The Crystal Structure of the Periplasmic Domain of the Escherichia coli Membrane Protein Insertase YidC Contains a Substrate Binding Cleft

Abstract

In bacteria the biogenesis of inner membrane proteins requires targeting and insertion factors such as the signal recognition particle and the Sec translocon. YidC is an essential membrane protein involved in the insertion of inner membrane proteins together with the Sec translocon, but also as a separate entity. YidC of Escherichia coli is a member of the conserved YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a large periplasmic domain (P1). We determined the crystal structure of the periplasmic domain of YidC from E. coli (P1D) at 1.8 Å resolution. The structure of P1D shows the conserved ␤-supersandwich fold of carbohydrate-binding proteins and an ␣-helical linker region at the C terminus that packs against the ␤-supersandwich by a highly conserved interface. P1D exhibits an elongated cleft of similar architecture as found in the structural homologs. However, the electrostatic properties and molecular details of the cleft make it unlikely to interact with carbohydrate substrates. The cleft in P1D is occupied by a polyethylene glycol molecule suggesting an elongated peptide or acyl chain as a natural ligand. The region of P1D previously reported to interact with SecF maps to a surface area in the vicinity of the cleft. The conserved C-terminal region of the P1 domain was reported to be essential for the membrane insertase function of YidC. The analysis of this region suggests a role in membrane interaction and/or in the regulation of YidC interaction with binding partners.

The Conserved Third Transmembrane Segment of YidC Contacts Nascent Escherichia coli Inner Membrane Proteins

“…Yet little structural information is available about YidC. The crystal structure of the major periplasmic domain in between TM1 and TM2 has been solved recently, but this domain is almost entirely dispensable for the insertase function (32,33). Furthermore, a low resolution electron cryo-microscopy image of the native YidC protein has been presented but provides too little detail to offer mechanistic insight (34).…”

Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase fromBacillus halodurans

“…The YidC proteins from Gram-negative bacteria possess an additional TM helix and a large periplasmic region formed by the N-termini of the core TM region. Structural information about YidC has been limited to the crystal structures of the large periplasmic domain and electron-microscopic studies (Oliver & Paetzel, 2008;Ravaud et al, 2008;Kohler et al, 2009;Seitl et al, 2014).…”

The YidC/Oxa1/Alb3 protein family: common principles and distinct features

“…The importance of core TMS2 (TMS3 in E. coli YidC) is also evident from chemical cross-linking to known YidC substrates (Klenner et al , 2008 ;Yu et al , 2008 ) all across the membrane helix, N-terminal domain is composed of an additional TMS followed by a large periplasmatic loop. Recently, the crystal structure of the periplasmatic domain of E. coli YidC was solved (Oliver and Paetzel , 2008 ;Ravaud et al , 2008 ). It confirmed the α -helical conformation of the functionally essential region preceding the first core TMS and revealed a potential protein binding cleft composed of a β -supersandwich fold flexibly linked to the TMSs via α -helices.…”