1
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Rao D, Zhu L, Liu W, Guo Z. Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB. J Phys Chem B 2024. [PMID: 39051443 DOI: 10.1021/acs.jpcb.4c02073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.
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Affiliation(s)
- Deming Rao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Lin Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
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2
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Zhao A, Teng X, Ma Y, Mu L, Han S, Wang S, Lei K, Ji L, Li P. First Clarification of the Mechanism of Action of the Apple Glycosyltransferase MdUGT91AJ2 Involved in the Detoxification Metabolism of the Triketone Herbicide Sulcotrione. PLANTS (BASEL, SWITZERLAND) 2024; 13:1796. [PMID: 38999636 PMCID: PMC11244407 DOI: 10.3390/plants13131796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024]
Abstract
Sulcotrione is a member of triketone herbicides, a class of HPPD (4-hydroxyphenylpyruvate dioxygenase) inhibitors with broad-spectrum herbicidal activity. Modifications of glycosylation mediated by glycosyltransferases (GT) are involved in plant detoxification. In this study, we analyzed chip data published online and found that eight glycosyltransferases from group A of the apple glycosyltransferase family 1 may be involved in the metabolic mechanism of detoxification of triketone herbicides. To verify this prediction, we induced apple seedlings with six types of triketone herbicides, and then detected the expression levels of eight glycosyltransferase genes through real-time PCR. We found that triketone herbicides induced up-regulation of eight glycosyltransferase genes to varying degrees, with MdUGT91AJ2 being the most significantly up-regulated by sulcotrione-induced glycosyltransferase gene expression. Then, through in vitro enzymatic reactions and HPLC identification of glycoside substrates, it was found that the glycosyltransferase MdUGT91AJ2 had the highest specific enzyme activity against the triketone herbicide sulcotrione. Furthermore, the in vivo mechanism of the glycosyltransferase MdUGT91AJ2 in the detoxification metabolism of sulcotrione was further validated by overexpressing the strain in the plant. HPLC analysis showed that the content of sulcotrione glycosides in the overexpressing strain of MdUGT91AJ2 was significantly higher than that in the wild type. This result indicated that the apple glycosyltransferase MdUGT91AJ2 can still glycosylate and modify sulfotrione in plants, and participate in its detoxification metabolism. In summary, this study identified for the first time a novel apple glycosyltransferase MdUGT91AJ2 and elucidated its mechanism of action in the detoxification and metabolism of the triketone herbicide sulfotriene.
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Affiliation(s)
- Aijuan Zhao
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Xiao Teng
- Rizhao Academy of Agricultural Science, Rizhao 276500, China;
| | - Yingxin Ma
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Lijun Mu
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Shibo Han
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Shumin Wang
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Kang Lei
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Lusha Ji
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
| | - Pan Li
- State Key Laboratory for Macromolecule Drugs and Large-Scale Manufacturing, School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China; (A.Z.); (Y.M.); (L.M.); (S.H.); (S.W.); (K.L.)
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3
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Ferreira P, Neves RPP, Miranda FP, Cunha AV, Havenith RWA, Ramos MJ, Fernandes PA. DszA Catalyzes C-S Bond Cleavage through N 5-Hydroperoxyl Formation. J Chem Inf Model 2024; 64:4218-4230. [PMID: 38684937 PMCID: PMC11134501 DOI: 10.1021/acs.jcim.4c00301] [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: 02/23/2024] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.
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Affiliation(s)
- Pedro Ferreira
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Rui P. P. Neves
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Filipa P. Miranda
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana V. Cunha
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, Antwerp 2000, Belgium
| | - Remco W. A. Havenith
- Stratingh
Institute for Chemistry and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, The Netherlands
- Ghent
Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan
281 (S3), Ghent B-9000, Belgium
| | - Maria J. Ramos
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A. Fernandes
- LAQV,REQUIMTE,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
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4
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Forrester TJB, Ovchinnikova OG, Li Z, Kitova EN, Nothof JT, Koizumi A, Klassen JS, Lowary TL, Whitfield C, Kimber MS. The retaining β-Kdo glycosyltransferase WbbB uses a double-displacement mechanism with an intermediate adduct rearrangement step. Nat Commun 2022; 13:6277. [PMID: 36271007 PMCID: PMC9587256 DOI: 10.1038/s41467-022-33988-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
WbbB, a lipopolysaccharide O-antigen synthesis enzyme from Raoultella terrigena, contains an N-terminal glycosyltransferase domain with a highly modified architecture that adds a terminal β-Kdo (3-deoxy-D-manno-oct-2-ulosonic acid) residue to the O-antigen saccharide, with retention of stereochemistry. We show, using mass spectrometry, that WbbB forms a covalent adduct between the catalytic nucleophile, Asp232, and Kdo. We also determine X-ray structures for the CMP-β-Kdo donor complex, for Kdo-adducts with D232N and D232C WbbB variants, for a synthetic disaccharide acceptor complex, and for a ternary complex with both a Kdo-adduct and the acceptor. Together, these structures show that the enzyme-linked Asp232-Kdo adduct rotates to reposition the Kdo into a second sub-site, which then transfers Kdo to the acceptor. Retaining glycosyltransferases were thought to use only the front-side SNi substitution mechanism; here we show that retaining glycosyltransferases can also potentially use double-displacement mechanisms, but incorporating an additional catalytic subsite requires rearrangement of the protein's architecture.
