4H5J

Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P64 form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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This is version 1.2 of the entry. See complete history


Literature

The structure of sec12 implicates potassium ion coordination in sar1 activation.

McMahon, C.Studer, S.M.Clendinen, C.Dann, G.P.Jeffrey, P.D.Hughson, F.M.

(2012) J Biol Chem 287: 43599-43606

  • DOI: https://doi.org/10.1074/jbc.M112.420141
  • Primary Citation of Related Structures:  
    4H5I, 4H5J

  • PubMed Abstract: 

    Coat protein II (COPII)-coated vesicles transport proteins and lipids from the endoplasmic reticulum to the Golgi. Crucial for the initiation of COPII coat assembly is Sec12, a guanine nucleotide exchange factor responsible for activating the small G protein Sar1. Once activated, Sar1/GTP binds to endoplasmic reticulum membranes and recruits COPII coat components (Sec23/24 and Sec13/31). Here, we report the 1.36 Å resolution crystal structure of the catalytically active, 38-kDa cytoplasmic portion of Saccharomyces cerevisiae Sec12. Sec12 adopts a β propeller fold. Conserved residues cluster around a loop we term the "K loop," which extends from the N-terminal propeller blade. Structure-guided site-directed mutagenesis, in conjunction with in vitro and in vivo functional studies, reveals that this region of Sec12 is catalytically essential, presumably because it makes direct contact with Sar1. Strikingly, the crystal structure also reveals that a single potassium ion stabilizes the K loop; bound potassium is, moreover, essential for optimum guanine nucleotide exchange activity in vitro. Thus, our results reveal a novel role for a potassium-stabilized loop in catalyzing guanine nucleotide exchange.


  • Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-exchange factor SEC12
A, B
365Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEC12SED2YNR026CN3244
UniProt
Find proteins for P11655 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11655 
Go to UniProtKB:  P11655
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11655
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.473α = 90
b = 189.473β = 90
c = 53.424γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2013-01-09
    Changes: Database references