1NF1

THE GAP RELATED DOMAIN OF NEUROFIBROMIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of the GAP-related domain from neurofibromin and its implications.

Scheffzek, K.Ahmadian, M.R.Wiesmuller, L.Kabsch, W.Stege, P.Schmitz, F.Wittinghofer, A.

(1998) EMBO J. 17: 4313-4327

  • DOI: 10.1093/emboj/17.15.4313

  • PubMed Abstract: 
  • Neurofibromin is the product of the NF1 gene, whose alteration is responsible for the pathogenesis of neurofibromatosis type 1 (NF1), one of the most frequent genetic disorders in man. It acts as a GTPase activating protein (GAP) on Ras; based on hom ...

    Neurofibromin is the product of the NF1 gene, whose alteration is responsible for the pathogenesis of neurofibromatosis type 1 (NF1), one of the most frequent genetic disorders in man. It acts as a GTPase activating protein (GAP) on Ras; based on homology to p120GAP, a segment spanning 250-400 aa and termed GAP-related domain (NF1GRD; 25-40 kDa) has been shown to be responsible for GAP activity and represents the only functionally defined segment of neurofibromin. Missense mutations found in NF1 patients map to NF1GRD, underscoring its importance for pathogenesis. X-ray crystallographic analysis of a proteolytically treated catalytic fragment of NF1GRD comprising residues 1198-1530 (NF1-333) of human neurofibromin reveals NF1GRD as a helical protein that resembles the corresponding fragment derived from p120GAP (GAP-334). A central domain (NF1c) containing all residues conserved among RasGAPs is coupled to an extra domain (NF1ex), which despite very limited sequence homology is surprisingly similar to the corresponding part of GAP-334. Numerous point mutations found in NF1 patients or derived from genetic screening protocols can be analysed on the basis of the three-dimensional structural model, which also allows identification of the site where structural changes in a differentially spliced isoform are to be expected. Based on the structure of the complex between Ras and GAP-334 described earlier, a model of the NF1GRD-Ras complex is proposed which is used to discuss the strikingly different properties of the Ras-p120GAP and Ras-neurofibromin interactions.


    Related Citations: 
    • The Gap-Related Domain of the Neurofibromatosis Type I Gene Product Interacts with Ras P21
      Martin, G.A.,Viskochil, D.,Bollag, G.,Mccabe, P.C.,Crosier, W.J.,Hausbruck, H.,Conroy, L.,Clark, R.,O'Connell, P.,Cawthon, R.M.,Innis, M.A.,Mccormick, F.
      (1990) Cell 63: 843
    • Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras:Gdp, Tetrafluoroaluminate and Gtpase-Activating Proteins
      Mittal, R.,Ahmadian, M.R.,Goody, R.S.,Wittinghofer, A.
      (1996) Science 273: 115
    • The Catalytic Domain of the Neurofibromatosis Type I Gene Product Stimulates Ras Gtpase and Complements Ira Mutants of S. Cerevisiae
      Xu, G.,Lin, B.,Tanaka, K.,Dunn, D.,Wod, D.,Gesteland, R.,White, R.,Weiss, R.,Tamanoi, F.
      (1990) Cell 63: 835
    • 3-Dimensional Structure of the Gtpase Activating Domain of Human P120Gap and Implications for the Interaction with Ras
      Scheffzek, K.,Lautwein, A.,Kabsch, W.,Ahmadian, M.R.,Wittinghofer, A.
      (1996) Nature 384: 591
    • Confirmation of the Arginine-Finger Hypothesis for the Gap-Stimulated GTP- Hydrolysis Reaction of Ras
      Ahmadian, M.R.,Stege, P.,Scheffzek, K.,Wittinghofer, A.
      (1997) Nat.Struct.Mol.Biol. 4: 686
    • The Neurofibromatosis Type I Gene and its Protein Product
      Gutmann, D.H.,Collins, F.S.
      (1993) Neuron 10: 335
    • The NF1 Locus Encodes a Protein Functionally Related to Mammalian Gap and Yeast Ira Proteins
      Ballester, R.,Marchuk, D.,Boguski, M.,Saulino, A.,Letcher, R.,Wigler, M.,Collins, F.
      (1990) Cell 63: 851
    • The Ras-Rasgap Complex: Structural Basis for Gtpase Activation and its Loss in Oncogenic Ras Mutants
      Scheffzek, K.,Ahmadian, M.R.,Kabsch, W.,Wiesmueller, L.,Lautwein, A.,Schmitz, F.,Wittinghofer, A.
      (1997) Science 277: 333
    • Structural Differences in the Minimal Catalytic Domains of the Gtpasse- Activating Proteins P120Gap and Neurofibromin
      Ahmadian, M.R.,Wiesmueller, L.,Lautwein, A.,Bischoff, F.R.,Wittinghofer, A.
      (1996) J.Biol.Chem. 271: 16409
    • Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis
      Pai, E.F.,Krengel, U.,Petsko, G.A.,Goody, R.S.,Kabsch, W.,Wittinghofer, A.
      (1990) Embo J. 9: 2351


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany. Klas.Scheffzek@mpi-dortmund.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (NEUROFIBROMIN)
A
333Homo sapiensGene Names: NF1
Find proteins for P21359 (Homo sapiens)
Go to Gene View: NF1
Go to UniProtKB:  P21359
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.266 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.250α = 90.00
b = 58.300β = 118.00
c = 74.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-20
    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: 2017-10-04
    Type: Refinement description