1FKM

CRYSTAL STRUCTURE OF THE YPT/RAB-GAP DOMAIN OF GYP1P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins.

Rak, A.Fedorov, R.Alexandrov, K.Albert, S.Goody, R.S.Gallwitz, D.Scheidig, A.J.

(2000) EMBO J. 19: 5105-5113

  • DOI: 10.1093/emboj/19.19.5105

  • PubMed Abstract: 
  • We present the 1.9 A resolution crystal structure of the catalytic domain of Gyp1p, a specific GTPase activating protein (GAP) for Ypt proteins, the yeast homologues of Rab proteins, which are involved in vesicular transport. Gyp1p is a member of a l ...

    We present the 1.9 A resolution crystal structure of the catalytic domain of Gyp1p, a specific GTPase activating protein (GAP) for Ypt proteins, the yeast homologues of Rab proteins, which are involved in vesicular transport. Gyp1p is a member of a large family of eukaryotic proteins with shared sequence motifs. Previously, no structural information was available for any member of this class of proteins. The GAP domain of Gyp1p was found to be fully alpha-helical. However, the observed fold does not superimpose with other alpha-helical GAPs (e.g. Ras- and Cdc42/Rho-GAP). The conserved and catalytically crucial arginine residue, identified by mutational analysis, is in a comparable position to the arginine finger in the Ras- and Cdc42-GAPs, suggesting that Gyp1p utilizes an arginine finger in the GAP reaction, in analogy to Ras- and Cdc42-GAPs. A model for the interaction between Gyp1p and the Ypt protein satisfying biochemical data is given.


    Related Citations: 
    • Identification of the Catalytic Domains and their Functionally Critical Arginine Residues of Two Yeast GTPase-activating Proteins Specific for Ypt/Rab Transport GTPases
      Albert, S.,Will, E.,Gallwitz, D.
      (1999) Embo J. 18: 5216


    Organizational Affiliation

    Max-Planck-Institute for Molecular Physiology, Department of Physical Biochemistry, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GYP1P)
A
396Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GYP1
Find proteins for Q08484 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08484
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.199 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.060α = 90.00
b = 74.060β = 90.00
c = 277.753γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
MAR345data collection
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation