6VSK

Crystal structure of the P-Rex1 DEP1 domain

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-02-11 Released: 2020-07-22 
  • Deposition Author(s): Tesmer, J., Ravala, S.K.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

The first DEP domain of the RhoGEF P-Rex1 autoinhibits activity and contributes to membrane binding.

Ravala, S.K.Hopkins, J.B.Plescia, C.B.Allgood, S.R.Kane, M.A.Cash, J.N.Stahelin, R.V.Tesmer, J.J.G.

(2020) J Biol Chem 295: 12635-12647

  • DOI: https://doi.org/10.1074/jbc.RA120.014534
  • Primary Citation of Related Structures:  
    6VSK

  • PubMed Abstract: 

    Phosphatidylinositol (3,4,5)-trisphosphate (PIP 3 )-dependent Rac exchanger 1 (P-Rex1) catalyzes the exchange of GDP for GTP on Rac GTPases, thereby triggering changes in the actin cytoskeleton and in transcription. Its overexpression is highly correlated with the metastasis of certain cancers. P-Rex1 recruitment to the plasma membrane and its activity are regulated via interactions with heterotrimeric Gβγ subunits, PIP 3 , and protein kinase A (PKA). Deletion analysis has further shown that domains C-terminal to its catalytic Dbl homology (DH) domain confer autoinhibition. Among these, the first dishevelled, Egl-10, and pleckstrin domain (DEP1) remains to be structurally characterized. DEP1 also harbors the primary PKA phosphorylation site, suggesting that an improved understanding of this region could substantially increase our knowledge of P-Rex1 signaling and open the door to new selective chemotherapeutics. Here we show that the DEP1 domain alone can autoinhibit activity in context of the DH/PH-DEP1 fragment of P-Rex1 and interacts with the DH/PH domains in solution. The 3.1 Å crystal structure of DEP1 features a domain swap, similar to that observed previously in the Dvl2 DEP domain, involving an exposed basic loop that contains the PKA site. Using purified proteins, we show that although DEP1 phosphorylation has no effect on the activity or solution conformation of the DH/PH-DEP1 fragment, it inhibits binding of the DEP1 domain to liposomes containing phosphatidic acid. Thus, we propose that PKA phosphorylation of the DEP1 domain hampers P-Rex1 binding to negatively charged membranes in cells, freeing the DEP1 domain to associate with and inhibit the DH/PH module.


  • Organizational Affiliation

    Departments of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3,4,5-trisphosphate-dependent Rac exchanger 1 protein94Homo sapiensMutation(s): 0 
Gene Names: PREX1KIAA1415
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TCU6 (Homo sapiens)
Explore Q8TCU6 
Go to UniProtKB:  Q8TCU6
PHAROS:  Q8TCU6
GTEx:  ENSG00000124126 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TCU6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.152α = 90
b = 103.152β = 90
c = 67.981γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA221289
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL122416
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL071818

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description