8IN6

Eisenia hydrolysis-enhancing protein from Aplysia kurodai complex with tannic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.

Sun, X.Ye, Y.Sakurai, N.Wang, H.Kato, K.Yu, J.Yuasa, K.Tsuji, A.Yao, M.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.88939
  • Primary Citation of Related Structures:  
    8IN1, 8IN3, 8IN4, 8IN6

  • PubMed Abstract: 

    The defensive-offensive associations between algae and herbivores determine marine ecology. Brown algae utilize phlorotannin as their chemical defense against the predator Aplysia kurodai , which uses β-glucosidase ( aku BGL) to digest the laminarin in algae into glucose. Moreover, A. kurodai employs Eisenia hydrolysis-enhancing protein (EHEP) as an offense to protect aku BGL activity from phlorotannin inhibition by precipitating phlorotannin. To underpin the molecular mechanism of this digestive-defensive-offensive system, we determined the structures of the apo and tannic acid (TNA, a phlorotannin analog) bound forms of EHEP, as well as the apo aku BGL. EHEP consisted of three peritrophin-A domains arranged in a triangular shape and bound TNA in the center without significant conformational changes. Structural comparison between EHEP and EHEP-TNA led us to find that EHEP can be resolubilized from phlorotannin precipitation at an alkaline pH, which reflects a requirement in the digestive tract. aku BGL contained two GH1 domains, only one of which conserved the active site. Combining docking analysis, we propose the mechanisms by which phlorotannin inhibits aku BGL by occupying the substrate-binding pocket, and EHEP protects aku BGL against this inhibition by binding with phlorotannin to free the aku BGL pocket.


  • Organizational Affiliation

    Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
25 kDa polyphenol-binding protein229Aplysia kurodaiMutation(s): 0 
UniProt
Find proteins for A0A1B4XTR1 (Aplysia kurodai)
Explore A0A1B4XTR1 
Go to UniProtKB:  A0A1B4XTR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B4XTR1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GGP (Subject of Investigation/LOI)
Query on GGP

Download Ideal Coordinates CCD File 
B [auth A]BETA-1,2,3,4,6-PENTA-O-GALLOYL-D-GLUCOPYRANOSE
C41 H32 O26
QJYNZEYHSMRWBK-CGKDMBANSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.463α = 90
b = 65.356β = 90
c = 67.173γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H01754
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101071
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101083

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release