures of MDH * PQQ * methanol, MDH * PQQH-, MDH * PQQH, sGDH * PQQ * glucose, sGDH * PQQH- (glucolactone, and sGDH * PQQH. The reaction PQQ-->PQQH- occurs with Glu 171-CO2- and His 144-Im as the base species in MDH and sGDH, respectively. The general-base-catalyzed hydroxyl proton abstraction from substrate concerted with hydride transfer to the C5 of PQQ is assisted by hydrogen-bonding to the C5=O by Wat1 and Arg 324 in MDH and by Wat89 and Arg 228 in sGDH. Asp 297-COOH would act as a proton donor for the reaction PQQH(-)-->PQQH, if formed by transfer of the proton from Glu 171-COOH to Asp 297-CO2- in MDH. For PQQH-->PQQH2, migration of H5 to the C4 oxygen may be assisted by a weak base like water (either by crystal water Wat97 or bulk solvent, hydrogen-bonded to Glu 171-CO2- in MDH and by Wat89 in sGDH).
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
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Gronert S, Keeffe JR. Identity Hydride-Ion Transfer from C−H Donors to C Acceptor Sites. Enthalpies of Hydride Addition and Enthalpies of Activation. Comparison with C···H···C Proton Transfer. An ab Initio Study. J Am Chem Soc 2005; 127:2324-33. [PMID: 15713112 DOI: 10.1021/ja044002l] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enthalpies of addition of hydride ion to eleven carbonyl acceptors (X-CHO), two conjugate addition sites (X-CH=CH2; X = CHO, NO2), eight carbenium ion acceptors, fulvene, borane, and SiH3(+) were calculated at the MP2/6-311+G level. Correlation between calculated and experimental enthalpies of addition of hydride ion is excellent. Transition states (ts) for the identity hydride transfers between the acceptors and their corresponding hydride adducts (hydride donors) were also calculated. The carbonyl and fulvene reactions have transition states with one imaginary frequency: the hydrogen transfer coordinate. The carbenium ions, borane, and SiH3(+) gave not transition states but stable compounds upon addition of the hydride donor. Computational differences between these hydride transfers and previously reported proton transfers include shorter partial C...H bonds and a tendency toward bent C...H...C angles for the hydride transfer ts and addition compound structures, particularly when a bent geometry improves interactions elsewhere in the structure. These and other differences are explained by modeling the hydride transfer ts and addition compounds as two-electron, three-center systems involving the transfer termini and the shared hydrogen but the proton transfer ts structures as four-electron, three-center systems. Charge and geometry measures suggest transition states in which these features change synchronously, again in contrast to many proton transfer reactions. For the X-CHO set, polar effects dominate enthalpies of hydride addition, with resonance effects also important for resonance donors; these preferentially stabilize the acceptor, reducing its hydride ion affinity. Activation enthalpies are dominated by resonance stabilization of the acceptors, greatly attenuated in the transition states.
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Affiliation(s)
- Scott Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132, USA.
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15
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Reddy SY, Bruice TC. Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: a computational approach. Proc Natl Acad Sci U S A 2004; 101:15887-92. [PMID: 15520392 PMCID: PMC528780 DOI: 10.1073/pnas.0407209101] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mechanism of methanol oxidation by quinoprotein methanol dehydrogenase (MDH.PQQ) in combination with methanol (MDH.PQQ.methanol) involves Glu-171--CO2(-) general base removal of the hydroxyl proton of methanol in concert with hydride equivalent transfer to the >C5=O quinone carbon of pyrroloquinoline quinone (PQQ) and rearrangement to hydroquinone (PQQH2) with release of formaldehyde. Molecular dynamics (MD) studies of the structures of MDH.PQQ.methanol in the presence of activator NH3 and inhibitor NH4(+) have been carried out. In the MD structure of MDH.PQQ.methanol.NH3, the hydrated NH3 resides at a distance of approximately 24 A away from methanol and the ortho-quinone portion of PQQ. As such, influence of NH3 on the oxidation reaction is not probable. We find that NH4(+) competes with the substrate by hydrogen-bonding to Glu-171CO2(-) such that the MDH.PQQ.methanol.NH4(+) complex is not reactive. Ammonia readily forms imines with quinone. Imines are present in solution as neutral (>C5=NH) and protonated (>C5=NH2(+)) species. MD simulations establish that the >C5=NH2(+) derivative of MDH.PQQ(NH2(+).methanol structure is unreactive because of the nonproductive means of methanol binding. The structure obtained by the MD simulations with the neutral >C5=NH imine of MDH.PQQ(NH).methanol structure is similar to the reactive MDH.PQQ.methanol complex. This active site geometry allows for catalysis of hydride equivalent transfer to the >C5=NH of PQQ(NH) by concerted Glu-171CO(2)(-) general-base removal of the H-OCH3 proton and Arg-324H+ general-acid proton transfer to the imine nitrogen. Enzyme-bound <C5(H)NH2 derivative of PQQ [PQQ(NH)] and CH(2)O product are formed.
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Affiliation(s)
- Swarnalatha Y Reddy
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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