Proteopedia - User contributions [en]

User:Lisa M. Marcheval/Sandbox 1484

2018-12-29T12:19:57Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
Please, click on this link to see the 3D structure of smbp protein : <scene name='80/803226/Smbp/4'>TextToBeDisplayed</scene>

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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-29T12:18:27Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<scene name='80/803226/Smbp/4'>TextToBeDisplayed</scene>

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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-29T12:17:53Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-29T12:13:09Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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<scene name='80/803226/Smbp/1'>Text To Be Displayed</scene> 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.

</StructureSection>
== 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

<scene name='80/803226/Smbp/1'>TextToBeDisplayed</scene>

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T10:15:55Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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 ==
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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T10:09:03Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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 ==
enhancement of aminoacylation efficiency of tmRNA, protection of tmRNA from degradation in the cell, and recruitment of tmRNA to the stalled ribosome.
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

== Relevance ==
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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T10:00:53Z

Lisa M. Marcheval:

==SmpB (refered as 3iyq in Protein Data Bank)==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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 ==
enhancement of aminoacylation efficiency of tmRNA, protection of tmRNA from degradation in the cell, and recruitment of tmRNA to the stalled ribosome.
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

== Disease ==

== Relevance ==
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.

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.
tmRNA/SmbP link : TLD is the crucial binding region of SmpB

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.

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. . 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.
- 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. Very important.
- 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.

</StructureSection>
== 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

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T09:27:18Z

Lisa M. Marcheval:

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T09:21:40Z

Lisa M. Marcheval:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
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 ==
enhancement of aminoacylation efficiency of tmRNA, protection of tmRNA from degradation in the cell, and recruitment of tmRNA to the stalled ribosome.
Stabilizing the 3D structure of tmRNA thanks to SmpB loop

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
http://www.pnas.org/content/104/20/8293
https://www.hindawi.com/journals/jna/2011/130581/

<references/>

User:Lisa M. Marcheval/Sandbox 1484

2018-12-27T09:06:19Z

Lisa M. Marcheval:

User:Lisa M. Marcheval/Sandbox 1484

2018-12-05T10:15:22Z

Lisa M. Marcheval: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Lisa M. Marcheval/Sandbox 1484'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Lisa M. Marcheval

2018-12-05T10:15:15Z

Lisa M. Marcheval:

* Full Real Name:
Lisa Mathilde Marcheval
* Position:
Student
* Institution (NO ABBREVIATIONS):
écope supérieure de biotechnologie de Strasbourg
* City, State/Province, Country:
strasbourg
* Field of Expertise or Study: /
*[[User:Lisa M. Marcheval/Sandbox 1484]]

User:Lisa M. Marcheval/Sandbox 1

2018-12-05T10:02:33Z

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Lisa M. Marcheval/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Lisa M. Marcheval

2018-12-05T10:01:17Z

Lisa M. Marcheval:

Atena Farhangian/sandboxA/

2018-12-05T09:45:10Z

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Atena Farhangian/sandboxA/'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>