2rql: Difference between revisions

Latest revision as of 19:15, 29 May 2024

Solution structure of the E. coli ribosome hibernation promoting factor HPF

Structural highlights

2rql is a 1 chain structure with sequence from Escherichia coli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HPF_ECOLI During stationary phase, promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes. May convert immature 90S particles formed by RMF into 100S ribosomes. May also function as a potential translational inhibitor.^[1] ^[2] ^[3] ^[4]

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 70S Escherichia coli ribosome dimerizes to form an inactive 100S ribosome during stationary phase, which is called "ribosome hibernation". The hibernation promoting factor HPF plays a crucial role in 100S ribosome formation. However, YfiA, a known paralog of HPF inhibits 100S formation, although it shares high sequence similarity. Here, we report the first solution structure of HPF as determined by multi-dimensional NMR. HPF adopts betaalphabetabetabetaalpha-fold and the overall structure is similar to YfiA as expected. However, detailed structure comparison based on the determined structure in this study revealed that there are remarkable differences around the C-terminal portion of helix alpha2, which is not predicted by homology modeling. Furthermore, some acidic residues conserved only in HPF are located at the rim of the common basic patch.

Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function.,Sato A, Watanabe T, Maki Y, Ueta M, Yoshida H, Ito Y, Wada A, Mishima M Biochem Biophys Res Commun. 2009 Nov 27;389(4):580-5. Epub 2009 Sep 10. PMID:19747895^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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:https://dx.doi.org/10.1111/j.1365-2443.2005.00903.x
↑ Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:https://dx.doi.org/10.1093/jb/mvm243
↑ Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:https://dx.doi.org/10.1111/j.1365-2443.2008.01272.x
↑ Sato A, Watanabe T, Maki Y, Ueta M, Yoshida H, Ito Y, Wada A, Mishima M. Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function. Biochem Biophys Res Commun. 2009 Nov 27;389(4):580-5. Epub 2009 Sep 10. PMID:19747895 doi:10.1016/j.bbrc.2009.09.022

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OCA

[1] 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

[2] 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:https://dx.doi.org/10.1111/j.1365-2443.2005.00903.x

[3] Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A. Role of HPF (hibernation promoting factor) in translational activity in Escherichia coli. J Biochem. 2008 Mar;143(3):425-33. doi: 10.1093/jb/mvm243. Epub 2008 Jan 2. PMID:18174192 doi:https://dx.doi.org/10.1093/jb/mvm243

[4] Yoshida H, Ueta M, Maki Y, Sakai A, Wada A. Activities of Escherichia coli ribosomes in IF3 and RMF change to prepare 100S ribosome formation on entering the stationary growth phase. Genes Cells. 2009 Feb;14(2):271-80. doi: 10.1111/j.1365-2443.2008.01272.x. Epub, 2008 Jan 15. PMID:19170772 doi:https://dx.doi.org/10.1111/j.1365-2443.2008.01272.x

[5] Sato A, Watanabe T, Maki Y, Ueta M, Yoshida H, Ito Y, Wada A, Mishima M. Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function. Biochem Biophys Res Commun. 2009 Nov 27;389(4):580-5. Epub 2009 Sep 10. PMID:19747895 doi:10.1016/j.bbrc.2009.09.022

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@@ Line 1: / Line 1: @@
 ==Solution structure of the E. coli ribosome hibernation promoting factor HPF==
-<StructureSection load='2rql' size='340' side='right'caption='[[2rql]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2rql' size='340' side='right'caption='[[2rql]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rql]] 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=2RQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RQL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rql]] 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=2RQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RQL FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hpf, ECs4082 ([https://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='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=2rql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rql OCA], [https://pdbe.org/2rql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rql RCSB], [https://www.ebi.ac.uk/pdbsum/2rql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rql ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/HPF_ECOLI HPF_ECOLI] During stationary phase, promotes and stabilizes dimerization of 70S ribosomes by the ribosome modulation factor (RMF), leading to the formation of inactive 100S ribosomes. May convert immature 90S particles formed by RMF into 100S ribosomes. May also function as a potential translational inhibitor.<ref>PMID:11168583</ref> <ref>PMID:16324148</ref> <ref>PMID:18174192</ref> <ref>PMID:19170772</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Mishima, M]]
+[[Category: Mishima M]]
-[[Category: Sato, A]]
+[[Category: Sato A]]
-[[Category: Hpf]]
-[[Category: Ribosome]]
-[[Category: Ribosome hibernation promoting factor]]
-[[Category: Translation]]

2rql: Difference between revisions

Latest revision as of 19:15, 29 May 2024

Solution structure of the E. coli ribosome hibernation promoting factor HPF

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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