User:Lisa M. Marcheval/Sandbox 1484
From Proteopedia
(Difference between revisions)
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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 == | ||
- | 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. | + | 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 | |
- | + | ||
- | the | + | - 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. | ||
- | 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. . 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. | ||
- | - Structural mimicry of a long-variable-arm tRNA by tmRNA with SmpB. | ||
- | - SmpB binding site. | ||
- | - 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. | ||
- | - Central loop : trypsin sensitive. Dynamically flexible when alone. | + | |
+ | - 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. | - 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. | + | - 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. | - 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 | ||
+ | |||
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 | ||
+ | |||
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)
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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