X-ray structure of a protein-conducting channel

Abstract

A conserved heterotrimeric membrane protein complex, the Sec61 or SecY complex, forms a protein-conducting channel, allowing polypeptides to be transferred across or integrated into membranes. We report the crystal structure of the complex from Methanococcus jannaschii at a resolution of 3.2 A. The structure suggests that one copy of the heterotrimer serves as a functional translocation channel. The alpha-subunit has two linked halves, transmembrane segments 1-5 and 6-10, clamped together by the gamma-subunit. A cytoplasmic funnel leading into the channel is plugged by a short helix. Plug displacement can open the channel into an 'hourglass' with a ring of hydrophobic residues at its constriction. This ring may form a seal around the translocating polypeptide, hindering the permeation of other molecules. The structure also suggests mechanisms for signal-sequence recognition and for the lateral exit of transmembrane segments of nascent membrane proteins into lipid, and indicates binding sites for partners that provide the driving force for translocation.

Identification of YidC Residues That Define Interactions with the Sec Apparatus

“…YidC is positioned at the lateral gate of SecY, which consists of SecY transmembrane segments 2b, 3, 7, and 8 (1,29). These SecY transmembrane segments are each highly conserved (1), and as determined by cross-linking analysis, each forms contacts with YidC (29).…”

“…The central hourglass-shaped hydrophilic channel is formed by SecY and is flanked by SecE and SecG. SecE, which is essential, is wrapped around the central channel, forming extensive contacts with SecY (1). Loss of SecE leads to instability of SecY (4,5).…”

“…For Sec-dependent YidC substrates, YidC is thought to facilitate the partitioning of nascent transmembrane segments from the SecY channel into the lipid bilayer as well as the proper bundling of transmembrane segments (27,28). Monomeric YidC associated with the Sec translocon is positioned at the lateral gate of SecY (29), which has been proposed to serve as the exit site of transmembrane segments from the translocation channel (1,30).…”

“…The core of the Sec apparatus in bacteria consists of a heterotrimer of the multipass membrane protein SecY and the singlepass transmembrane proteins SecE and SecG (1)(2)(3). The central hourglass-shaped hydrophilic channel is formed by SecY and is flanked by SecE and SecG.…”

Role of the Carboxy Terminus of SecA in Iron Acquisition, Protein Translocation, and Virulence of the Bacterial Pathogen Acinetobacter baumannii

“…Most proteins are translocated in an unfolded state across the cytoplasmic membrane by the Sec system, while fully folded and/or cofactor-containing proteins are usually transported via the Tat pathway. The study of the Sec-dependent transport system, which was pioneered using Escherichia coli as a working model (14,15), shows that it is composed of a cytoplasmic membrane protein-conducting channel consisting of SecY, SecE, and SecG (16,17), as well as SecA (18), an ATPase that associates with the conducting channel and phospholipids in the cytoplasmic membrane and functions as a driving motor for protein translocation in an energy-dependent process (19,20). Proteins destined for export by the Sec-dependent mechanism are targeted to the protein-conducting channel either cotranslationally or posttranslationally (19).…”