2VH9

CRYSTAL STRUCTURE OF NXG1-DELTAYNIIG IN COMPLEX WITH XLLG, A XYLOGLUCAN DERIVED OLIGOSACCHARIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report



Literature

Analysis of Nasturtium Tmnxg1 Complexes by Crystallography and Molecular Dynamics Provides Detailed Insight Into Substrate Recognition by Family Gh16 Xyloglucan Endo-Transglycosylases and Endo-Hydrolases.

Mark, P.Baumann, M.J.Eklof, J.M.Gullfot, F.Michel, G.Kallas, A.M.Teeri, T.T.Brumer, H.Czjzek, M.

(2009) Proteins 75: 820

  • DOI: 10.1002/prot.22291
  • Primary Citation of Related Structures:  
    2VH9

  • PubMed Abstract: 
  • Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting proce ...

    Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting processes as diverse as germination, morphogenesis, and fruit ripening. A high-resolution, three-dimensional structure of a nasturtium (Tropaeolum majus) endo-xyloglucanase loop mutant, TmNXG1-DeltaYNIIG, with an oligosaccharide product bound in the negative active-site subsites, has been solved by X-ray crystallography. Comparison of this novel complex to that of the strict xyloglucan endo-transglycosylase PttXET16-34 from hybrid aspen (Populus tremula x tremuloides), previously solved with a xylogluco-oligosaccharide bound in the positive subsites, highlighted key protein structures that affect the disparate catalytic activities displayed by these closely related enzymes. Combination of these "partial" active-site complexes through molecular dynamics simulations in water allowed modeling of wild-type TmNXG1, TmNXG1-DeltaYNIIG, and wild-type PttXET16-34 in complex with a xyloglucan octadecasaccharide spanning the entire catalytic cleft. A comprehensive analysis of these full-length complexes underscored the importance of various loops lining the active site. Subtle differences leading to a tighter hydrogen bonding pattern on the negative (glycosyl donor) binding subsites, together with loop flexibility on the positive (glycosyl acceptor) binding subsites appear to favor hydrolysis over transglycosylation in GH16 xyloglucan-active enzymes.


    Organizational Affiliation

    School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre. S 106 91 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULASEAB290Tropaeolum majusMutation(s): 0 
EC: 3.2.1.151 (PDB Primary Data), 3.2.1.4 (PDB Primary Data), 2.4.1.207 (UniProt)
Find proteins for Q07524 (Tropaeolum majus)
Explore Q07524 
Go to UniProtKB:  Q07524
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose
C, D, F, G
3 N/A
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose
E, H
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

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A, B
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.54α = 90
b = 100.54β = 90
c = 61.13γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-25
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Atomic model, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Derived calculations
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary