2IBM

A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.321 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Novel Dimer Interface and Conformational Changes Revealed by an X-ray Structure of B. subtilis SecA.

Zimmer, J.Li, W.Rapoport, T.A.

(2006) J.Mol.Biol. 364: 259-265

  • DOI: 10.1016/j.jmb.2006.08.044

  • PubMed Abstract: 
  • The SecA ATPase moves polypeptides post-translationally across the plasma membrane of eubacteria, but the mechanism of transport is still unclear. We describe the crystal structure of a novel dimeric form of Bacillus subtilis SecA. Dimerization of Se ...

    The SecA ATPase moves polypeptides post-translationally across the plasma membrane of eubacteria, but the mechanism of transport is still unclear. We describe the crystal structure of a novel dimeric form of Bacillus subtilis SecA. Dimerization of SecA occurs at the prominent groove formed by the nucleotide binding domain 2 (nbd2) and the preprotein cross-linking (ppx) domain. The dimer interface is very large, burying approximately 5400 A(2) of solvent accessible surface per monomer. Single cysteine disulfide cross-linking shows the presence of this novel SecA dimer in solution. In addition, other dimers also exist in solution, arguing that they all are in equilibrium with monomeric SecA and supporting the idea that the monomer may be the functional species. Dimerization of SecA causes an alpha-helix of one subunit to convert to a short beta-strand that participates in beta-sheet formation with strands in the other subunit. This conversion of secondary structure elements occurs close to the connection between the nbd1 and ppx domains, a potential site of interaction with translocation substrate. Comparing the different X-ray structures of B. subtilis SecA suggests that small changes in the nucleotide binding domains could be amplified via helix 1 of the helical scaffold domain (hsd) to generate larger movements of the domains involved in polypeptide binding.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Preprotein translocase secA subunit
A, B
780Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: secA (div+)
Find proteins for P28366 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P28366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.321 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 125.834α = 90.00
b = 166.833β = 90.00
c = 211.990γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance