5JIF

Crystal structure of mouse hepatitis virus strain DVIM Hemagglutinin-Esterase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.

Bakkers, M.J.Zeng, Q.Feitsma, L.J.Hulswit, R.J.Li, Z.Westerbeke, A.van Kuppeveld, F.J.Boons, G.J.Langereis, M.A.Huizinga, E.G.de Groot, R.J.

(2016) Proc.Natl.Acad.Sci.USA 113: E3111-E3119

  • DOI: 10.1073/pnas.1519881113
  • Primary Citation of Related Structures:  

  • PubMed 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 d ...

    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.


    Organizational Affiliation

    Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CH Utrecht, The Netherlands;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemagglutinin-esterase
A, B
381Murine coronavirus (strain DVIM)Mutation(s): 0 
Gene Names: HE
EC: 3.1.1.53
Find proteins for O92367 (Murine coronavirus (strain DVIM))
Go to UniProtKB:  O92367
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.523α = 90.00
b = 88.819β = 90.00
c = 122.163γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
EVAL15data reduction
PHASERphasing
EVAL15data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organization for Scientific ResearchNetherlandsECHO 711.011.006

Revision History 

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2016-06-08
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence
  • Version 1.4: 2019-04-03
    Type: Data collection, Source and taxonomy