3VLA

Crystal structure of edgp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.128 

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This is version 2.1 of the entry. See complete history


Literature

Structural basis for inhibition of xyloglucan-specific endo-beta-1,4-glucanase (XEG) by XEG-protein inhibitor

Yoshizawa, T.Shimizu, T.Hirano, H.Sato, M.Hashimoto, H.

(2012) J Biol Chem 287: 18710-18716

  • DOI: https://doi.org/10.1074/jbc.M112.350520
  • Primary Citation of Related Structures:  
    3VL8, 3VL9, 3VLA, 3VLB

  • PubMed Abstract: 

    Microorganisms such as plant pathogens secrete glycoside hydrolases (GHs) to digest the polysaccharide chains of plant cell walls. The degradation of cell walls by these enzymes is a crucial step for nutrition and invasion. To protect the cell wall from these enzymes, plants secrete glycoside hydrolase inhibitor proteins (GHIPs). Xyloglucan-specific endo-β-1,4-glucanase (XEG), a member of GH family 12 (GH12), could be a great threat to many plants because xyloglucan is a major component of the cell wall in most plants. Understanding the inhibition mechanism of XEG by GHIP is therefore of great importance in the field of plant defense, but to date the mechanism and specificity of GHIPs remain unclear. We have determined the crystal structure of XEG in complex with extracellular dermal glycoprotein (EDGP), a carrot GHIP that inhibits XEG. The structure reveals that the conserved arginines of EDGP intrude into the active site of XEG and interact with the catalytic glutamates of the enzyme. We have also determined the crystal structure of the XEG-xyloglucan complex. These structures show that EDGP closely mimics the XEG-xyloglucan interaction. Although EDGP shares structural similarity to a wheat GHIP (Triticum aestivum xylanase inhibitor-IA (TAXI-IA)) that inhibits GH11 family xylanases, the arrangement of GH and GHIP in the XEG-EDGP complex is distinct from that in the xylanase-TAXI-IA complex. Our findings imply that plants have evolved structures of GHIPs to inhibit different GH family members that attack their cell walls.


  • Organizational Affiliation

    Graduate School of Nanobioscience, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EDGP413Daucus carotaMutation(s): 0 
Gene Names: EDGP1
UniProt
Find proteins for Q05929 (Daucus carota)
Explore Q05929 
Go to UniProtKB:  Q05929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05929
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.128 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.102α = 90
b = 130.102β = 90
c = 44.544γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references
  • Version 1.2: 2013-08-14
    Changes: Database references
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary