User:Lisa M. Marcheval/Sandbox 1484

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Stabilizing the 3D structure of tmRNA thanks to SmpB loop
Stabilizing the 3D structure of tmRNA thanks to SmpB loop
Correspond to the anti-codon and D stem of the L-shaped tRNA : acting as an anticodon arm of tRNA for GTP hydrolysis of EF-Tu on the ribosome
Correspond to the anti-codon and D stem of the L-shaped tRNA : acting as an anticodon arm of tRNA for GTP hydrolysis of EF-Tu on the ribosome
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== Disease ==
 
== Relevance ==
== Relevance ==
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== Structural highlights ==
== Structural highlights ==
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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.
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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.
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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.
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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.
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SmpB/ribosome link : 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.
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interaction of the C-terminal tail of SmpB with the mRNA path in the ribosome occurs after hydrolysis of GTP by EF-Tu
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tmRNA/SmbP link : TLD is the crucial binding region of SmpB
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the C-terminal tail of SmpB mimics mRNA in the A-site and P-site and that these binding sites reflect the pre- and posttranslocation steps of trans-translation.
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- 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.
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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.
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- The association of SmpB and tRNA will provide a structural mimicry of a long-variable-arm tRNA.
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- 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.
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interaction of the C-terminal tail of SmpB with the mRNA path in the ribosome occurs after hydrolysis of GTP by EF-Tu
 
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- Beta-barrel : (revealed from two bacterial species) adapted to interact with the tmRNA to facilitate their association with translational components. . Strongly bound to the single-stranded D loop with phe 107 and Val 31. Form a consecutive stacking structure by interacting with the side chain of arg35 and C48 of tmRNA.
 
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- Structural mimicry of a long-variable-arm tRNA by tmRNA with SmpB.
 
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- SmpB binding site.
 
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- Amino acid residues : participate in the base stacking.
 
- Arg 35, phe 107 and VAL 31 play role of the D-arm bases in the canonical tRNA.
- Arg 35, phe 107 and VAL 31 play role of the D-arm bases in the canonical tRNA.
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- Central loop : trypsin sensitive. Dynamically flexible when alone.
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- Central loop : trypsin sensitive. Dynamically flexible when alone.
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- Loop of SmpB : important tRNA identity determinant of alanyl tRNa synthetase. Close to the conserved helix of the Ala RS RRD1 domain.
- Loop of SmpB : important tRNA identity determinant of alanyl tRNa synthetase. Close to the conserved helix of the Ala RS RRD1 domain.
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- 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. Very important.
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- 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.
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- 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.
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- 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.
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- Beta 7 strand : structurally correspond to the anticodon loop.
- Beta 7 strand : structurally correspond to the anticodon loop.
we could accurately specify the location of the SmpB on the ribosome by superimposition.
we could accurately specify the location of the SmpB on the ribosome by superimposition.
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https://www.frontiersin.org/articles/10.3389/fmicb.2014.00421/full
https://www.frontiersin.org/articles/10.3389/fmicb.2014.00421/full
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http://www.jbc.org/content/280/7/5503.full
http://www.jbc.org/content/280/7/5503.full
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https://en.wikipedia.org/wiki/Transfer_RNA
https://en.wikipedia.org/wiki/Transfer_RNA
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https://www.sciencedirect.com/science/article/pii/S0014579302023335
https://www.sciencedirect.com/science/article/pii/S0014579302023335
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https://www.uniprot.org/uniprot/P0A832
https://www.uniprot.org/uniprot/P0A832
<references/>
<references/>

Revision as of 10:09, 27 December 2018

SmpB (refered as 3iyq in Protein Data Bank)

Caption for this structure

Drag the structure with the mouse to rotate

References

http://www.pnas.org/content/104/20/8293

https://www.hindawi.com/journals/jna/2011/130581/

https://www.frontiersin.org/articles/10.3389/fmicb.2014.00421/full

http://www.jbc.org/content/280/7/5503.full

https://en.wikipedia.org/wiki/Transfer_RNA

https://www.sciencedirect.com/science/article/pii/S0014579302023335

https://www.uniprot.org/uniprot/P0A832


Proteopedia Page Contributors and Editors (what is this?)

Lisa M. Marcheval

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