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Structural basis of catalysis and substrate recognition by the NAD(H)-dependent α-d-glucuronidase from the glycoside hydrolase family 4. Biochem J 2021; 478:943-959. [PMID: 33565573 DOI: 10.1042/bcj20200824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/03/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022]
Abstract
Members of the glycoside hydrolase family 4 (GH4) employ an unusual glycosidic bond cleavage mechanism utilizing NAD(H) and a divalent metal ion, under reducing conditions. These enzymes act upon a diverse range of glycosides, and unlike most other GH families, homologs here are known to accommodate both α- and β-anomeric specificities within the same active site. Here, we report the catalytic properties and the crystal structures of TmAgu4B, an α-d-glucuronidase from the hyperthermophile Thermotoga maritima. The structures in three different states include the apo form, the NADH bound holo form, and the ternary complex with NADH and the reaction product d-glucuronic acid, at 2.15, 1.97 and 1.85 Å resolutions, respectively. These structures reveal the step-wise route of conformational changes required in the active site to achieve the catalytically competent state, and illustrate the direct role of residues that determine the reaction mechanism. Furthermore, a structural transition of a helical region in the active site to a turn geometry resulting in the rearrangement of a unique arginine residue governs the exclusive glucopyranosiduronic acid recognition in TmAgu4B. Mutational studies show that modifications of the glycone binding site geometry lead to catalytic failure and indicate overlapping roles of specific residues in catalysis and substrate recognition. The data highlight hitherto unreported molecular features and associated active site dynamics that determine the structure-function relationships within the unique GH4 family.
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Eixelsberger T, Horvat D, Gutmann A, Weber H, Nidetzky B. Reaktion von UDP-Apiose/UDP-Xylose-Synthase mit isotopenmarkierten Substraten: Hinweise auf einen Mechanismus mit gekoppelter Oxidation und Aldolspaltung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Thomas Eixelsberger
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Doroteja Horvat
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Alexander Gutmann
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
| | - Hansjörg Weber
- Institut für Organische Chemie; Technische Universität Graz; NAWI Graz; Stremayrgasse 16 8010 Graz Österreich
| | - Bernd Nidetzky
- Institut für Biotechnologie und Bioprozesstechnik; Technische Universität Graz; NAWI Graz; Petersgasse 12 8010 Graz Österreich
- Austrian Centre of Industrial Biotechnology (acib); Petersgasse 14 8010 Graz Österreich
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Eixelsberger T, Horvat D, Gutmann A, Weber H, Nidetzky B. Isotope Probing of the UDP-Apiose/UDP-Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage. Angew Chem Int Ed Engl 2017; 56:2503-2507. [PMID: 28102965 PMCID: PMC5324594 DOI: 10.1002/anie.201609288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/09/2016] [Indexed: 12/05/2022]
Abstract
The C-branched sugar d-apiose (Api) is essential for plant cell-wall development. An enzyme-catalyzed decarboxylation/pyranoside ring-contraction reaction leads from UDP-α-d-glucuronic acid (UDP-GlcA) to the Api precursor UDP-α-d-apiose (UDP-Api). We examined the mechanism of UDP-Api/UDP-α-d-xylose synthase (UAXS) with site-selectively 2 H-labeled and deoxygenated substrates. The analogue UDP-2-deoxy-GlcA, which prevents C-2/C-3 aldol cleavage as the plausible initiating step of pyranoside-to-furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme-NAD+ and retro-aldol sugar ring-opening occur coupled in a single rate-limiting step leading to decarboxylation. Rearrangement and ring-contracting aldol addition in an open-chain intermediate then give the UDP-Api aldehyde, which is intercepted via reduction by enzyme-NADH.
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Doroteja Horvat
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Alexander Gutmann
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
| | - Hansjörg Weber
- Institute of Organic ChemistryGraz University of TechnologyNAWI GrazStremayrgasse 98010GrazAustria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyNAWI GrazPetersgasse 128010GrazAustria
- Austrian Centre of Industrial Biotechnology (acib)Petersgasse 148010GrazAustria
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Pélissier MC, Sebban-Kreuzer C, Guerlesquin F, Brannigan JA, Bourne Y, Vincent F. Structural and functional characterization of the Clostridium perfringens N-acetylmannosamine-6-phosphate 2-epimerase essential for the sialic acid salvage pathway. J Biol Chem 2014; 289:35215-24. [PMID: 25320079 DOI: 10.1074/jbc.m114.604272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pathogenic bacteria are endowed with an arsenal of specialized enzymes to convert nutrient compounds from their cell hosts. The essential N-acetylmannosamine-6-phosphate 2-epimerase (NanE) belongs to a convergent glycolytic pathway for utilization of the three amino sugars, GlcNAc, ManNAc, and sialic acid. The crystal structure of ligand-free NanE from Clostridium perfringens reveals a modified triose-phosphate isomerase (β/α)8 barrel in which a stable dimer is formed by exchanging the C-terminal helix. By retaining catalytic activity in the crystalline state, the structure of the enzyme bound to the GlcNAc-6P product identifies the topology of the active site pocket and points to invariant residues Lys(66) as a putative single catalyst, supported by the structure of the catalytically inactive K66A mutant in complex with substrate ManNAc-6P. (1)H NMR-based time course assays of native NanE and mutated variants demonstrate the essential role of Lys(66) for the epimerization reaction with participation of neighboring Arg(43), Asp(126), and Glu(180) residues. These findings unveil a one-base catalytic mechanism of C2 deprotonation/reprotonation via an enolate intermediate and provide the structural basis for the development of new antimicrobial agents against this family of bacterial 2-epimerases.
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Affiliation(s)
- Marie-Cécile Pélissier
- From the Aix-Marseille University, AFMB UMR7257, 163 avenue de Luminy 13288 Marseille, France, the CNRS, AFMB UMR7257, 163 avenue de Luminy, 13288 Marseille, France
| | - Corinne Sebban-Kreuzer
- the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, and
| | - Françoise Guerlesquin
- the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS UMR7255, Aix-Marseille Université, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, and
| | - James A Brannigan
- the Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Yves Bourne
- From the Aix-Marseille University, AFMB UMR7257, 163 avenue de Luminy 13288 Marseille, France, the CNRS, AFMB UMR7257, 163 avenue de Luminy, 13288 Marseille, France
| | - Florence Vincent
- From the Aix-Marseille University, AFMB UMR7257, 163 avenue de Luminy 13288 Marseille, France, the CNRS, AFMB UMR7257, 163 avenue de Luminy, 13288 Marseille, France,
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Martinez Cuesta S, Furnham N, Rahman SA, Sillitoe I, Thornton JM. The evolution of enzyme function in the isomerases. Curr Opin Struct Biol 2014; 26:121-30. [PMID: 25000289 PMCID: PMC4139412 DOI: 10.1016/j.sbi.2014.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 06/02/2014] [Accepted: 06/10/2014] [Indexed: 01/14/2023]
Abstract
The advent of computational approaches to measure functional similarity between enzymes adds a new dimension to existing evolutionary studies based on sequence and structure. This paper reviews research efforts aiming to understand the evolution of enzyme function in superfamilies, presenting a novel strategy to provide an overview of the evolution of enzymes belonging to an individual EC class, using the isomerases as an exemplar.
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Affiliation(s)
- Sergio Martinez Cuesta
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - Nicholas Furnham
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Syed Asad Rahman
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.
