7F3N

Structure of PopP2 in apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Secondary-structure switch regulates the substrate binding of a YopJ family acetyltransferase.

Xia, Y.Zou, R.Escouboue, M.Zhong, L.Zhu, C.Pouzet, C.Wu, X.Wang, Y.Lv, G.Zhou, H.Sun, P.Ding, K.Deslandes, L.Yuan, S.Zhang, Z.M.

(2021) Nat Commun 12: 5969-5969

  • DOI: https://doi.org/10.1038/s41467-021-26183-1
  • Primary Citation of Related Structures:  
    7F3N

  • PubMed Abstract: 

    The Yersinia outer protein J (YopJ) family effectors are widely deployed through the type III secretion system by both plant and animal pathogens. As non-canonical acetyltransferases, the enzymatic activities of YopJ family effectors are allosterically activated by the eukaryote-specific ligand inositol hexaphosphate (InsP6). However, the underpinning molecular mechanism remains undefined. Here we present the crystal structure of apo-PopP2, a YopJ family member secreted by the plant pathogen Ralstonia solanacearum. Structural comparison of apo-PopP2 with the InsP6-bound PopP2 reveals a substantial conformational readjustment centered in the substrate-binding site. Combining biochemical and computational analyses, we further identify a mechanism by which the association of InsP6 with PopP2 induces an α-helix-to-β-strand transition in the catalytic core, resulting in stabilization of the substrate recognition helix in the target protein binding site. Together, our study uncovers the molecular basis governing InsP6-mediated allosteric regulation of YopJ family acetyltransferases and further expands the paradigm of fold-switching proteins.


  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, 510632, Guangzhou, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type III effector protein popp2343Ralstonia pseudosolanacearum GMI1000Mutation(s): 0 
Gene Names: popP2RSc0868
UniProt
Find proteins for Q8Y125 (Ralstonia nicotianae (strain GMI1000))
Explore Q8Y125 
Go to UniProtKB:  Q8Y125
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8Y125
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.36α = 90
b = 89.36β = 90
c = 79.871γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
Cootmodel building
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description