5W3X

Crystal structure of PopP2 in complex with IP6, AcCoA and the WRKY domain of RRS1-R .

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.3 of the entry. See complete history. 


Literature

Mechanism of host substrate acetylation by a YopJ family effector.

Zhang, Z.M., Ma, K.W., Gao, L., Hu, Z., Schwizer, S., Ma, W., Song, J.

(2017) Nat Plants 3: 17115-17115

  • DOI: 10.1038/nplants.2017.115
  • Primary Citation of Related Structures:  
    5W3T, 5W3X, 5W3Y, 5W40

  • PubMed Abstract: 

    • The Yersinia outer protein J (YopJ) family of bacterial effectors depends on a novel acetyltransferase domain to acetylate signalling proteins from plant and animal hosts. However, the underlying mechanism is unclear. Here, we report the crystal structures of PopP2, a YopJ effector produced by the plant pathogen Ralstonia solanacearum, in complex with inositol hexaphosphate (InsP 6 ), acetyl-coenzyme A (AcCoA) and/or substrate Resistance to Ralstonia solanacearum 1 (RRS1-R) WRKY ...

    The Yersinia outer protein J (YopJ) family of bacterial effectors depends on a novel acetyltransferase domain to acetylate signalling proteins from plant and animal hosts. However, the underlying mechanism is unclear. Here, we report the crystal structures of PopP2, a YopJ effector produced by the plant pathogen Ralstonia solanacearum, in complex with inositol hexaphosphate (InsP 6 ), acetyl-coenzyme A (AcCoA) and/or substrate Resistance to Ralstonia solanacearum 1 (RRS1-R) WRKY . PopP2 recognizes the WRKYGQK motif of RRS1-R WRKY to position a targeted lysine in the active site for acetylation. Importantly, the PopP2-RRS1-R WRKY association is allosterically regulated by InsP 6 binding, suggesting a previously unidentified role of the eukaryote-specific cofactor in substrate interaction. Furthermore, we provide evidence for the reaction intermediate of PopP2-mediated acetylation, an acetyl-cysteine covalent adduct, lending direct support to the 'ping-pong'-like catalytic mechanism proposed for YopJ effectors. Our study provides critical mechanistic insights into the virulence activity of YopJ class of acetyltransferases.

    Organizational Affiliation: 

    Environmental Toxicology Program, University of California, Riverside, California 92521, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PopP2 proteinA, C352Ralstonia solanacearumMutation(s): 0 
Gene Names: popp, RUN1985_v1_1190012
UniProt
Find proteins for A0A0S4VB05 (Ralstonia solanacearum)
Explore A0A0S4VB05 
Go to UniProtKB:  A0A0S4VB05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S4VB05
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Disease resistance protein RRS1B, D80Arabidopsis thalianaMutation(s): 0 
Gene Names: RRS1, RCH2, RRS1-R, WRKY52
UniProt
Find proteins for C4B7M5 (Arabidopsis thaliana)
Explore C4B7M5 
Go to UniProtKB:  C4B7M5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4B7M5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO
Download Ideal Coordinates CCD File 
F [auth A],
I [auth C]		ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N		 Ligand Interaction
IHP
Query on IHP
Download Ideal Coordinates CCD File 
E [auth A],
H [auth C]		INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
J [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
G [auth B],
K [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.539α = 71.54
b = 87.542β = 84.04
c = 87.548γ = 84
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM119721

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2020-10-14
    Changes: Structure summary