|
|
| (4 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli== | | ==Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli== |
| - | <StructureSection load='1n3g' size='340' side='right' caption='[[1n3g]], [[NMR_Ensembles_of_Models | 29 NMR models]]' scene=''> | + | <StructureSection load='1n3g' size='340' side='right'caption='[[1n3g]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1n3g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N3G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1n3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N3G FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3g OCA], [http://pdbe.org/1n3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n3g RCSB], [http://www.ebi.ac.uk/pdbsum/1n3g PDBsum]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3g OCA], [https://pdbe.org/1n3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n3g RCSB], [https://www.ebi.ac.uk/pdbsum/1n3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3g ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RAIA_ECOLI RAIA_ECOLI]] During stationary phase, prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases. In addition, during environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation initiation and increase translation accuracy. When normal growth conditions are restored, is quickly released from the ribosome. Inhibits translation initiation by blocking the A-site (aminoacyl-tRNA site) and P-site (peptidyl-tRNA site) of the ribosome. Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations. Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of RaiA in vivo.<ref>PMID:10535924</ref> <ref>PMID:11168583</ref> <ref>PMID:11375931</ref> <ref>PMID:15219834</ref> <ref>PMID:16324148</ref> <ref>PMID:15502846</ref> | + | [https://www.uniprot.org/uniprot/YFIA_ECOLI YFIA_ECOLI] During stationary phase, prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases. In addition, during environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation initiation and increase translation accuracy. When normal growth conditions are restored, is quickly released from the ribosome. Inhibits translation initiation by blocking the A-site (aminoacyl-tRNA site) and P-site (peptidyl-tRNA site) of the ribosome. Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations. Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of RaiA in vivo.<ref>PMID:10535924</ref> <ref>PMID:11168583</ref> <ref>PMID:11375931</ref> <ref>PMID:15219834</ref> <ref>PMID:15502846</ref> <ref>PMID:16324148</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n3g_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n3g_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| - | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n3g ConSurf]. |
| | <div style="clear:both"></div> | | <div style="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| Line 30: |
Line 32: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Bayer, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Kalinin, A]] | + | [[Category: Bayer P]] |
| - | [[Category: Rak, A]] | + | [[Category: Kalinin A]] |
| - | [[Category: Shcherbakov, D]] | + | [[Category: Rak A]] |
| - | [[Category: Cold shock]]
| + | [[Category: Shcherbakov D]] |
| - | [[Category: Dsrbd]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: Translation inhibitor]]
| + | |
| Structural highlights
Function
YFIA_ECOLI During stationary phase, prevents 70S dimer formation, probably in order to regulate translation efficiency during transition between the exponential and the stationary phases. In addition, during environmental stress such as cold shock or excessive cell density at stationary phase, stabilizes the 70S ribosome against dissociation, inhibits translation initiation and increase translation accuracy. When normal growth conditions are restored, is quickly released from the ribosome. Inhibits translation initiation by blocking the A-site (aminoacyl-tRNA site) and P-site (peptidyl-tRNA site) of the ribosome. Counteracts miscoding (translation errors) particularly efficiently at magnesium concentrations close to those observed in vivo but less efficiently at higher concentrations. Counteraction of miscoding was shown to be stronger than inhibition of translation, suggesting that the former activity could be the main function of RaiA in vivo.[1] [2] [3] [4] [5] [6]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli was determined by nuclear magnetic resonance with a RMSD of 0.6A. Yfia shows a global beta-alpha-beta-beta-beta-alpha folding topology similar to its homologue HI0257 of Haemophilus influenzae and the double-strand-binding domain of Drosophila Staufen protein. Yfia and HI0257 differ in their surface charges and in the composition of their flexible C-termini, indicating their specificity to different target molecules. Both proteins exhibit a hydrophobic and polar region, which probably functions as interaction site for protein complex formation. Despite their similarity to the dsRBD fold, Yfia does not bind to model fragments of 16S ribosomal RNA as determined by NMR titration and gel shift experiments.
Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli.,Rak A, Kalinin A, Shcherbakov D, Bayer P Biochem Biophys Res Commun. 2002 Dec 20;299(5):710-4. PMID:12470636[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Agafonov DE, Kolb VA, Nazimov IV, Spirin AS. A protein residing at the subunit interface of the bacterial ribosome. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12345-9. PMID:10535924
- ↑ Maki Y, Yoshida H, Wada A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells. 2000 Dec;5(12):965-74. PMID:11168583
- ↑ Agafonov DE, Kolb VA, Spirin AS. Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage. EMBO Rep. 2001 May;2(5):399-402. PMID:11375931 doi:http://dx.doi.org/10.1093/embo-reports/kve091
- ↑ Agafonov DE, Spirin AS. The ribosome-associated inhibitor A reduces translation errors. Biochem Biophys Res Commun. 2004 Jul 23;320(2):354-8. PMID:15219834 doi:http://dx.doi.org/10.1016/j.bbrc.2004.05.171
- ↑ Vila-Sanjurjo A, Schuwirth BS, Hau CW, Cate JH. Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol. 2004 Nov;11(11):1054-9. Epub 2004 Oct 24. PMID:15502846 doi:http://dx.doi.org/10.1038/nsmb850
- ↑ Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A. Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells. 2005 Dec;10(12):1103-12. PMID:16324148 doi:http://dx.doi.org/10.1111/j.1365-2443.2005.00903.x
- ↑ Rak A, Kalinin A, Shcherbakov D, Bayer P. Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli. Biochem Biophys Res Commun. 2002 Dec 20;299(5):710-4. PMID:12470636
|
