User:Lisa M. Marcheval/Sandbox 1484

Please, click on this link to see the 3D structure of smbp protein :

SmpB, also called Small Protein B, is a protein involved in the trans-translation phenomenon. Indeed, SmpB works with tmRNA and translation factors as EF-Tu in order to unblock the ribosome and the mRNA.

SmpB-bound tmRNA functionally mimics a canonical tRNA as a ribonucleoprotein complex (tRNP), during aminoacylation and entry into the ribosome.Moreover, SmpB is the first protein that has been shown to mimic mRNA. SmpB is also the first protein of which stepwise movements in the ribosome are assumed to mimic those of tRNA in the translating ribosome.

Function

SmpB possess different roles in the cell. Indeed, this protein is part of the enhancement of aminoacylation efficiency of tmRNA, the protection of tmRNA from degradation in the cell, and the recruitment of tmRNA to the stalled ribosome.Moreover, SmpB can stabilize the 3D structure of tmRNA thanks to its loop. And this protein correspond to the anti-codon and D stem of the L-shaped tRNA : SmpB acts as an anticodon arm of tRNA for GTP hydrolysis of EF-Tu on the ribosome

Relevance

For this protein, there are highly conserved among all bacteria and some organelle genomes

Structural highlights

NMR studies have revealed that SmpB consists of an antiparallel β-barrel core with three helices and flexible C-terminal tail residues that are disordered in solution.

Upon entrance of tmRNA into the stalled ribosome, the C-terminal tail of SmpB may recognize the vacant A-site free of mRNA to trigger trans translation.

After peptidyl transfer to Ala-tmRNA occurring essentially in the same manner as that in canonical translation, translocation of peptidyl-Ala-tmRNA/SmpB from the A-site to the P-site may occur. During this event, the extended C-terminal tail folds around the region of the codon-anticodon interaction in the P-site, which drives out mRNA from the P-site.

interaction of the C-terminal tail of SmpB with the mRNA path in the ribosome occurs after hydrolysis of GTP by EF-Tu

- Beta-barrel : (revealed from two bacterial species) adapted to interact with the tmRNA to facilitate their association with translational components.TLD is the crucial binding region of SmpB. Strongly bound to the single-stranded D loop with phe 107 and Val 31 it will form a consecutive stacking structure by interacting with the side chain of arg35 and C48 of tmRNA.

- The association of SmpB and tRNA will provide a structural mimicry of a long-variable-arm tRNA.

- SmpB binding site : there are two SmpB-binding sites on the ribosome; one is around the P-site of the small ribosomal subunit and the other is under the L7/L12 stalk of the large ribosomal subunit.

- Arg 35, phe 107 and VAL 31 play role of the D-arm bases in the canonical tRNA.

- Central loop : trypsin sensitive. Dynamically flexible when alone.

- Loop of SmpB : important tRNA identity determinant of alanyl tRNa synthetase. Close to the conserved helix of the Ala RS RRD1 domain.

- C-terminal region : close to the decoding region of the 30s ribosomal subunit in the A site if ribosome. Corresponding to the 3’ part of the anticodon loop.

- Beta 5 strand : orient the linker helix P2a in the proper direction = the tmRNA could be moved from the A site to the P site of ribosome, after dissociation of SmpB.

- Beta 7 strand : structurally correspond to the anticodon loop.

we could accurately specify the location of the SmpB on the ribosome by superimposition.