3BS6

1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC

Summary for 3BS6

• Entry DOI: 10.2210/pdb3bs6/pdb
• Descriptor: Inner membrane protein oxaA, CALCIUM ION, TETRAETHYLENE GLYCOL, ... (7 entities in total)
• Functional Keywords: yidc/oxa1/alb3 family, membrane insertion, chaperone, sec translocon, periplasmic domain, beta supersandwich fold, helical linker domain, membrane protein, protein transport
• Biological source: Escherichia coli
• Cellular location: Cell inner membrane; Multi-pass membrane protein: P25714
• Total number of polymer chains: 2
• Total formula weight: 63449.20

Authors

Ravaud, S.,Sinning, I. (deposition date: 2007-12-22, release date: 2008-02-12, Last modification date: 2024-10-30)

Primary citation

Ravaud, S.,Stjepanovic, G.,Wild, K.,Sinning, I.
The Crystal Structure of the Periplasmic Domain of the Escherichia coli Membrane Protein Insertase YidC Contains a Substrate Binding Cleft
J.Biol.Chem., 283:9350-9358, 2008

PubMed 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 A resolution. The structure of P1D shows the conserved beta-supersandwich fold of carbohydrate-binding proteins and an alpha-helical linker region at the C terminus that packs against the beta-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.

PubMed: 18234665
DOI: 10.1074/jbc.M710493200

Experimental method

X-RAY DIFFRACTION (1.8 Å)