title: Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.
abstract: Hemagglutinin-esterases (HEs) are bimodular envelope proteins of orthomyxoviruses, toroviruses, and coronaviruses with a carbohydrate-binding "lectin" domain appended to a receptor-destroying sialate-O-acetylesterase ("esterase"). In concert, these domains facilitate dynamic virion attachment to cell-surface sialoglycans. Most HEs (type I) target 9-O-acetylated sialic acids (9-O-Ac-Sias), but one group of coronaviruses switched to using 4-O-Ac-Sias instead (type II). This specificity shift required quasisynchronous adaptations in the Sia-binding sites of both lectin and esterase domains. Previously, a partially disordered crystal structure of a type II HE revealed how the shift in lectin ligand specificity was achieved. How the switch in esterase substrate specificity was realized remained unresolved, however. Here, we present a complete structure of a type II HE with a receptor analog in the catalytic site and identify the mutations underlying the 9-O- to 4-O-Ac-Sia substrate switch. We show that (i) common principles pertaining to the stereochemistry of protein-carbohydrate interactions were at the core of the transition in lectin ligand and esterase substrate specificity; (ii) in consequence, the switch in O-Ac-Sia specificity could be readily accomplished via convergent intramolecular coevolution with only modest architectural changes in lectin and esterase domains; and (iii) a single, inconspicuous Ala-to-Ser substitution in the catalytic site was key to the emergence of the type II HEs. Our findings provide fundamental insights into how proteins "see" sugars and how this affects protein and virus evolution.
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Mark J G
authors.initials: MJ
authors.lastname: Bakkers
authors.affiliation: Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Qinghong
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Louris J
authors.initials: LJ
authors.lastname: Feitsma
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Ruben J G
authors.initials: RJ
authors.lastname: Hulswit
authors.affiliation: Department of Chemistry, University of Georgia, Athens, GA 30602; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands;
authors.forename: Zeshi
authors.initials: Z
authors.lastname: Li
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Aniek
authors.initials: A
authors.lastname: Westerbeke
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Frank J M
authors.initials: FJ
authors.lastname: van Kuppeveld
authors.affiliation: Department of Chemistry, University of Georgia, Athens, GA 30602; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602.
authors.forename: Geert-Jan
authors.initials: GJ
authors.lastname: Boons
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;
authors.forename: Martijn A
authors.initials: MA
authors.lastname: Langereis
authors.affiliation: Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; r.j.degroot@uu.nl e.g.huizinga@uu.nl.
authors.forename: Eric G
authors.identifier: 0000-0001-6928-8426
authors.initials: EG
authors.lastname: Huizinga
authors.affiliation: Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands; r.j.degroot@uu.nl e.g.huizinga@uu.nl.
authors.forename: Raoul J
authors.initials: RJ
authors.lastname: de Groot
mesh_terms: D000818:Animals; D001665:Binding Sites; D020134:Catalytic Domain; D003106:Colon / Q000378:metabolism; D017934:Coronavirus / Q000201:enzymology*; D018360:Crystallography, X-Ray; D006389:Hemagglutinins, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D037102:Lectins / Q000737:chemistry / Q000378:metabolism*; D051379:Mice; D062105:Molecular Docking Simulation; D009154:Mutation / Q000235:genetics*; D000085064:Receptors, Coronavirus; D011991:Receptors, Virus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012794:Sialic Acids / Q000737:chemistry / Q000378:metabolism*; D013237:Stereoisomerism; D013379:Substrate Specificity; D014760:Viral Fusion Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D006389:Hemagglutinins, Viral; D037102:Lectins; D000085064:Receptors, Coronavirus; D011991:Receptors, Virus; D012794:Sialic Acids; D014760:Viral Fusion Proteins; C060814:hemagglutinin esterase
keywords: coronavirus; crystal structure; hemagglutinin-esterase; sialate-O-acetyl esterase; sialic acid