8TWS | pdb_00008tws

AvrB bound with UDP-rhamnose and RIN4 C-NOI motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.336 (Depositor), 0.336 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 
    0.285 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Pseudomonas effector AvrB is a glycosyltransferase that rhamnosylates plant guardee protein RIN4.

Peng, W.Garcia, N.Servage, K.A.Kohler, J.J.Ready, J.M.Tomchick, D.R.Fernandez, J.Orth, K.

(2024) Sci Adv 10: eadd5108-eadd5108

  • DOI: https://doi.org/10.1126/sciadv.add5108
  • Primary Citation Related Structures: 
    8TWJ, 8TWO, 8TWS, 8TXF

  • PubMed Abstract: 

    The plant pathogen Pseudomonas syringae encodes a type III secretion system avirulence effector protein, AvrB, that induces a form of programmed cell death called the hypersensitive response in plants as a defense mechanism against systemic infection. Despite the well-documented catalytic activities observed in other Fido ( Fi c, Do c, and AvrB) proteins, the enzymatic activity and target substrates of AvrB have remained elusive. Here, we show that AvrB is an unprecedented glycosyltransferase that transfers rhamnose from UDP-rhamnose to a threonine residue of the Arabidopsis guardee protein RIN4. We report structures of various enzymatic states of the AvrB-catalyzed rhamnosylation reaction of RIN4, which reveal the structural and mechanistic basis for rhamnosylation by a Fido protein. Collectively, our results uncover an unexpected reaction performed by a prototypical member of the Fido superfamily while providing important insights into the plant hypersensitive response pathway and foreshadowing more diverse chemistry used by Fido proteins and their substrates.


  • Organizational Affiliation
    • Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 40.24 kDa 
  • Atom Count: 2,550 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 353 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Avirulence protein B323Pseudomonas syringaeMutation(s): 0 
Gene Names: avrB
UniProt
Find proteins for P13835 (Pseudomonas savastanoi pv. glycinea)
Explore P13835 
Go to UniProtKB:  P13835
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13835
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RPM1-interacting protein 430Arabidopsis thalianaMutation(s): 0 
Gene Names: RIN4At3g25070MJL12_1
UniProt
Find proteins for Q8GYN5 (Arabidopsis thaliana)
Explore Q8GYN5 
Go to UniProtKB:  Q8GYN5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GYN5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AWU
(Subject of Investigation/LOI)

Query on AWU



Download:Ideal Coordinates CCD File
C [auth A][[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
C15 H24 N2 O16 P2
DRDCJEIZVLVWNC-SLBWPEPYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.336 (Depositor), 0.336 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.279 (DCC) 
  • R-Value Observed: 0.285 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.622α = 90
b = 123.58β = 90
c = 45.552γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134945

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release