5C2J

Complex structure of the GAP domain of MgcRacGAP and Cdc42


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA.

Murayama, K.Kato-Murayama, M.Hosaka, T.Kitamura, T.Yokoyama, S.Shirouzu, M.

(2024) J Struct Biol 216: 108151-108151

  • DOI: https://doi.org/10.1016/j.jsb.2024.108151
  • Primary Citation of Related Structures:  
    3WPQ, 3WPS, 5C2J, 5C2K

  • PubMed Abstract: 

    MgcRacGAP is a GTPase-activating protein (GAP) for the Rho family GTPases. During cytokinesis, MgcRacGAP localizes to the midbody, where it activates the GTPase activity of Rho family GTPases to facilitate cytokinesis. In the midbody, Aurora B phosphorylates Ser387 within the GAP domain of human MgcRacGAP, a modification that is suggested to influence GTPase preference. However, there are conflicting reports, with some studies indicating that Ser387 phosphorylation does not alter the GTPase preference of MgcRacGAP. This controversy highlights the need for a deeper understanding of the molecular interactions involved, which can be clarified through structural analyses. In the present study, we determined the crystal structures of the wild-type MgcRacGAP GAP domain complexed with CDC42•GDP•AlF 4 - and the S378D phosphomimetic mutant GAP domain fused with RHOA•GDP•AlF 4 - . Additionally, crystal structures of the GAP domains were determined for the S387D and S387A mutants. Our analysis revealed that neither GTPase binding nor S387D mutation affected the overall structure of the GAP domain. However, comparison of the CDC42•MgcRacGAP (wild-type) complex with the RHOA-MgcRacGAP(S378D) fusion protein structure indicated that the S387D mutation caused positional shifts in both CDC42 and RHOA relative to MgcRacGAP. These shifts reduced interactions with CDC42 more severely than those with RHOA. In fact, the S387D mutation decreased the GTPase-activating activity of MgcRacGAP toward CDC42, while its impact on RHOA was only moderate. This difference in the rate of activity reduction may play an important role in GTPase preference.


  • Organizational Affiliation

    Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, 2-1 Seiryo, Aoba, Sendai 980-8575, Japan; RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rac GTPase-activating protein 1208Homo sapiensMutation(s): 0 
Gene Names: RACGAP1KIAA1478MGCRACGAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H5 (Homo sapiens)
Explore Q9H0H5 
Go to UniProtKB:  Q9H0H5
PHAROS:  Q9H0H5
GTEx:  ENSG00000161800 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0H5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 42 homolog198Mus musculusMutation(s): 0 
Gene Names: Cdc42
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60766 (Mus musculus)
Explore P60766 
Go to UniProtKB:  P60766
IMPC:  MGI:106211
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60766
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.324α = 90
b = 74.237β = 96.67
c = 55.423γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary
  • Version 1.4: 2024-12-04
    Changes: Database references