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1l4s

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Revision as of 08:12, 23 February 2022

Solution structure of ribosome associated factor Y

Structural highlights

1l4s is a 1 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	YFIA ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[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

Escherichia coli protein Y (pY) binds to the small ribosomal subunit and stabilizes ribosomes against dissociation when bacteria experience environmental stress. pY inhibits translation in vitro, most probably by interfering with the binding of the aminoacyl-tRNA to the ribosomal A site. Such a translational arrest may mediate overall adaptation of cells to environmental conditions. We have determined the 3D solution structure of a 112-residue pY and have studied its backbone dynamic by NMR spectroscopy. The structure has a betaalphabetabetabetaalpha topology and represents a compact two-layered sandwich of two nearly parallel alpha helices packed against the same side of a four-stranded beta sheet. The 23 C-terminal residues of the protein are disordered. Long-range angular constraints provided by residual dipolar coupling data proved critical for precisely defining the position of helix 1. Our data establish that the C-terminal region of helix 1 and the loop linking this helix with strand beta2 show significant conformational exchange in the ms- micro s time scale, which may have relevance to the interaction of pY with ribosomal subunits. Distribution of the conserved residues on the protein surface highlights a positively charged region towards the C-terminal segments of both alpha helices, which most probably constitutes an RNA binding site. The observed betaalphabetabetabetaalpha topology of pY resembles the alphabetabetabetaalpha topology of double-stranded RNA-binding domains, despite limited sequence similarity. It appears probable that functional properties of pY are not identical to those of dsRBDs, as the postulated RNA-binding site in pY does not coincide with the RNA-binding surface of the dsRBDs.

Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.,Ye K, Serganov A, Hu W, Garber M, Patel DJ Eur J Biochem. 2002 Nov;269(21):5182-91. PMID:12392550^[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
↑ 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
↑ 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
↑ Ye K, Serganov A, Hu W, Garber M, Patel DJ. Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur J Biochem. 2002 Nov;269(21):5182-91. PMID:12392550

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l4s"

@@ Line 3: / Line 3: @@
 <StructureSection load='1l4s' size='340' side='right'caption='[[1l4s]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1l4s]] 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=1L4S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L4S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1l4s]] is a 1 chain structure with sequence from [https://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=1L4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L4S FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YFIA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YFIA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1l4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4s OCA], [http://pdbe.org/1l4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l4s RCSB], [http://www.ebi.ac.uk/pdbsum/1l4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4s ProSAT]</span></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=1l4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l4s OCA], [https://pdbe.org/1l4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l4s RCSB], [https://www.ebi.ac.uk/pdbsum/1l4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l4s ProSAT]</span></td></tr>
 </table>
 == 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/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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1l4s

From Proteopedia

Revision as of 08:12, 23 February 2022

Solution structure of ribosome associated factor Y

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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