Substrate binding mode and catalytic mechanism of human heparan sulfate d-glucuronyl C5 epimerase

Autor: Emeline Richard, Véronique Roig-Zamboni, Hugues Lortat-Jacob, Firas Fadel, Jérôme Hénault, Adeline Goulet, Christine Le Narvor, Yves Bourne, David Bonnaffé, Vincent Delauzun, C. Debarnot, Yoan R. Monneau, Bernard Priem, Romain R. Vivès
Přispěvatelé: Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-11-IDEX-0003,IPS,Idex Paris-Saclay(2011), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), LCOM eG2M, Inst Chim Mol & Mat Orsay, LabEx LERMIT,UMR 8182, Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur les Macromolécules Végétales (CERMAV ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bourne, Yves, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, Idex Paris-Saclay - - IPS2011 - ANR-11-IDEX-0003 - IDEX - VALID
Jazyk: angličtina
Rok vydání: 2019
Předmět:
MESH: Heparin
[SDV.BIO]Life Sciences [q-bio]/Biotechnology
[SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology
Oligosaccharides
Isomerase
Uronic acid
catalytic mechanism
Crystallography
X-Ray
01 natural sciences
[SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity
Substrate Specificity
chemistry.chemical_compound
MESH: Structure-Activity Relationship
Glucuronic Acid
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases
Trisaccharide
[SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biochemistry [q-bio.BM]
chemistry.chemical_classification
[SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology
0303 health sciences
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases
Multidisciplinary
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
biology
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Structural Biology [q-bio.BM]
Nuclear magnetic resonance spectroscopy
Heparan sulfate
Biological Sciences
MESH: Carbohydrate Epimerases
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biomolecules [q-bio.BM]
MESH: Glucuronic Acid
[SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology
MESH: HEK293 Cells
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
[SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases
heparan sulfate
substrate distortion
Stereochemistry
[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Structural Biology [q-bio.BM]
Catalysis
Structure-Activity Relationship
03 medical and health sciences
Humans
Binding site
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biochemistry [q-bio.BM]
[SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity
030304 developmental biology
X-ray crystallography
Binding Sites
MESH: Humans
Heparin
010405 organic chemistry
Mandelate racemase
[SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology
Active site
MESH: Catalysis
MESH: Crystallography
X-Ray
[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
0104 chemical sciences
[SDV.BIO] Life Sciences [q-bio]/Biotechnology
HEK293 Cells
chemistry
MESH: Binding Sites
C5 epimerization
biology.protein
[SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology
MESH: Substrate Specificity
[SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Carbohydrate Epimerases
MESH: Oligosaccharides
Zdroj: Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2019, 116 (14), pp.6760-6765. ⟨10.1073/pnas.1818333116⟩
Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2019, pp.201818333. ⟨10.1073/pnas.1818333116⟩
Proceedings of the National Academy of Sciences of the United States of America, 2019, 116 (14), pp.6760-6765. ⟨10.1073/pnas.1818333116⟩
ISSN: 0027-8424
1091-6490
Popis: Heparan sulfate (HS) is a linear, complex polysaccharide that modulates the biological activities of proteins through binding sites made by a series of Golgi-localized enzymes. Of these, glucuronyl C5-epimerase (Glce) catalyzes C5-epimerization of the HS component, d -glucuronic acid (GlcA), into l -iduronic acid (IdoA), which provides internal flexibility to the polymer and forges protein-binding sites to ensure polymer function. Here we report crystal structures of human Glce in the unbound state and of an inactive mutant, as assessed by real-time NMR spectroscopy, bound with a (GlcA-GlcNS) n substrate or a (IdoA-GlcNS) n product. Deep infiltration of the oligosaccharides into the active site cleft imposes a sharp kink within the central GlcNS-GlcA/IdoA-GlcNS trisaccharide motif. An extensive network of specific interactions illustrates the absolute requirement of N -sulfate groups vicinal to the epimerization site for substrate binding. At the epimerization site, the GlcA/IdoA rings are highly constrained in two closely related boat conformations, highlighting ring-puckering signatures during catalysis. The structure-based mechanism involves the two invariant acid/base residues, Glu499 and Tyr578, poised on each side of the target uronic acid residue, thus allowing reversible abstraction and readdition of a proton at the C5 position through a neutral enol intermediate, reminiscent of mandelate racemase. These structures also shed light on a convergent mechanism of action between HS epimerases and lyases and provide molecular frameworks for the chemoenzymatic synthesis of heparin or HS analogs.
Databáze: OpenAIRE
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