Crystal Structure of the catalytic nucleophile mutant of VvEG16 in complex with cellotetraose

Experimental Data Snapshot

  • Resolution: 0.97 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 

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Crystallographic insight into the evolutionary origins of xyloglucan endotransglycosylases and endohydrolases.

McGregor, N.Yin, V.Tung, C.C.Van Petegem, F.Brumer, H.

(2017) Plant J 89: 651-670

  • DOI: https://doi.org/10.1111/tpj.13421
  • Primary Citation of Related Structures:  
    5DZE, 5DZF, 5DZG, 5SV8

  • PubMed Abstract: 

    The xyloglucan endotransglycosylase/hydrolase (XTH) gene family encodes enzymes of central importance to plant cell wall remodeling. The evolutionary history of plant XTH gene products is incompletely understood vis-à-vis the larger body of bacterial endoglycanases in Glycoside Hydrolase Family 16 (GH16). To provide molecular insight into this issue, high-resolution X-ray crystal structures and detailed enzyme kinetics of an extant transitional plant endoglucanase (EG) were determined. Functionally intermediate between plant XTH gene products and bacterial licheninases of GH16, Vitis vinifera EG16 (VvEG16) effectively catalyzes the hydrolysis of the backbones of two dominant plant cell wall matrix glycans, xyloglucan (XyG) and β(1,3)/β(1,4)-mixed-linkage glucan (MLG). Crystallographic complexes with extended oligosaccharide substrates reveal the structural basis for the accommodation of both unbranched, mixed-linked (MLG) and highly decorated, linear (XyG) polysaccharide chains in a broad, extended active-site cleft. Structural comparison with representative bacterial licheninases, a xyloglucan endotranglycosylase (XET), and a xyloglucan endohydrolase (XEH) outline the functional ramifications of key sequence deletions and insertions across the phylogenetic landscape of GH16. Although the biological role(s) of EG16 orthologs remains to be fully resolved, the present biochemical and tertiary structural characterization provides key insight into plant cell wall enzyme evolution, which will continue to inform genomic analyses and functional studies across species.

  • Organizational Affiliation

    Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
endo-glucanase207Vitis viniferaMutation(s): 1 
Gene Names: VIT_15s0048g01850
Find proteins for F6I323 (Vitis vinifera)
Explore F6I323 
Go to UniProtKB:  F6I323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6I323
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G41724ZD
GlyCosmos:  G41724ZD
GlyGen:  G41724ZD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BGC

Download Ideal Coordinates CCD File 
C [auth A]beta-D-glucopyranose
C6 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 0.97 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.15α = 90
b = 52.02β = 90
c = 83.06γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary