Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase

Abstract

Bacterial YidC, an evolutionally conserved membrane protein, functions as a membrane protein chaperone in cooperation with the Sec translocon and as an independent insertase for membrane proteins. In Gram-negative bacteria, the transmembrane and periplasmic regions of YidC interact with the Sec proteins, forming a multi-protein complex for Sec-dependent membrane protein integration. Here, we report the crystal structure of full-length Escherichia coli YidC. The structure reveals that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature of YidC, as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase, and provided structural insight into the multi-protein complex.

Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein

“…The importance of the cavity was also supported by photo-cross-linking experiments showing that the inner surface of the cavity of SpoIIIJ interacts with substrate protein in vivo (21). Together with the crystal structure of E. coli YidC (22), it is suggested that having a hydrophilic and positively charged cavity is a feature shared by the YidC family members.…”

YidC/Alb3/Oxa1 Family of Insertases

“…The crystal structure of the Gram-negative E. coli YidC was also reported (PDB ID 3WVF) in late 2014 to 3.2 Å by Kumazaki et al (93). Like the Gram-positive B. halodurans structure, the five conserved core TMs are tightly packed in the periplasmic half of the membrane and spread out in the cytoplasmic half (Fig.…”

“…Others are found on the exterior region of these TMs as well as in the hydrophilic groove located on other TM segments (93) (Fig. 2).…”

Role of the Cytosolic Loop C2 and the C Terminus of YidC in Ribosome Binding and Insertion Activity

“…Crystal structures of YidC proteins from B. halodurans and E. coli (20,40), as well as co-evolution based modeling (27), demonstrate that the large cytosolic loop C1 is folded into a helical hairpin that protrudes from the membrane plane with a tilt determined by an N-terminal proline residue (position 371 within E. coli YidC). Point mutations Y370A and Y377A at the N-terminal end of the loop inactivate YidC in vivo (27), whereas mutations, but not deletions, within the hairpin did not interfere with YidC functionality.…”