PDBsum entry 2ibm

Protein transport

PDB id: 2ibm

Contents

Protein chains

780 a.a. *

Ligands

ADP

* Residue conservation analysis

PDB id:

2ibm

Name:

Protein transport

Title:

A novel dimer interface and conformational changes revealed by an x- ray structure of b. Subtilis seca

Structure:

Preprotein translocase seca subunit. Chain: a, b. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Gene: seca, div+. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

3.20Å R-factor: 0.321 R-free: 0.323

Authors:

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

Key ref:

J.Zimmer et al. (2006). A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA. J Mol Biol, 364, 259-265. PubMed id: 16989859 DOI: 10.1016/j.jmb.2006.08.044

Date:

11-Sep-06 Release date: 14-Nov-06

Protein chains

P28366  (SECA_BACSU) -  Protein translocase subunit SecA from Bacillus subtilis (strain 168)

Seq: 841 a.a.

Struc: 780 a.a.

Enzyme reactions

• Enzyme class: E.C.7.4.2.8 - protein-secreting ATPase.
• Reaction: ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2

ATP + H2O + cellular proteinSide 1 = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + cellular proteinSide 2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2006.08.044

J Mol Biol 364:259-265 (2006)

PubMed id: 16989859

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

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

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 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.

Selected figure(s)

Figure 1.
Figure 1. Dimeric structure of B. subtilis SecA. (a) Dimerization of SecA occurs at the prominent groove formed by nbd2 and the ppx domain. Chain a is in gray and chain b is color-coded for the individual domains of SecA. (b) Dimer interface of chain a and b: residues 551 to 554 of subunit a form a novel parallel β-sheet with the highly conserved region connecting nbd1 to the ppx domain (residues 221 to 224). (c) The equivalent dimer interface of chain b and a: the α-helical conformation of residues 552 to 559 of chain b is seen in all previously determined SecA structures. All Figures were generated using Pymol [http://pymol.sourceforge.net/].

Figure 3.
Figure 3. Interactions within the helical scaffold domain and within the dimer interface. (a) The swiveling of the C-terminal domain of helix 1 of hsd is propagated via van der Waals interactions between Ile610 and Trp724. The conserved salt bridge between Arg614 and Asp721 is broken in the new structure presented here. Arrows indicate the direction of movement of secondary structure elements. Right panel: a magnified view of the B. subtilis SecA structure (pdb code 1M6N, gray) superimposed on subunit a of the new SecA dimer (orange). (b) Asn588 of helix 1 in the helical scaffold domain is located at the dimer interface. Replacement by cysteine can be used to form disulfide-linked monomers.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 259-265) copyright 2006.

Figures were selected by an automated process.