1
|
Kaushik S, Rameshwari R, Chapadgaonkar SS. The in-silico study of the structural changes in the Arthrobacter globiformis choline oxidase induced by high temperature. J Genet Eng Biotechnol 2024; 22:100348. [PMID: 38494262 PMCID: PMC10980864 DOI: 10.1016/j.jgeb.2023.100348] [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: 11/27/2023] [Accepted: 12/03/2023] [Indexed: 03/19/2024]
Abstract
BACKGROUND Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry. PROCESS This research paper presents the in-silico study and analysis of the structural changes of A. globiformis choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in Fig. 1. RESULTS Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs Arthrobacter globiformis choline oxidase showed that active site residues are highly conserved. The available crystal structure of A. globiformis choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW)1 was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase. CONCLUSION Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.
Collapse
Affiliation(s)
- Sonia Kaushik
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Rashmi Rameshwari
- Department of Biotechnology, School of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India.
| | | |
Collapse
|
2
|
Kaushik S, Rameshwari R, Chapadgaonkar SS. Enzyme engineering of choline oxidase for improving stability. J Biomol Struct Dyn 2024:1-13. [PMID: 38319016 DOI: 10.1080/07391102.2024.2309650] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024]
Abstract
Functioning as a flavoprotein, choline oxidase facilitates the transformation of choline into glycine betaine. Notably, choline oxidase and its resultant product, glycine betaine, find extensive applications across various industries and fields of study. However, its high sensitivity and tendency to lose functional activity at high temperatures reduces its industrial usage. MD simulation and mutation studies have revealed the role of certain residues responsible for the enzyme's thermal instability. This study focuses on inducing thermal stability to choline oxidase of A. globiformis through computational approaches at a maximum temperature of 60 °C. MD simulation analysis showed that Trp 331, Val 464 and Ser 101 contribute to structural instability, leading to the instability at 60 °C. Mutation of these residues with phenylalanine residues and simulation of the mutated enzyme at 60 °C exhibited thermostability and insignificant residual fluctuation. The re-docking and MM/GBSA analyses further validated the mutated enzyme's binding affinity and catalytic activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sonia Kaushik
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | - Rashmi Rameshwari
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, India
| | | |
Collapse
|
3
|
Dulchavsky M, Mitra R, Wu K, Li J, Boer K, Liu X, Zhang Z, Vasquez C, Clark CT, Funckes K, Shankar K, Bonnet-Zahedi S, Siddiq M, Sepulveda Y, Suhandynata RT, Momper JD, Calabrese AN, George O, Stull F, Bardwell JCA. Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme. Nat Chem Biol 2023; 19:1406-1414. [PMID: 37770699 PMCID: PMC10611581 DOI: 10.1038/s41589-023-01426-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 08/23/2023] [Indexed: 09/30/2023]
Abstract
The flavoenzyme nicotine oxidoreductase (NicA2) is a promising injectable treatment to aid in the cessation of smoking, a behavior responsible for one in ten deaths worldwide. NicA2 acts by degrading nicotine in the bloodstream before it reaches the brain. Clinical use of NicA2 is limited by its poor catalytic activity in the absence of its natural electron acceptor CycN. Without CycN, NicA2 is instead oxidized slowly by dioxygen (O2), necessitating unfeasibly large doses in a therapeutic setting. Here, we report a genetic selection strategy that directly links CycN-independent activity of NicA2 to growth of Pseudomonas putida S16. This selection enabled us to evolve NicA2 variants with substantial improvement in their rate of oxidation by O2. The encoded mutations cluster around a putative O2 tunnel, increasing flexibility and accessibility to O2 in this region. These mutations further confer desirable clinical properties. A variant form of NicA2 is tenfold more effective than the wild type at degrading nicotine in the bloodstream of rats.
Collapse
Affiliation(s)
- Mark Dulchavsky
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Rishav Mitra
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Wu
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Joshua Li
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Karli Boer
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Xiaomeng Liu
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhiyao Zhang
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Cristian Vasquez
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | | | - Kaitrin Funckes
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Kokila Shankar
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Selene Bonnet-Zahedi
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Mohammad Siddiq
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yadira Sepulveda
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
| | - Raymond T Suhandynata
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Jeremiah D Momper
- School of Pharmacy and Pharmaceutical Science, University of California, San Diego, La Jolla, CA, USA
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, S chool of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Olivier George
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
4
|
Hiraka K, Yoshida H, Tsugawa W, Asano R, La Belle JT, Ikebukuro K, Sode K. Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper. Protein Sci 2022; 31:e4434. [PMID: 36173159 PMCID: PMC9490804 DOI: 10.1002/pro.4434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/09/2022]
Abstract
l-Lactate oxidase (LOx) is a flavin mononucleotide (FMN)-dependent triose phosphate isomerase (TIM) barrel fold enzyme that catalyzes the oxidation of l-lactate using oxygen as a primary electron acceptor. Although reductive half-reaction mechanism of LOx has been studied by structure-based kinetic studies, oxidative half-reaction and substrate/product-inhibition mechanisms were yet to be elucidated. In this study, the structure and enzymatic properties of wild-type and mutant LOxs from Enterococcus hirae (EhLOx) were investigated. EhLOx structure showed the common TIM-barrel fold with flexible loop region. Noteworthy observations were that the EhLOx crystal structures prepared by co-crystallization with product, pyruvate, revealed the complex structures with "d-lactate form ligand," which was covalently bonded with a Tyr211 side chain. This observation provided direct evidence to suggest the product-inhibition mode of EhLOx. Moreover, this structure also revealed a flip motion of Met207 side chain, which is located on the flexible loop region as well as Tyr211. Through a saturation mutagenesis study of Met207, one of the mutants Met207Leu showed the drastically decreased oxidase activity but maintained dye-mediated dehydrogenase activity. The structure analysis of EhLOx Met207Leu revealed the absence of flipping in the vicinity of FMN, unlike the wild-type Met207 side chain. Together with the simulation of the oxygen-accessible channel prediction, Met207 may play as an oxygen gatekeeper residue, which contributes oxygen uptake from external enzyme to FMN. Three clades of LOxs are proposed based on the difference of the Met207 position and they have different oxygen migration pathway from external enzyme to active center FMN.
Collapse
Affiliation(s)
- Kentaro Hiraka
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
- College of Science, Engineering and TechnologyGrand Canyon UniversityPhoenixArizonaUSA
| | - Hiromi Yoshida
- Department of Basic Life Science, Faculty of MedicineKagawa UniversityKagawaJapan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Jeffrey T. La Belle
- College of Science, Engineering and TechnologyGrand Canyon UniversityPhoenixArizonaUSA
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of EngineeringTokyo University of Agriculture and TechnologyTokyoJapan
| | - Koji Sode
- Joint Department of Biomedical EngineeringThe University of North Carolina at Chapel Hill and North Carolina State UniversityChapel HillNorth CarolinaUSA
| |
Collapse
|
5
|
Vyas B, Bhowmik R, Akhter M, Ahmad FJ. Identification, analysis of deleterious SNPs of the human GSR gene and their effects on the structure and functions of associated proteins and other diseases. Sci Rep 2022; 12:5474. [PMID: 35361806 PMCID: PMC8971378 DOI: 10.1038/s41598-022-09295-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/08/2022] [Indexed: 11/27/2022] Open
Abstract
Hereditary glutathione reductase deficiency, caused by mutations of the GSR gene, is an autosomal recessive disorder characterized by decreased glutathione disulfide (GSSG) reduction activity and increased thermal instability. This study implemented computational analysis to screen the most likely mutation that might be associated with hereditary glutathione reductase deficiency and other diseases. Using ten online computational tools, the study revealed four nsSNPs among the 17 nsSNPs identified as most deleterious and disease associated. Structural analyses and evolutionary confirmation study of native and mutant GSR proteins using the HOPE project and ConSruf. HOPE revealed more flexibility in the native GSR structure than in the mutant structure. The mutation in GSR might be responsible for changes in the structural conformation and function of the GSR protein and might also play a significant role in inducing hereditary glutathione reductase deficiency. LD and haplotype studies of the gene revealed that the identified variations rs2978663 and rs8190955 may be responsible for obstructive heart defects (OHDs) and hereditary anemia, respectively. These interethnic differences in the frequencies of SNPs and haplotypes might help explain the unpredictability that has been reported in association studies and can contribute to predicting the pharmacokinetics and pharmacodynamics of drugs that make use of GSR.
Collapse
Affiliation(s)
- Bharti Vyas
- School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India
| | - Ratul Bhowmik
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mymoona Akhter
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
| | - Farhan Jalees Ahmad
- School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India.,Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| |
Collapse
|
6
|
Abstract
Choline oxidase catalyzes the four-electron, two-step, flavin-mediated oxidation of choline to glycine betaine. The enzyme is important both for medical and biotechnological reasons, because glycine betaine is one among a limited number of compatible solutes used by cells to counteract osmotic pressure. From a fundamental standpoint, choline oxidase has emerged as one of the paradigm enzymes for the oxidation of alcohols catalyzed by flavoproteins. Mechanistic, structural, and computational studies have elucidated the mechanism of action of the enzyme from Arthrobacter globiformis at the molecular level. Both choline and oxygen access to the active site cavity are gated and tightly controlled. Amino acid residues involved in substrate binding, and their contribution, have been identified. The mechanism of choline oxidation, with a hydride transfer reaction, an asynchronous transition state, the formation and stabilization of an alkoxide transient species, and a quantum mechanical mode of reaction, has been elucidated. The importance of nonpolar side chains for oxygen localization and of the positive charge harbored on the substrate for activation of oxygen for reaction with the reduced flavin have been recognized. Interesting phenomena, like the formation of a metastable photoinduced flavin-protein adduct, the reversible formation of a bicovalent flavoprotein, and the trapping of the enzyme in inactive conformations, have been described. This review summarizes the current status of our understanding on the structure-function-dynamics of choline oxidase.
Collapse
Affiliation(s)
- Giovanni Gadda
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States; Department of Biology, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, United States.
| |
Collapse
|
7
|
Alteration of Electron Acceptor Preferences in the Oxidative Half-Reaction of Flavin-Dependent Oxidases and Dehydrogenases. Int J Mol Sci 2020; 21:ijms21113797. [PMID: 32471202 PMCID: PMC7312611 DOI: 10.3390/ijms21113797] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 11/30/2022] Open
Abstract
In this review, recent progress in the engineering of the oxidative half-reaction of flavin-dependent oxidases and dehydrogenases is discussed, considering their current and future applications in bioelectrochemical studies, such as for the development of biosensors and biofuel cells. There have been two approaches in the studies of oxidative half-reaction: engineering of the oxidative half-reaction with oxygen, and engineering of the preference for artificial electron acceptors. The challenges for engineering oxidative half-reactions with oxygen are further categorized into the following approaches: (1) mutation to the putative residues that compose the cavity where oxygen may be located, (2) investigation of the vicinities where the reaction with oxygen may take place, and (3) investigation of possible oxygen access routes to the isoalloxazine ring. Among these approaches, introducing a mutation at the oxygen access route to the isoalloxazine ring represents the most versatile and effective strategy. Studies to engineer the preference of artificial electron acceptors are categorized into three different approaches: (1) engineering of the charge at the residues around the substrate entrance, (2) engineering of a cavity in the vicinity of flavin, and (3) decreasing the glycosylation degree of enzymes. Among these approaches, altering the charge in the vicinity where the electron acceptor may be accessed will be most relevant.
Collapse
|
8
|
Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| |
Collapse
|
9
|
Su D, Yuan H, Gadda G. A Reversible, Charge-Induced Intramolecular C4a-S-Cysteinyl-Flavin in Choline Oxidase Variant S101C. Biochemistry 2017; 56:6677-6690. [DOI: 10.1021/acs.biochem.7b00958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dan Su
- 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
| | - Hongling Yuan
- 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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Evidence for proton tunneling and a transient covalent flavin-substrate adduct in choline oxidase S101A. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1470-1478. [PMID: 28843728 DOI: 10.1016/j.bbapap.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 11/20/2022]
Abstract
The effect of temperature on the reaction of alcohol oxidation catalyzed by choline oxidase was investigated with the S101A variant of choline oxidase. Anaerobic enzyme reduction in a stopped-flow spectrophotometer was biphasic using either choline or 1,2-[2H4]-choline as a substrate. The limiting rate constants klim1 and klim2 at saturating substrate were well separated (klim1/klim2>9), and were >15-fold slower than for wild-type choline oxidase. Solvent deuterium kinetic isotope effects (KIEs) ~4 established that klim1 probes the proton transfer from the substrate hydroxyl to a catalytic base. Primary substrate deuterium KIEs ≥7 demonstrated that klim2 reports on hydride transfer from the choline alkoxide to the flavin. Between 15°C and 39°C the klim1 and klim2 values increased with increasing temperature, allowing for the analyses of H+ and H- transfers using Eyring and Arrhenius formalisms. Temperature-independent KIE on the klim1 value (H2Oklim1/D2Oklim1) suggests that proton transfer occurs within a highly reorganized tunneling-ready-state with a narrow distribution of donor-acceptor distances. Eyring analysis of the klim2 value gave lines with the slope(choline)>slope(D-choline), suggesting kinetic complexity. Spectral evidence for the transient occurrence of a covalent flavin-substrate adduct during the first phase of the anaerobic reaction of S101A CHO with choline is presented, supporting the notion that an important role of amino acid residues in the active site of flavin-dependent enzymes is to eliminate alternative reactions of the versatile enzyme-bound flavin for the reaction that needs to be catalyzed.
Collapse
|
12
|
Tremey E, Stines-Chaumeil C, Gounel S, Mano N. Designing an O2
-Insensitive Glucose Oxidase for Improved Electrochemical Applications. ChemElectroChem 2017. [DOI: 10.1002/celc.201700646] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emilie Tremey
- CNRS, CRPP - UPR 8641; 115 Avenue du Docteur Schweitzer 33600 Pessac France
- Univ Bordeaux; 146 rue Léo Saignat 33076 Bordeaux Cedex France
| | - Claire Stines-Chaumeil
- CNRS, CRPP - UPR 8641; 115 Avenue du Docteur Schweitzer 33600 Pessac France
- Univ Bordeaux; 146 rue Léo Saignat 33076 Bordeaux Cedex France
| | - Sébastien Gounel
- CNRS, CRPP - UPR 8641; 115 Avenue du Docteur Schweitzer 33600 Pessac France
- Univ Bordeaux; 146 rue Léo Saignat 33076 Bordeaux Cedex France
| | - Nicolas Mano
- CNRS, CRPP - UPR 8641; 115 Avenue du Docteur Schweitzer 33600 Pessac France
- Univ Bordeaux; 146 rue Léo Saignat 33076 Bordeaux Cedex France
| |
Collapse
|
13
|
Salvi F, Rodriguez I, Hamelberg D, Gadda G. Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase. Biochemistry 2016; 55:1473-84. [PMID: 26907558 DOI: 10.1021/acs.biochem.5b01356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.
Collapse
Affiliation(s)
- Francesca Salvi
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Isela Rodriguez
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug Design, and ∥Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302, United States
| |
Collapse
|
14
|
Koch C, Neumann P, Valerius O, Feussner I, Ficner R. Crystal Structure of Alcohol Oxidase from Pichia pastoris. PLoS One 2016; 11:e0149846. [PMID: 26905908 PMCID: PMC4764120 DOI: 10.1371/journal.pone.0149846] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
FAD-dependent alcohol oxidases (AOX) are key enzymes of methylotrophic organisms that can utilize lower primary alcohols as sole source of carbon and energy. Here we report the crystal structure analysis of the methanol oxidase AOX1 from Pichia pastoris. The crystallographic phase problem was solved by means of Molecular Replacement in combination with initial structure rebuilding using Rosetta model completion and relaxation against an averaged electron density map. The subunit arrangement of the homo-octameric AOX1 differs from that of octameric vanillyl alcohol oxidase and other dimeric or tetrameric alcohol oxidases, due to the insertion of two large protruding loop regions and an additional C-terminal extension in AOX1. In comparison to other alcohol oxidases, the active site cavity of AOX1 is significantly reduced in size, which could explain the observed preference for methanol as substrate. All AOX1 subunits of the structure reported here harbor a modified flavin adenine dinucleotide, which contains an arabityl chain instead of a ribityl chain attached to the isoalloxazine ring.
Collapse
Affiliation(s)
- Christian Koch
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Georg-August-University Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology und Genetics, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Georg-August-University Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- * E-mail:
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute for Microbiology und Genetics, Georg-August-University, Griesebachstr. 8, 37077, Goettingen, Germany
- Georg-August-University Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Georg-August-University Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology und Genetics, Georg-August-University, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Georg-August-University Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| |
Collapse
|
15
|
Chai AF, Bulloch EMM, Evans GL, Lott JS, Baker EN, Johnston JM. A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket. ACTA ACUST UNITED AC 2015; 71:862-72. [PMID: 25849397 DOI: 10.1107/s1399004715001650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/25/2015] [Indexed: 11/10/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. Access to iron in host macrophages depends on iron-chelating siderophores called mycobactins and is strongly correlated with Mtb virulence. Here, the crystal structure of an Mtb enzyme involved in mycobactin biosynthesis, MbtN, in complex with its FAD cofactor is presented at 2.30 Å resolution. The polypeptide fold of MbtN conforms to that of the acyl-CoA dehydrogenase (ACAD) family, consistent with its predicted role of introducing a double bond into the acyl chain of mycobactin. Structural comparisons and the presence of an acyl carrier protein, MbtL, in the same gene locus suggest that MbtN acts on an acyl-(acyl carrier protein) rather than an acyl-CoA. A notable feature of the crystal structure is the tubular density projecting from N(5) of FAD. This was interpreted as a covalently bound polyethylene glycol (PEG) fragment and resides in a hydrophobic pocket where the substrate acyl group is likely to bind. The pocket could accommodate an acyl chain of 14-21 C atoms, consistent with the expected length of the mycobactin acyl chain. Supporting this, steady-state kinetics show that MbtN has ACAD activity, preferring acyl chains of at least 16 C atoms. The acyl-binding pocket adopts a different orientation (relative to the FAD) to other structurally characterized ACADs. This difference may be correlated with the apparent ability of MbtN to catalyse the formation of an unusual cis double bond in the mycobactin acyl chain.
Collapse
Affiliation(s)
- Ai-Fen Chai
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Esther M M Bulloch
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Genevieve L Evans
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - J Shaun Lott
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Edward N Baker
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jodie M Johnston
- Laboratory of Structural Biology, School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| |
Collapse
|
16
|
Smitherman C, Rungsrisuriyachai K, Germann MW, Gadda G. Identification of the Catalytic Base for Alcohol Activation in Choline Oxidase. Biochemistry 2014; 54:413-21. [DOI: 10.1021/bi500982y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Crystal Smitherman
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Kunchala Rungsrisuriyachai
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Markus W. Germann
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Biotechnology and Drug
Design, ∥Center for Diagnostics and Therapeutics, and ⊥Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-3965, United States
| |
Collapse
|
17
|
Aldonolactone oxidoreductases. Methods Mol Biol 2014; 1146:95-111. [PMID: 24764090 DOI: 10.1007/978-1-4939-0452-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Vitamin C is a widely used vitamin. Here we review the occurrence and properties of aldonolactone oxidoreductases, an important group of flavoenzymes responsible for the ultimate production of vitamin C and its analogs in animals, plants, and single-cell organisms.
Collapse
|
18
|
Krondorfer I, Lipp K, Brugger D, Staudigl P, Sygmund C, Haltrich D, Peterbauer CK. Engineering of pyranose dehydrogenase for increased oxygen reactivity. PLoS One 2014; 9:e91145. [PMID: 24614932 PMCID: PMC3948749 DOI: 10.1371/journal.pone.0091145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 02/07/2014] [Indexed: 11/22/2022] Open
Abstract
Pyranose dehydrogenase (PDH), a member of the GMC family of flavoproteins, shows a very broad sugar substrate specificity but is limited to a narrow range of electron acceptors and reacts extremely slowly with dioxygen as acceptor. The use of substituted quinones or (organo)metals as electron acceptors is undesirable for many production processes, especially of food ingredients. To improve the oxygen reactivity, site-saturation mutagenesis libraries of twelve amino acids around the active site of Agaricus meleagris PDH were expressed in Saccharomyces cerevisiae. We established high-throughput screening assays for oxygen reactivity and standard dehydrogenase activity using an indirect Amplex Red/horseradish peroxidase and a DCIP/D-glucose based approach. The low number of active clones confirmed the catalytic role of H512 and H556. Only one position was found to display increased oxygen reactivity. Histidine 103, carrying the covalently linked FAD cofactor in the wild-type, was substituted by tyrosine, phenylalanine, tryptophan and methionine. Variant H103Y was produced in Pichia pastoris and characterized and revealed a five-fold increase of the oxygen reactivity.
Collapse
Affiliation(s)
- Iris Krondorfer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Katharina Lipp
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- University of Applied Sciences Wiener Neustadt – Campus Tulln, Tulln, Austria
| | - Dagmar Brugger
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Petra Staudigl
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
- * E-mail:
| |
Collapse
|
19
|
Salvi F, Wang YF, Weber IT, Gadda G. Structure of choline oxidase in complex with the reaction product glycine betaine. ACTA ACUST UNITED AC 2014; 70:405-13. [DOI: 10.1107/s1399004713029283] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022]
Abstract
Choline oxidase fromArthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose–methanol–choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand–enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250–255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.
Collapse
|
20
|
Salvi F, Gadda G. Human choline dehydrogenase: medical promises and biochemical challenges. Arch Biochem Biophys 2013; 537:243-52. [PMID: 23906661 PMCID: PMC7094428 DOI: 10.1016/j.abb.2013.07.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/24/2013] [Accepted: 07/16/2013] [Indexed: 01/17/2023]
Abstract
Human choline dehydrogenase (CHD) is located in the inner membrane of mitochondria primarily in liver and kidney and catalyzes the oxidation of choline to glycine betaine. Its physiological role is to regulate the concentrations of choline and glycine betaine in the blood and cells. Choline is important for regulation of gene expression, the biosynthesis of lipoproteins and membrane phospholipids and for the biosynthesis of the neurotransmitter acetylcholine; glycine betaine plays important roles as a primary intracellular osmoprotectant and as methyl donor for the biosynthesis of methionine from homocysteine, a required step for the synthesis of the ubiquitous methyl donor S-adenosyl methionine. Recently, CHD has generated considerable medical attention due to its association with various human pathologies, including male infertility, homocysteinuria, breast cancer and metabolic syndrome. Despite the renewed interest, the biochemical characterization of the enzyme has lagged behind due to difficulties in the obtainment of purified, active and stable enzyme. This review article summarizes the medical relevance and the physiological roles of human CHD, highlights the biochemical knowledge on the enzyme, and provides an analysis based on the comparison of the protein sequence with that of bacterial choline oxidase, for which structural and biochemical information is available.
Collapse
Affiliation(s)
- Francesca Salvi
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-3965, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-3965, United States
- Department of Biology, Georgia State University, Atlanta, GA 30302-3965, United States
- The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302-3965, United States
| |
Collapse
|
21
|
Pathway of glycine betaine biosynthesis in Aspergillus fumigatus. EUKARYOTIC CELL 2013; 12:853-63. [PMID: 23563483 DOI: 10.1128/ec.00348-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The choline oxidase (CHOA) and betaine aldehyde dehydrogenase (BADH) genes identified in Aspergillus fumigatus are present as a cluster specific for fungal genomes. Biochemical and molecular analyses of this cluster showed that it has very specific biochemical and functional features that make it unique and different from its plant and bacterial homologs. A. fumigatus ChoAp catalyzed the oxidation of choline to glycine betaine with betaine aldehyde as an intermediate and reduced molecular oxygen to hydrogen peroxide using FAD as a cofactor. A. fumigatus Badhp oxidized betaine aldehyde to glycine betaine with reduction of NAD(+) to NADH. Analysis of the AfchoAΔ::HPH and AfbadAΔ::HPH single mutants and the AfchoAΔAfbadAΔ::HPH double mutant showed that AfChoAp is essential for the use of choline as the sole nitrogen, carbon, or carbon and nitrogen source during the germination process. AfChoAp and AfBadAp were localized in the cytosol of germinating conidia and mycelia but were absent from resting conidia. Characterization of the mutant phenotypes showed that glycine betaine in A. fumigatus functions exclusively as a metabolic intermediate in the catabolism of choline and not as a stress protectant. This study in A. fumigatus is the first molecular, cellular, and biochemical characterization of the glycine betaine biosynthetic pathway in the fungal kingdom.
Collapse
|
22
|
Mugo AN, Kobayashi J, Yamasaki T, Mikami B, Ohnishi K, Yoshikane Y, Yagi T. Crystal structure of pyridoxine 4-oxidase from Mesorhizobium loti. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:953-63. [PMID: 23501672 DOI: 10.1016/j.bbapap.2013.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 03/04/2013] [Indexed: 10/27/2022]
Abstract
Pyridoxine 4-oxidase (PNOX) from Mesorhizobium loti is a monomeric glucose-methanol-choline (GMC) oxidoreductase family enzyme, catalyzes FAD-dependent oxidation of pyridoxine (PN) into pyridoxal, and is the first enzyme in pathway I for the degradation of PN. The tertiary structures of PNOX with a C-terminal His6-tag and PNOX-pyridoxamine (PM) complex were determined at 2.2Å and at 2.1Å resolutions, respectively. The overall structure consisted of FAD-binding and substrate-binding domains. In the active site, His460, His462, and Pro504 were located on the re-face of the isoalloxazine ring of FAD. PM binds to the active site through several hydrogen bonds. The side chains of His462 and His460 are located at 2.7 and 3.1Å from the N4' atom of PM. The activities of His460Ala and His462Ala mutant PNOXs were very low, and 460Ala/His462Ala double mutant PNOX exhibited no activity. His462 may act as a general base for the abstraction of a proton from the 4'-hydroxyl of PN. His460 may play a role in the binding and positioning of PN. The C4' atom in PM is located at 3.2Å, and the hydride ion from the C4' atom may be transferred to the N5 atom of the isoalloxazine ring. The comparison of active site residues in GMC oxidoreductase shows that Pro504 in PNOX corresponds to Asn or His of the conserved His-Asn or His-His pair in other GMC oxidoreductases. The function of the novel proline residue was discussed.
Collapse
Affiliation(s)
- Andrew Njagi Mugo
- Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi, Japan
| | | | | | | | | | | | | |
Collapse
|
23
|
Tan TC, Spadiut O, Wongnate T, Sucharitakul J, Krondorfer I, Sygmund C, Haltrich D, Chaiyen P, Peterbauer CK, Divne C. The 1.6 Å crystal structure of pyranose dehydrogenase from Agaricus meleagris rationalizes substrate specificity and reveals a flavin intermediate. PLoS One 2013; 8:e53567. [PMID: 23326459 PMCID: PMC3541233 DOI: 10.1371/journal.pone.0053567] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022] Open
Abstract
Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-Å crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.
Collapse
Affiliation(s)
- Tien Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Spadiut
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Thanyaporn Wongnate
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand
| | - Iris Krondorfer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christoph Sygmund
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Clemens K. Peterbauer
- Food Biotechnology Laboratory, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
24
|
Kim JY, Won GY, Lee S. Effects of Microsolvation on the Stability of Zwitterionic Valine. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.11.3797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
25
|
Chaiyen P, Fraaije MW, Mattevi A. The enigmatic reaction of flavins with oxygen. Trends Biochem Sci 2012; 37:373-80. [DOI: 10.1016/j.tibs.2012.06.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/19/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022]
|
26
|
Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Role of Active Site Histidines in the Two Half-Reactions of the Aryl-Alcohol Oxidase Catalytic Cycle. Biochemistry 2012; 51:6595-608. [DOI: 10.1021/bi300505z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fátima Lucas
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
| | - Patricia Ferreira
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and
Molecular and Cellular Biology and Institute of Biocomputation and
Physics of Complex Systems, University of Zaragoza, E-50009 Zaragoza, Spain
| | - Victor Guallar
- Joint BSC-IRB
Research Program
in Computational Biology, Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Angel T. Martínez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, E-28040
Madrid, Spain
| |
Collapse
|
27
|
Gadda G. Oxygen Activation in Flavoprotein Oxidases: The Importance of Being Positive. Biochemistry 2012; 51:2662-9. [DOI: 10.1021/bi300227d] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- 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
| |
Collapse
|
28
|
Hernández-Ortega A, Lucas F, Ferreira P, Medina M, Guallar V, Martínez AT. Modulating O2 reactivity in a fungal flavoenzyme: involvement of aryl-alcohol oxidase Phe-501 contiguous to catalytic histidine. J Biol Chem 2011; 286:41105-14. [PMID: 21940622 DOI: 10.1074/jbc.m111.282467] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aryl-alcohol oxidase (AAO) is a flavoenzyme responsible for activation of O(2) to H(2)O(2) in fungal degradation of lignin. The AAO crystal structure shows a buried active site connected to the solvent by a hydrophobic funnel-shaped channel, with Phe-501 and two other aromatic residues forming a narrow bottleneck that prevents the direct access of alcohol substrates. However, ligand diffusion simulations show O(2) access to the active site following this channel. Site-directed mutagenesis of Phe-501 yielded a F501A variant with strongly reduced O(2) reactivity. However, a variant with increased reactivity, as shown by kinetic constants and steady-state oxidation degree, was obtained by substitution of Phe-501 with tryptophan. The high oxygen catalytic efficiency of F501W, ∼2-fold that of native AAO and ∼120-fold that of F501A, seems related to a higher O(2) availability because the turnover number was slightly decreased with respect to the native enzyme. Free diffusion simulations of O(2) inside the active-site cavity of AAO (and several in silico Phe-501 variants) yielded >60% O(2) population at 3-4 Å from flavin C4a in F501W compared with 44% in AAO and only 14% in F501A. Paradoxically, the O(2) reactivity of AAO decreased when the access channel was enlarged and increased when it was constricted by introducing a tryptophan residue. This is because the side chain of Phe-501, contiguous to the catalytic histidine (His-502 in AAO), helps to position O(2) at an adequate distance from flavin C4a (and His-502 Nε). Phe-501 substitution with a bulkier tryptophan residue resulted in an increase in the O(2) reactivity of this flavoenzyme.
Collapse
Affiliation(s)
- Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain
| | | | | | | | | | | |
Collapse
|
29
|
RoseFigura JM, Puehringer S, Schwarzenbacher R, Toyama H, Klinman JP. Characterization of a protein-generated O₂ binding pocket in PqqC, a cofactorless oxidase catalyzing the final step in PQQ production. Biochemistry 2011; 50:1556-66. [PMID: 21155540 DOI: 10.1021/bi1015474] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PQQ is an exogenous, tricyclic, quino-cofactor for a number of bacterial dehydrogenases. The final step of PQQ formation is catalyzed by PqqC, a cofactorless oxidase. This study focuses on the activation of molecular oxygen in an enzyme active site without metal or cofactor and has identified a specific oxygen binding and activating pocket in PqqC. The active site variants H154N, Y175F,S, and R179S were studied with the goal of defining the site of O(2) binding and activation. Using apo-glucose dehydrogenase to assay for PQQ production, none of the mutants in this "O(2) core" are capable of PQQ/PQQH(2) formation. Spectrophotometric assays give insight into the incomplete reactions being catalyzed by these mutants. Active site variants Y175F, H154N, and R179S form a quinoid intermediate (Figure 1) anaerobically. Y175S is capable of proceeding further from quinoid to quinol, whereas Y175F, H154N, and R179S require O(2) to produce the quinol species. None of the mutations precludes substrate/product binding or oxygen binding. Assays for the oxidation of PQQH(2) to PQQ show that these O(2) core mutants are incapable of catalyzing a rate increase over the reaction in buffer, whereas H154N can catalyze the oxidation of PQQH(2) to PQQ in the presence of H(2)O(2) as an electron acceptor. Taken together, these data indicate that none of the targeted mutants can react fully to form quinone even in the presence of bound O(2). The data indicate a successful separation of oxidative chemistry from O(2) binding. The residues H154, Y175, and R179 are proposed to form a core O(2) binding structure that is essential for efficient O(2) activation.
Collapse
Affiliation(s)
- Jordan M RoseFigura
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | | | | | | | | |
Collapse
|
30
|
Yuan H, Gadda G. Importance of a Serine Proximal to the C(4a) and N(5) Flavin Atoms for Hydride Transfer in Choline Oxidase. Biochemistry 2011; 50:770-9. [DOI: 10.1021/bi101837u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Giovanni Gadda
- Department of Chemistry
- Department of Biology
- The Center for Biotechnology and Drug Design
| |
Collapse
|
31
|
Giagou T, Meyer MP. Mechanism of the Swern oxidation: significant deviations from transition state theory. J Org Chem 2010; 75:8088-99. [PMID: 21043525 DOI: 10.1021/jo101636w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deprotonation of the alkoxysulfonium intermediate has been shown to be rate-determining in the Swern oxidation of benzyl alcohol. Directly following this rate-determining step is the intramolecular syn-β-elimination of the ylide. In the present study, intramolecular (2)H kinetic isotope effects (KIEs) are used to gain insight into this syn-β-elimination step. As a result of the stereogenic sulfur center in the ylide intermediate, two diastereomeric transition states (endo-TS1 and exo-TS1) must be assumed to contribute to the intramolecular KIE. The intramolecular (2)H KIE determined at -78 °C is 2.82 ± 0.06. Attempts to reproduce this measurement computationally using transition state theory and a Bell tunneling correction yielded a value (1.58) far below that determined experimentally. Computational analysis is complicated by the existence of two distinct transition structures owing to the stereogenic center. Two extremes of Curtin-Hammett kinetics are explored using energies, vibrational frequencies, and moments of inertia from computed transition structures. Neither Curtin-Hammett scenario can reproduce the observed KIE to any acceptable degree of fidelity. Evidence based upon previous kinetics measurements and calculations upon a model system suggests that the stereogenic sulfur center is not likely to undergo inversion to a significant degree at the temperatures at which the Swern oxidation is performed here. Proceeding under the assumption of no stereoinversion at the sulfur center, calculations predict a nearly linear Arrhenius plot for the KIE--even with the inclusion of a one-dimensional tunneling correction. By contrast, the experimentally determined temperature dependence shows a significant concave upward curvature indicative of the influence of tunneling. Notably, KIEs measured in CCl(4), CHCl(3), CH(2)Cl(2), dichloroethane, and chlorobenzene at -23 °C showed little variance. This finding discounted the possible influence from dynamical effects due to incomplete vibrational relaxation. An ad hoc amplification of the imaginary frequencies corresponding to the first-order saddle points corresponding to endo-TS1 and exo-TS1 allowed us to reproduce the experimental temperature dependence of the KIE using only two adjustable parameters applied to a kinetic scenario that involves four isotopomeric transition states. The cumulative data and computational modeling strongly suggest that, even though the intramolecular (2)H KIE observed in these experiments is small, this reaction requires a multidimensional description of the tunneling phenomenon to accurately reproduce experimental trends.
Collapse
Affiliation(s)
- Thomas Giagou
- School of Natural Sciences, University of California, Merced, P.O. Box 5200 North Lake Road, Merced, California 95343, USA
| | | |
Collapse
|
32
|
Yuan H, Fu G, Brooks PT, Weber I, Gadda G. Steady-State Kinetic Mechanism and Reductive Half-Reaction of d-Arginine Dehydrogenase from Pseudomonas aeruginosa. Biochemistry 2010; 49:9542-50. [DOI: 10.1021/bi101420w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Irene Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| |
Collapse
|
33
|
Jamil F, Afza Gardner QTA, Bashir Q, Rashid N, Akhtar M. Mechanistic and Stereochemical Studies of Glycine Oxidase from Bacillus subtilis Strain R5. Biochemistry 2010; 49:7377-83. [DOI: 10.1021/bi100553n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farrukh Jamil
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | | | - Qamar Bashir
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
| |
Collapse
|
34
|
Finnegan S, Yuan H, Wang YF, Orville AM, Weber IT, Gadda G. Structural and kinetic studies on the Ser101Ala variant of choline oxidase: catalysis by compromise. Arch Biochem Biophys 2010; 501:207-13. [PMID: 20561507 DOI: 10.1016/j.abb.2010.06.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 06/10/2010] [Accepted: 06/10/2010] [Indexed: 11/27/2022]
Abstract
The oxidation of choline catalyzed by choline oxidase includes two reductive half-reactions where FAD is reduced by the alcohol substrate and by an aldehyde intermediate transiently formed in the reaction. Each reductive half-reaction is followed by an oxidative half-reaction where the reduced flavin is oxidized by oxygen. Here, we have used mutagenesis to prepare the Ser101Ala mutant of choline oxidase and have investigated the impact of this mutation on the structural and kinetic properties of the enzyme. The crystallographic structure of the Ser101Ala enzyme indicates that the only differences between the mutant and wild-type enzymes are the lack of a hydroxyl group on residue 101 and a more planar configuration of the flavin in the mutant enzyme. Kinetics established that replacement of Ser101 with alanine yields a mutant enzyme with increased efficiencies in the oxidative half-reactions and decreased efficiencies in the reductive half-reactions. This is accompanied by a significant decrease in the overall rate of turnover with choline. Thus, this mutation has revealed the importance of a specific residue for the optimization of the overall turnover of choline oxidase, which requires fine-tuning of four consecutive half-reactions for the conversion of an alcohol to a carboxylic acid.
Collapse
Affiliation(s)
- Steffan Finnegan
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA
| | | | | | | | | | | |
Collapse
|