6JGD

Crystal structure of barley exohydrolaseI W286Y mutant in complex with methyl 6-thio-beta-gentiobioside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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 ...

    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

    Jiangsu Collaborative Innovation Centre for Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huai'an, China. maria.hrmova@adelaide.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1609Hordeum vulgare subsp. vulgareMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside
B
2N/AN/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14290QQ
GlyCosmos:  G14290QQ
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE (Subject of Investigation/LOI)
Query on 1PE

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
Q [auth A],
R [auth A],
S [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
T [auth A]
U [auth A]
V [auth A]
W [auth A]
X [auth A]
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.231α = 90
b = 101.231β = 90
c = 180.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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: Advisory, Data collection, Database references, Experimental preparation, Refinement description