1M74

Crystal structure of Mg-ADP-bound SecA from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nucleotide Control of Interdomain Interactions in the Conformational Reaction Cycle of SecA

Hunt, J.F.Weinkauf, S.Henry, L.Fak, J.J.McNicholas, P.Oliver, D.B.Deisenhofer, J.

(2002) Science 297: 2018-2026

  • DOI: 10.1126/science.1074424
  • Primary Citation of Related Structures:  
    1M6N, 1M74

  • PubMed Abstract: 
  • The SecA adenosine triphosphatase (ATPase) mediates extrusion of the amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible binding to the SecYEG translocon. We have determined the crystal structure of SecA with ...

    The SecA adenosine triphosphatase (ATPase) mediates extrusion of the amino termini of secreted proteins from the eubacterial cytosol based on cycles of reversible binding to the SecYEG translocon. We have determined the crystal structure of SecA with and without magnesium-adenosine diphosphate bound to the high-affinity ATPase site at 3.0 and 2.7 angstrom resolution, respectively. Candidate sites for preprotein binding are located on a surface containing the SecA epitopes exposed to the periplasm upon binding to SecYEG and are thus positioned to deliver preprotein to SecYEG. Comparisons with structurally related ATPases, including superfamily I and II ATP-dependent helicases, suggest that the interaction geometry of the tandem motor domains in SecA is modulated by nucleotide binding, which is shown by fluorescence anisotropy experiments to reverse an endothermic domain-dissociation reaction hypothesized to gate binding to SecYEG.


    Related Citations: 
    • Ping-pong cross-validation in real space: a method to increase the phasing power of a partial model without risk of phase bias
      Hunt, J.F., Deisenhofer, J.
      (2002) To be published --: --
    • Conformational stabilization and crystallization of the SecA translocation ATPase from Bacillus subtilis
      Weinkauf, S., Hunt, J.F., Scheuring, J., Henry, L., Fak, J.J., Oliver, D.B., Deisenhofer, J.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 559

    Organizational Affiliation

    Department of Biological Sciences, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA. hunt@sid.bio.columbia.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Preprotein translocase secAA802Bacillus subtilisMutation(s): 0 
Gene Names: Div
Find proteins for P28366 (Bacillus subtilis (strain 168))
Explore P28366 
Go to UniProtKB:  P28366
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ADPKd :  100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.245α = 90
b = 131.245β = 90
c = 150.453γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance