Figure 8.
At the ribosome, the interaction partners of a signal sequence change with the length of the nascent chains. Depicted are molecular contacts of the signal sequence of pOmpA at the ribosomal exit site. The large ribosomal subunit is outlined in the top panel. Protein L23 located at the orifice of the ribosomal exit tunnel is indicated. The exiting pOmpA chain is illustrated by a cylinder (signal sequence) followed by a solid line, which represents the part of mature OmpA predicted to have emerged from the ribosome (its size is given in number of amino acids in parentheses). The structure labeled SRP is meant to represent Ffh, the 4.5S RNA is not shown. SecA and TF are indicated. Cross-links are illustrated by stars; for pOmpA-89, cross-links at residues 3 and 11 of the signal sequence are simultaneously depicted. Whereas Ffh and TF have been shown to use L23 as docking site, the presumed ribosomal-binding site of SecA has not been identified. Different from the model showing Ffh and TF simultaneously bound to L23, recent data suggest competitive binding between Ffh and TF to L23 (Ullers et al., 2003). This has also been shown for Ffh and SecA with respect to pOmpA-66 (unpublished data), for which reason binding of the signal sequence to either protein was drawn as two alternative situations (labeled A and B). It should be noted that only single adducts were obtained. Therefore in cases in which the model suggests interaction of the signal sequence with two binding partners (e.g., pOmpA-89), these should be taken as representing two separate populations of adducts. The identified cross-linking partners of the signal sequence are Ffh for pOmpA-50; Ffh and SecA for pOmpA-66; Ffh, SecA, TF, and L23 for pOmpA-89; and TF for pOmpA-105. Upon removal of TF, pOmpA-126 (not depicted) was found cross-linked to L23 and Ffh. The bottom scheme invokes the hypothetical possibility of two TF molecules associating with two different sites of a single nascent chain.