5KLP

Crystal structure of HopZ1a in complex with IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family.

Zhang, Z.M.Ma, K.W.Yuan, S.Luo, Y.Jiang, S.Hawara, E.Pan, S.Ma, W.Song, J.

(2016) Nat.Struct.Mol.Biol. 23: 847-852

  • DOI: 10.1038/nsmb.3279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Effectors secreted by the type III secretion system are essential for bacterial pathogenesis. Members of the Yersinia outer-protein J (YopJ) family of effectors found in diverse plant and animal pathogens depend on a protease-like catalytic triad to ...

    Effectors secreted by the type III secretion system are essential for bacterial pathogenesis. Members of the Yersinia outer-protein J (YopJ) family of effectors found in diverse plant and animal pathogens depend on a protease-like catalytic triad to acetylate host proteins and produce virulence. However, the structural basis for this noncanonical acetyltransferase activity remains unknown. Here, we report the crystal structures of the YopJ effector HopZ1a, produced by the phytopathogen Pseudomonas syringae, in complex with the eukaryote-specific cofactor inositol hexakisphosphate (IP6) and/or coenzyme A (CoA). Structural, computational and functional characterizations reveal a catalytic core with a fold resembling that of ubiquitin-like cysteine proteases and an acetyl-CoA-binding pocket formed after IP6-induced structural rearrangements. Modeling-guided mutagenesis further identified key IP6-interacting residues of Salmonella effector AvrA that are required for acetylating its substrate. Our study reveals the structural basis of a novel class of acetyltransferases and the conserved allosteric regulation of YopJ effectors by IP6.


    Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, Riverside, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orf34
A, B, C
342Pseudomonas syringae pv. syringaeMutation(s): 10 
Find proteins for Q6VE93 (Pseudomonas syringae pv. syringae)
Go to UniProtKB:  Q6VE93
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B, C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
IHP
Query on IHP

Download SDF File 
Download CCD File 
A, B, C
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.153α = 90.00
b = 99.777β = 103.44
c = 71.915γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-24 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Zhang, Z.-M., Song, J.

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2016-08-31
    Type: Database references
  • Version 1.3: 2016-09-21
    Type: Database references
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description