PROSITE documentation PDOC00612

Protein secY signatures

The eubacterial secY protein [1] plays an important role in protein export. It interacts with the signal sequences of secretory proteins as well as with two other components of the protein translocation system: secA and secE. SecY is an integral plasma membrane protein of 419 to 492 amino acid residues that apparently contains ten transmembrane segments. Such a structure probably confers to secY a 'translocator' function, providing a channel for periplasmic and outer-membrane precursor proteins.

Homologs of secY are found in archaebacteria [2]. SecY is also encoded in the chloroplast genome of some algae [3] where it could be involved in a prokaryotic-like protein export system across the two membranes of the chloroplast endoplasmic reticulum (CER) which is present in chromophyte and cryptophyte algae.

In eukaryotes, the evolutionary related protein sec61-α plays a role in protein translocation through the endoplasmic reticulum; it is part of a trimeric complex that also consist of sec61-β and γ [4].

We have developed two signature patterns for secY proteins. The first corresponds to the second transmembrane region, which is the most conserved section of these proteins. The second spans the C-terminal part of the fourth transmembrane region, a short intracellular loop, and the N-terminal part of the fifth transmembrane region.