2WBL

Three-dimensional structure of a binary ROP-PRONE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

3D Structure of a Binary Rop-Prone Complex: The Final Intermediate for a Complete Set of Molecular Snapshots of the Ropgef Reaction.

Thomas, C.Fricke, I.Weyand, M.Berken, A.

(2009) Biol Chem 390: 427

  • DOI: 10.1515/BC.2009.049
  • Primary Citation of Related Structures:  
    2WBL

  • PubMed Abstract: 
  • Guanine nucleotide exchange factors (GEFs) catalyze the activation of GTP-binding proteins (G proteins) in a multi-step reaction comprising intermediary complexes with and without nucleotide. Rho proteins of plants (ROPs) are activated by novel RopGEFs with a catalytic PRONE domain ...

    Guanine nucleotide exchange factors (GEFs) catalyze the activation of GTP-binding proteins (G proteins) in a multi-step reaction comprising intermediary complexes with and without nucleotide. Rho proteins of plants (ROPs) are activated by novel RopGEFs with a catalytic PRONE domain. We have previously characterized structures of GDP-bound ROP and a ternary complex between plant-specific ROP nucleotide exchanger (PRONE) and ROP including loosely bound GDP. Now, we complete the molecular snapshots of the RopGEF reaction with the nucleotide-free ROP-PRONE structure at 2.9 A. The binary complex surprisingly closely resembles the preceding ternary intermediate including an unusually intact P-loop in the G protein. A striking difference is the prominent contact of the invariant P-loop lysine to a conserved switch II glutamate in ROP, favoring a key role of this interaction in driving out the nucleotide. The nucleotide-free state is supported by additional interactions involving the essential WW-motif in PRONE. We propose that this GEF region stabilizes the intact P-loop conformation, which facilitates re-association with a new nucleotide and further promotes the overall exchange reaction. With our novel structure, we provide further insights into the nucleotide exchange mechanism and present a first example of the complete GEF reaction at a molecular level.


    Related Citations: 
    • Structural Evidence for a Common Intermediate in Small G Protein-Gef Reactions.
      Thomas, C., Fricke, I., Scrima, A., Berken, A., Wittinghofer, A.
      (2007) Mol Cell 25: 141

    Organizational Affiliation

    Department of Structural Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHO OF PLANTS GUANINE NUCLEOTIDE EXCHANGE FACTOR 8A, B365Arabidopsis thalianaMutation(s): 0 
Gene Names: ROPGEF8At3g24620MOB24.21
UniProt
Find proteins for Q9LV40 (Arabidopsis thaliana)
Explore Q9LV40 
Go to UniProtKB:  Q9LV40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LV40
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAC-LIKE GTP-BINDING PROTEIN ARAC2C, D180Arabidopsis thalianaMutation(s): 0 
Gene Names: ARAC2ROP7At5g45970MCL19.1
UniProt
Find proteins for Q38903 (Arabidopsis thaliana)
Explore Q38903 
Go to UniProtKB:  Q38903
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38903
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.55α = 90
b = 110.22β = 90
c = 151.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2011-10-12
    Changes: Database references, Derived calculations