5M6X

Crystal Structure of human RhoGAP mutated in its arginine finger (R85A) in complex with RhoA.GDP.MgF3- human


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, (19) F NMR, and DFT Approaches.

Jin, Y.Molt, R.W.Pellegrini, E.Cliff, M.J.Bowler, M.W.Richards, N.G.J.Blackburn, G.M.Waltho, J.P.

(2017) Angew Chem Int Ed Engl 56: 9732-9735

  • DOI: https://doi.org/10.1002/anie.201703074
  • Primary Citation of Related Structures:  
    5M6X, 5M70

  • PubMed Abstract: 

    We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF 3 - , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O 3G and thence to P G . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAP Arg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.


  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rho GTPase-activating protein 1A,
C [auth H]
240Homo sapiensMutation(s): 1 
Gene Names: ARHGAP1CDC42GAPRHOGAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07960 (Homo sapiens)
Explore Q07960 
Go to UniProtKB:  Q07960
PHAROS:  Q07960
GTEx:  ENSG00000175220 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07960
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein RhoAB,
D [auth I]
192Homo sapiensMutation(s): 0 
Gene Names: RHOAARH12ARHARHO12
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens)
Explore P61586 
Go to UniProtKB:  P61586
PHAROS:  P61586
GTEx:  ENSG00000067560 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61586
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.47α = 90
b = 66.69β = 95.41
c = 76.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description