3RAP

The small G protein Rap2 in a non catalytic complex with GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the small G protein Rap2 in a non-catalytic complex with GTP.

Menetrey, J.Cherfils, J.

(1999) Proteins 37: 465-473


  • PubMed Abstract: 
  • We report a novel crystal form of the small G protein Rap2A in complex with GTP which has no GTPase activity in the crystal. The asymmetric unit contains two complexes which show that a conserved switch I residue, Tyr 32, contributes an extra hydroge ...

    We report a novel crystal form of the small G protein Rap2A in complex with GTP which has no GTPase activity in the crystal. The asymmetric unit contains two complexes which show that a conserved switch I residue, Tyr 32, contributes an extra hydrogen bond to the gamma-phosphate of GTP as compared to related structures with GTP analogs. Since GTP is not hydrolyzed in the crystal, this interaction is unlikely to contribute to the intrinsic GTPase activity. The comparison of other G protein structures to the Rap2-GTP complex suggests that an equivalent interaction is likely to exist in their GTP form, whether unbound or bound to an effector. This interaction has to be released to allow the GAP-activated GTPase, and presumably the intrinsic GTPase activity as well. We also discuss the definition of the flexible regions and their hinges in the light of this structure and the expanding database of G protein structures. We propose that the switch I and switch II undergo either partial or complete disorder-to-order transitions according to their cellular status, thus defining a complex energy landscape comprising more than two conformational states. We observe in addition that the region connecting the switch I and switch II is flexible in Rap2 and other G proteins. This region may be important for protein-protein interactions and possibly behave as a conformational lever arm, as characterized for Arf. Taken together, these observations suggest that the structural mechanisms of small G proteins are significantly driven by entropy-based free energy changes.


    Related Citations: 
    • Crystal Structures of the Small G Protein Rap2A in Complex with its Substrate GTP, with GDP and with GTPgS
      Cherfils, J.,Menetrey, J.,Lebras, G.,Lebras, G.,Janoueix-Lerosey, I.,De Gunzburg, J.,Garel, J.R.,Auzat, I.
      (1997) Embo J. 16: 5582


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (G protein RAP2A)
R, S
167Homo sapiensMutation(s): 0 
Gene Names: RAP2A
Find proteins for P10114 (Homo sapiens)
Go to Gene View: RAP2A
Go to UniProtKB:  P10114
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download SDF File 
Download CCD File 
R, S
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
R, S
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.010α = 90.00
b = 59.830β = 97.07
c = 68.440γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-08
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection
  • Version 1.4: 2018-04-11
    Type: Data collection