PDBsum entry 2ipc

Transport protein

PDB id: 2ipc

Contents

Protein chains

939 a.a. *

Waters ×1370

* Residue conservation analysis

PDB id:

2ipc

Name:

Transport protein

Title:

Crystal structure of the translocation atpase seca from thermus thermophilus reveals a parallel, head-to-head dimer

Structure:

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

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: seca. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.221 R-free: 0.255

Authors:

D.G.Vassylyev,H.Mori,M.N.Vassylyeva,T.Tsukazaki,Y.Kimura,T.H.Tahirov, K.Ito,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

D.G.Vassylyev et al. (2006). Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer. J Mol Biol, 364, 248-258. PubMed id: 17059823 DOI: 10.1016/j.jmb.2006.09.061

Date:

12-Oct-06 Release date: 28-Nov-06

Protein chains

Q5SIW3  (SECA_THET8) -  Protein translocase subunit SecA from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 997 a.a.

Struc: 939 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

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

reference

DOI no: 10.1016/j.jmb.2006.09.061

J Mol Biol 364:248-258 (2006)

PubMed id: 17059823

Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer.

D.G.Vassylyev, H.Mori, M.N.Vassylyeva, T.Tsukazaki, Y.Kimura, T.H.Tahirov, K.Ito.

ABSTRACT

The mechanism of pre-protein export through the bacterial cytoplasmic membrane, in which the SecA ATPase plays a crucial role as an "energy supplier", is poorly understood. In particular, biochemical and structural studies provide contradictory data as to the oligomeric state of SecA when it is integrated into the active trans-membrane translocase. Here, we report the 2.8 A resolution crystal structure of the Thermus thermophilus SecA protein (TtSecA). Whereas the structure of the TtSecA monomer closely resembles that from other bacteria, the oligomeric state of TtSecA is strikingly distinct. In contrast to the antiparallel (head-to-tail) dimerization reported previously for the other bacterial systems, TtSecA forms parallel (head-to-head) dimers that are reminiscent of open scissors. The dimer interface is abundant in bulky Arg and Lys side-chains from both subunits, which stack on one another to form an unusual "basic zipper" that is highly conserved, as revealed by homology modeling and sequence analysis. The basic zipper is sealed on both ends by two pairs of the salt bridges formed between the basic side-chains from the zipper and two invariant acidic residues. The organization of the dimers, in which the two pre-protein binding domains are located proximal to each other at the tip of the "scissors", might allow a concerted mode of substrate recognition while the opening/closing of the scissors might facilitate translocation.

Selected figure(s)

Figure 1.
Figure 1. The TtSecA structure. (a) The ribbon diagram of the parallel dimer. The two distinct views are shown. BH, the bridge helix. (b) Superposition of the TtSecA and RNA polymerase bridge helices.

Figure 4.
Figure 4. Implications for translocation. (a) The surface representation of the TtSecA dimer (gray) showing the cavity formed between the PPXD and C-terminal domains exposing a large number of the hydrophobic residues (yellow) that might constitute a putative pre-protein (red ellipse) binding site. (b) Sequence alignment showing conservation of the hydrophobic residues (yellow boxes) in the cavity.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 248-258) copyright 2006.

Figures were selected by the author.