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Affiliation(s)
- Taylor J. B. Forrester
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Olga G. Ovchinnikova
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Zhixiong Li
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Elena N. Kitova
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Jeremy T. Nothof
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Akihiko Koizumi
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - John S. Klassen
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada
| | - Todd L. Lowary
- grid.17089.370000 0001 2190 316XDepartment of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2 Canada ,grid.506934.d0000 0004 0633 7878Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529 Taiwan ,grid.19188.390000 0004 0546 0241Institute of Biochemical Sciences, National Taiwan University, Section 4, #1, Roosevelt Road, Taipei, 10617 Taiwan
| | - Chris Whitfield
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
| | - Matthew S. Kimber
- grid.34429.380000 0004 1936 8198Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1 Canada
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5
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Paparella A, Cahill SM, Aboulache BL, Schramm VL. Clostridioides difficile TcdB Toxin Glucosylates Rho GTPase by an S Ni Mechanism and Ion Pair Transition State. ACS Chem Biol 2022; 17:2507-2518. [PMID: 36038138 PMCID: PMC9486934 DOI: 10.1021/acschembio.2c00408] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Toxins TcdA and TcdB from Clostridioides difficile glucosylate human colon Rho GTPases. TcdA and TcdB glucosylation of RhoGTPases results in cytoskeletal changes, causing cell rounding and loss of intestinal integrity. Clostridial toxins TcdA and TcdB are proposed to catalyze glucosylation of Rho GTPases with retention of stereochemistry from UDP-glucose. We used kinetic isotope effects to analyze the mechanisms and transition-state structures of the glucohydrolase and glucosyltransferase activities of TcdB. TcdB catalyzes Rho GTPase glucosylation with retention of stereochemistry, while hydrolysis of UDP-glucose by TcdB causes inversion of stereochemistry. Kinetic analysis revealed TcdB glucosylation via the formation of a ternary complex with no intermediate, supporting an SNi mechanism with nucleophilic attack and leaving group departure occurring on the same face of the glucose ring. Kinetic isotope effects combined with quantum mechanical calculations revealed that the transition states of both glucohydrolase and glucosyltransferase activities of TcdB are highly dissociative. Specifically, the TcdB glucosyltransferase reaction proceeds via an SNi mechanism with the formation of a distinct oxocarbenium phosphate ion pair transition state where the glycosidic bond to the UDP leaving group breaks prior to attack of the threonine nucleophile from Rho GTPase.
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6
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Coines J, Cuxart I, Teze D, Rovira C. Computer Simulation to Rationalize “Rational” Engineering of Glycoside Hydrolases and Glycosyltransferases. J Phys Chem B 2022; 126:802-812. [PMID: 35073079 PMCID: PMC8819650 DOI: 10.1021/acs.jpcb.1c09536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Glycoside hydrolases
and glycosyltransferases are the main classes
of enzymes that synthesize and degrade carbohydrates, molecules essential
to life that are a challenge for classical chemistry. As such, considerable
efforts have been made to engineer these enzymes and make them pliable
to human needs, ranging from directed evolution to rational design,
including mechanism engineering. Such endeavors fall short and are
unreported in numerous cases, while even success is a necessary but
not sufficient proof that the chemical rationale behind the design
is correct. Here we review some of the recent work in CAZyme mechanism
engineering, showing that computational simulations are instrumental
to rationalize experimental data, providing mechanistic insight into
how native and engineered CAZymes catalyze chemical reactions. We
illustrate this with two recent studies in which (i) a glycoside hydrolase
is converted into a glycoside phosphorylase and (ii) substrate specificity
of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.
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Affiliation(s)
- Joan Coines
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Cuxart
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - David Teze
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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7
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Magalhães RP, Fernandes HS, Sousa SF. The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02271g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We described the catalytic mechanism of IsPETase, a polyethylene-terephthalate degrading enzyme. The reaction was found to progress in four steps, divided in two events: formation of the first transition intermediate and hydrolysis of the adduct.
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Affiliation(s)
- Rita P. Magalhães
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Henrique S. Fernandes
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO – Applied Molecular Biosciences Unit, BioSIM – Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
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