Crystal structure of barley exohydrolaseI W434Y mutant in complex with methyl 2-thio-beta-sophoroside.

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

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The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases.

Luang, S.Fernandez-Luengo, X.Nin-Hill, A.Streltsov, V.A.Schwerdt, J.G.Alonso-Gil, S.Ketudat Cairns, J.R.Pradeau, S.Fort, S.Marechal, J.D.Masgrau, L.Rovira, C.Hrmova, M.

(2022) Nat Commun 13: 5577-5577

  • DOI: https://doi.org/10.1038/s41467-022-33180-5
  • Primary Citation of Related Structures:  
    6JG1, 6JG2, 6JG6, 6JG7, 6JGA, 6JGB, 6JGC, 6JGD, 6JGE, 6JGG, 6JGK, 6JGL, 6JGN, 6JGO, 6JGP, 6JGQ, 6JGR, 6JGS, 6JGT, 6K6V, 6KUF, 6L1J, 6LBB, 6LBV, 6LC5

  • PubMed Abstract: 

    In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.

  • Organizational Affiliation

    School of Agriculture, Food and Wine, and Waite Research Institute, University of Adelaide, Waite Research Precinct, Glen Osmond, SA, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1609Hordeum vulgare subsp. vulgareMutation(s): 1 
Find proteins for Q9XEI3 (Hordeum vulgare subsp. vulgare)
Explore Q9XEI3 
Go to UniProtKB:  Q9XEI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XEI3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-2)-methyl 2-thio-beta-D-glucopyranoside
Glycosylation Resources
GlyTouCan:  G67616SG
GlyCosmos:  G67616SG
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
C3 H8 O3
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.457α = 90
b = 100.457β = 90
c = 181.889γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Data collection, Database references, Experimental preparation, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description