2ihr: Difference between revisions

Latest revision as of 10:11, 30 August 2023

RF2 of Thermus thermophilus

Structural highlights

2ihr is a 1 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RF2_THET8 Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (Probable). In endogenous ribosomes interacts with P-site tRNA and 23S rRNA (PubMed:18988853, PubMed:20421507). In the presence of truncated mRNA in the 70S ribosome, ArfA and RF2 interact such that the GGQ peptide hydrolysis motif of RF2 rises into the peptidyl-transferase center and releases the ribosome (By similarity). Recruited to stalled E.coli 70S ribosomes by E.coli ArfA, but cannot be functionally accomodated in the peptidyl-transferase center (PubMed:27934701, PubMed:28077875). Note T.thermophilus probably does not encode arfA (Ref.1).[UniProtKB:P07012]^[1] ^[2] ^[3] ^[4] ^[5] [UniProtKB:P07012]

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

Prokaryotic class I release factors (RFs) respond to mRNA stop codons and terminate protein synthesis. They interact with the ribosomal decoding site and the peptidyl-transferase centre bridging these 75 A distant ribosomal centres. For this an elongated RF conformation, with partially unfolded core domains II.III.IV is required, which contrasts the known compact RF crystal structures. The crystal structure of Thermus thermophilus RF2 was determined and compared with solution structure of T. thermophilus and Escherichia coli RF2 by microcalorimetry, circular dichroism spectroscopy and small angle X-ray scattering. The structure of T. thermophilus RF2 in solution at 20 degrees C is predominantly compact like the crystal structure. Thermodynamic analysis point to an initial melting of domain I, which is independent from the melting of the core. The core domains II.III.IV melt cooperatively at the respective physiological temperatures for T. thermophilus and E. coli. Thermodynamic analyses and the X-ray scattering results for T. thermophilus RF2 in solution suggest that the compact conformation of RF2 resembles a physiological state in absence of the ribosome.

Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies.,Zoldak G, Redecke L, Svergun DI, Konarev PV, Voertler CS, Dobbek H, Sedlak E, Sprinzl M Nucleic Acids Res. 2007;35(4):1343-53. Epub 2007 Feb 1. PMID:17272297^[6]

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

References

↑ Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. Insights into translational termination from the structure of RF2 bound to the ribosome. Science. 2008 Nov 7;322(5903):953-6. PMID:18988853 doi:https://dx.doi.org/322/5903/953
↑ Jin H, Kelley AC, Loakes D, Ramakrishnan V. Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. Proc Natl Acad Sci U S A. 2010 Apr 26. PMID:20421507
↑ James NR, Brown A, Gordiyenko Y, Ramakrishnan V. Translational termination without a stop codon. Science. 2016 Dec 16;354(6318):1437-1440. Epub 2016 Dec 1. PMID:27934701 doi:https://dx.doi.org/10.1126/science.aai9127
↑ Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Nature. 2017 Jan 11. doi: 10.1038/nature21053. PMID:28077875 doi:https://dx.doi.org/10.1038/nature21053
↑ Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005 Dec 29;123(7):1255-66. PMID:16377566 doi:https://dx.doi.org/10.1016/j.cell.2005.09.039
↑ Zoldak G, Redecke L, Svergun DI, Konarev PV, Voertler CS, Dobbek H, Sedlak E, Sprinzl M. Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies. Nucleic Acids Res. 2007;35(4):1343-53. Epub 2007 Feb 1. PMID:17272297 doi:10.1093/nar/gkl696

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OCA

[1] Weixlbaumer A, Jin H, Neubauer C, Voorhees RM, Petry S, Kelley AC, Ramakrishnan V. Insights into translational termination from the structure of RF2 bound to the ribosome. Science. 2008 Nov 7;322(5903):953-6. PMID:18988853 doi:https://dx.doi.org/322/5903/953

[2] Jin H, Kelley AC, Loakes D, Ramakrishnan V. Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. Proc Natl Acad Sci U S A. 2010 Apr 26. PMID:20421507

[3] James NR, Brown A, Gordiyenko Y, Ramakrishnan V. Translational termination without a stop codon. Science. 2016 Dec 16;354(6318):1437-1440. Epub 2016 Dec 1. PMID:27934701 doi:https://dx.doi.org/10.1126/science.aai9127

[4] Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H. Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Nature. 2017 Jan 11. doi: 10.1038/nature21053. PMID:28077875 doi:https://dx.doi.org/10.1038/nature21053

[5] Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005 Dec 29;123(7):1255-66. PMID:16377566 doi:https://dx.doi.org/10.1016/j.cell.2005.09.039

[6] Zoldak G, Redecke L, Svergun DI, Konarev PV, Voertler CS, Dobbek H, Sedlak E, Sprinzl M. Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies. Nucleic Acids Res. 2007;35(4):1343-53. Epub 2007 Feb 1. PMID:17272297 doi:10.1093/nar/gkl696

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@@ Line 3: / Line 3: @@
 <StructureSection load='2ihr' size='340' side='right'caption='[[2ihr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ihr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IHR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ihr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IHR FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YP_005821 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=2ihr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ihr OCA], [https://pdbe.org/2ihr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ihr RCSB], [https://www.ebi.ac.uk/pdbsum/2ihr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ihr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/Q5SM01_THET8 Q5SM01_THET8]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (By similarity).
+[https://www.uniprot.org/uniprot/RF2_THET8 RF2_THET8] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (Probable). In endogenous ribosomes interacts with P-site tRNA and 23S rRNA (PubMed:18988853, PubMed:20421507). In the presence of truncated mRNA in the 70S ribosome, ArfA and RF2 interact such that the GGQ peptide hydrolysis motif of RF2 rises into the peptidyl-transferase center and releases the ribosome (By similarity). Recruited to stalled E.coli 70S ribosomes by E.coli ArfA, but cannot be functionally accomodated in the peptidyl-transferase center (PubMed:27934701, PubMed:28077875). Note T.thermophilus probably does not encode arfA (Ref.1).[UniProtKB:P07012]<ref>PMID:18988853</ref> <ref>PMID:20421507</ref> <ref>PMID:27934701</ref> <ref>PMID:28077875</ref> <ref>PMID:16377566</ref> [UniProtKB:P07012]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
 [[Category: Large Structures]]
-[[Category: Dobbek, H]]
+[[Category: Thermus thermophilus]]
-[[Category: Sprinzl, M]]
+[[Category: Dobbek H]]
-[[Category: Voertler, C S]]
+[[Category: Sprinzl M]]
-[[Category: Mixed alpha-beta]]
+[[Category: Voertler CS]]
-[[Category: Translation]]

2ihr: Difference between revisions

Latest revision as of 10:11, 30 August 2023

RF2 of Thermus thermophilus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

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