2JPH

NMR solution structure of the Rho GTPase binding domain of human plexin-b1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into Oncogenic Mutations of Plexin-B1 Based on the Solution Structure of the Rho GTPase Binding Domain

Tong, Y.Hota, P.K.Hamaneh, M.B.Buck, M.

(2008) Structure 16: 246-258

  • DOI: 10.1016/j.str.2007.12.012

  • PubMed Abstract: 
  • The plexin family of transmembrane receptors are important for axon guidance, angiogenesis, but also in cancer. Recently, plexin-B1 somatic missense mutations were found in both primary tumors and metastases of breast and prostate cancers, with sever ...

    The plexin family of transmembrane receptors are important for axon guidance, angiogenesis, but also in cancer. Recently, plexin-B1 somatic missense mutations were found in both primary tumors and metastases of breast and prostate cancers, with several mutations mapping to the Rho GTPase binding domain (RBD) in the cytoplasmic region of the receptor. Here we present the NMR solution structure of this domain, confirming that the protein has both a ubiquitin-like fold and surface features. Oncogenic mutations T1795A and T1802A are located in a loop region, perturb the average structure locally, and have no effect on Rho GTPase binding affinity. Mutations L1815F and L1815P are located at the Rho GTPase binding site and are associated with a complete loss of binding for Rac1 and Rnd1. Both are found to disturb the conformation of the beta3-beta4 sheet and the orientation of surrounding side chains. Our study suggests that the oncogenic behavior of the mutants can be rationalized with reference to the structure of the RBD of plexin-B1.


    Related Citations: 
    • When monomers are preferred: a strategy for the identification and disruption of weakly oligomerized proteins.
      Tong, Y.,Hughes, D.,Placanica, L.,Buck, M.
      (2005) Structure 13: 7
    • The Semaphorin 4D receptor Plexin-B1 is a GTPase activating protein for R-Ras.
      Oinuma, I.,Ishikawa, Y.,Katoh, H.,Negishi, M.
      (2004) Science 305: 862
    • Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain
      Tong, Y.,Chugha, P.,Hota, P.K.,Alviani, R.S.,Li, M.,Tempel, W.,Shen, L.,Park, H.W.,Buck, M.
      (2007) J.Biol.Chem. 282: 37215
    • Plexin-B semaphorin receptors interact directly with active Rac and regulate the actin cytoskeleton by activating Rho.
      Driessens, M.H.,Nobes, C.D.,Self, A.,Jordens, I.,Goodman, C.S.,Hall, A.
      (2001) CURR.BIOL. 11: 339
    • 1H, 15N and 13C Resonance assignments and secondary structure determination reveal that the minimal Rac1 GTPase binding domain of plexin-B1 has a ubiquitin fold.
      Tong, Y.,Buck, M.
      (2005) J.Biomol.NMR 31: 369
    • The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner.
      Vikis, H.G.,Li, W.,He, Z.,Guan, K.L.
      (2000) Proc.Natl.Acad.Sci.USA 97: 12457


    Organizational Affiliation

    Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plexin-B1
A
123Homo sapiensMutation(s): 1 
Gene Names: PLXNB1 (KIAA0407, PLXN5, SEP)
Find proteins for O43157 (Homo sapiens)
Go to Gene View: PLXNB1
Go to UniProtKB:  O43157
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 
  • Olderado: 2JPH Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-05-11 
  • Released Date: 2008-03-18 
  • Deposition Author(s): Tong, Y., Buck, M.

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance