2E7S

Crystal structure of the yeast Sec2p GEF domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Asymmetric Coiled-Coil Structure with Guanine Nucleotide Exchange Activity

Sato, Y., Shirakawa, R., Horiuchi, H., Dohmae, N., Fukai, S., Nureki, O.

(2007) Structure 15: 245-252

  • DOI: 10.1016/j.str.2007.01.003
  • Primary Citation of Related Structures:  
    2E7S

  • PubMed Abstract: 

    • Vesicular traffic during exocytosis is regulated by Rab GTPase, Sec4p in yeast, which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. The GEF activity is localized in the N-terminal 160 residues of Sec2p, which lacks sequence ...

    Vesicular traffic during exocytosis is regulated by Rab GTPase, Sec4p in yeast, which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. The GEF activity is localized in the N-terminal 160 residues of Sec2p, which lacks sequence similarity with any other GEFs with known structures, and thereby the guanine nucleotide exchange mechanism by Sec2p remains unknown. Here, we report the crystal structure of the Sec2p GEF domain at 3.0 A resolution. The structure unexpectedly consists of a homodimeric, parallel coiled coil that extends over 180 A. Pull-down and guanine nucleotide exchange analyses on a series of deletion and point mutants of Sec2p unveiled the catalytic residues for its GEF activity as well as the Sec4p binding site, thus presenting a nucleotide exchange mechanism by a simple coiled coil. The present functional analyses allow us to build the Sec2p:Sec4p complex model, which explains the specificity for Rab GTPases by their respective GEF proteins.

    Organizational Affiliation: 

    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Yokohama-shi, Kanagawa, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rab guanine nucleotide exchange factor SEC2A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T135Saccharomyces cerevisiaeMutation(s): 1 
Find proteins for P17065 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17065 
Go to UniProtKB:  P17065
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,TL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.937α = 90
b = 176.569β = 90
c = 181.453γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance