5KLP

Crystal structure of HopZ1a in complex with IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1038/nsmb.3279
  • Primary Citation of Related Structures:  
    5KLP, 5KLQ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orf34
A, B, C
342Pseudomonas syringae pv. syringaeMutation(s): 10 
UniProt
Find proteins for Q6VE93 (Pseudomonas syringae pv. syringae)
Explore Q6VE93 
Go to UniProtKB:  Q6VE93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VE93
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
IHP Binding MOAD:  5KLP Kd: 2.27e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.153α = 90
b = 99.777β = 103.44
c = 71.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2016-08-31
    Changes: Database references
  • Version 1.3: 2016-09-21
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.5: 2020-10-14
    Changes: Structure summary