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Eixelsberger T, Sykora S, Egger S, Brunsteiner M, Kavanagh KL, Oppermann U, Brecker L, Nidetzky B. Structure and mechanism of human UDP-xylose synthase: evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid. J Biol Chem 2012; 287:31349-58. [PMID: 22810237 PMCID: PMC3438964 DOI: 10.1074/jbc.m112.386706] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
UDP-xylose synthase (UXS) catalyzes decarboxylation of UDP-d-glucuronic acid to UDP-xylose. In mammals, UDP-xylose serves to initiate glycosaminoglycan synthesis on the protein core of extracellular matrix proteoglycans. Lack of UXS activity leads to a defective extracellular matrix, resulting in strong interference with cell signaling pathways. We present comprehensive structural and mechanistic characterization of the human form of UXS. The 1.26-Å crystal structure of the enzyme bound with NAD+ and UDP reveals a homodimeric short-chain dehydrogenase/reductase (SDR), belonging to the NDP-sugar epimerases/dehydratases subclass. We show that enzymatic reaction proceeds in three chemical steps via UDP-4-keto-d-glucuronic acid and UDP-4-keto-pentose intermediates. Molecular dynamics simulations reveal that the d-glucuronyl ring accommodated by UXS features a marked 4C1chair to BO,3boat distortion that facilitates catalysis in two different ways. It promotes oxidation at C4 (step 1) by aligning the enzymatic base Tyr147 with the reactive substrate hydroxyl and it brings the carboxylate group at C5 into an almost fully axial position, ideal for decarboxylation of UDP-4-keto-d-glucuronic acid in the second chemical step. The protonated side chain of Tyr147 stabilizes the enolate of decarboxylated C4 keto species (2H1half-chair) that is then protonated from the Si face at C5, involving water coordinated by Glu120. Arg277, which is positioned by a salt-link interaction with Glu120, closes up the catalytic site and prevents release of the UDP-4-keto-pentose and NADH intermediates. Hydrogenation of the C4 keto group by NADH, assisted by Tyr147 as catalytic proton donor, yields UDP-xylose adopting the relaxed 4C1chair conformation (step 3).
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Affiliation(s)
- Thomas Eixelsberger
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, A-8010 Graz, Austria
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Huang W, Llano J, Gauld JW. Redox mechanism of glycosidic bond hydrolysis catalyzed by 6-phospho-alpha-glucosidase: a DFT study. J Phys Chem B 2010; 114:11196-206. [PMID: 20698522 DOI: 10.1021/jp102399h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glycosidic bonds are remarkably resistant to cleavage by chemical hydrolysis. Glycoside hydrolases catalyze their selective hydrolysis in oligosaccharides, polysaccharides, and glycoconjugates by following nonredox catalytic pathways or a net redox-neutral catalytic pathway using NAD(+) and divalent metal ions as cofactors. GlvA (6-phospho-alpha-glucosidase) is a glycosidase belonging to family GH4 and follows a regioselective redox-neutral mechanism of glycosidic-bond hydrolysis that favors alpha- over beta-glycosides. Its proposed catalytic mechanism can be divided into two half-reactions: the first one activates the glucopyranose ring by successively forming intermediates that are oxidized at the 3-, 2-, and 1-positions of the ring, which ultimately facilitate the heterolytic deglycosylation. The second half-reaction is essentially the reverse of the first half-reaction, beginning with the pyranose ring hydroxylation at the anomeric carbon, and it is followed by 3-reduction and regeneration of the active forms of the catalytic site and its cofactors. We investigated the NAD(+)-dependent redox mechanism of glycosidic bond hydrolysis as catalyzed by GlvA through the combined application of density functional theory and a self-consistent reaction field to a large active-site model obtained from the crystallographic structure of the enzyme, then we applied natural bond orbital and second-order perturbation analyses to monitor the electron flow and change in oxidation state on each atomic center along the reaction coordinate to rationalize the energetics and regioselectivity of this catalytic mechanism. We find that in GlvA, the redox catalytic mechanism of hydrolysis is driven by the gradual strengthening of the axial endo-anomeric component within the hexose ring along the reaction coordinate to facilitate the heterolytic dissociation of the axial C1-O bond. In addition, the combined influence of specific components of the generalized anomeric effect fully explains the regioselectivity observed in the catalytic activity of GlvA.
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Affiliation(s)
- Wenjuan Huang
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
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