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 receptordestroying 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 proteincarbohydrate 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.A mong host cell surface determinants for pathogen adherence, sialic acids (Sias) rank prominently (1, 2). Representatives of at least 11 families of vertebrate viruses use Sia as primary entry receptor and/or attachment factor (3, 4). Viral adherence to sialoglycans, however, comes with inherent complexities related to (i) the sheer ubiquity of receptor determinants that may act as "decoys" when present on off-target cells and non-cell-associated glycoconjugates, and (ii) the dense clustering that is characteristic to glycotopes and that may augment the apparent affinity of ligandlectin interactions by orders of magnitude (5, 6). Viruses may avoid inadvertent virion binding to nonproductive sites by being selective for particular sialoglycan subtypes so that attachment is dependent on Sia linkage type, the underlying glycan chain, and/or the absence or presence of specific postsynthetic Sia modifications (2, 7, 8). Moreover, as an apparent strategy to evade irremediable binding to decoy receptors, viral sialolectins typically are of low affinity, with dissociation constants in the millimolar range (reviewed in ref.3). In consequence, virion-Sia interactions are intrinsically dynamic and the affinity of the virolectins would appear to be fine-tuned such as to ensure reversibility of virion attachment. In most viruses, reversibility is exclusively subject to the lectin-ligand binding equilibrium. Some, howev...

Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus

“…3A). This may be due to stabilization of the interaction at low temperature, as was previously described for several other Sia-binding viruses (19,20). NA treatment of several cell types revealed that Sia supports CV-A24v infection of HCE and HAP1 cells, but not of HeLa cells (Fig.…”

Mutation of the Second Sialic Acid-Binding Site, Resulting in Reduced Neuraminidase Activity, Preceded the Emergence of H7N9 Influenza A Virus

“…Only a single study showed that the ability of NA to bind red blood cells corresponded to the cleavage efficiencies of other multivalent substrates (26). Enhancement of catalytic efficiency resulting from catalytic and carbohydrate-binding domains interacting simultaneously with a polyvalent substrate appears to be a general feature of most glycoside hydrolases, as most of these enzymes have been shown to contain lectin domains, including eukaryotic and bacterial NA proteins (44), as well as other viral-receptordestroying enzymes (45,46). The 2nd SIA-binding site, which is adjacent to the actual NA active site, may enhance the catalytic efficiency of NA by recruiting and keeping multivalent sialosides close to the active site (26,43).…”

Structural insights into coronavirus entry

“…2A) (Hulswit et al, 2019;Tortorici et al, 2019). This site is conserved in all other CoVs known to attach to 9-O-Ac-Sia (β-CoVs, lineage A) and shares architectural similarity with the ligand-binding pockets of CoV hemagglutinin-esterases and influenza virus C/D hemagglutinin-esterase-fusion glycoproteins, highlighting common structural principles of recognition (Bakkers et al, 2017(Bakkers et al, , 2016 Hulswit et al, 2019;Rosenthal et al, 1998;Tortorici et al, 2019). The current consensus in the field is that HCoV-OC43 only utilizes 9-O-Ac-sialosides as host receptors.…”

“…The CoV virion contains at least four structural proteins: spike (S), envelope (E), membrane (M) and nucleocapsid (N). In contrast to other β-CoV lineages, lineage A CoVs also encode a hemagglutinin-esterase which serves as receptor-destroying enzyme to facilitate release of viral progeny from infected cells and escape from attachment to non-permissive host cells or decoys (Bakkers et al, 2017(Bakkers et al, , 2016. S is a class 1 viral fusion protein that promotes host attachment and fusion of the viral and cellular membranes during entry (Bosch et al, 2003).…”