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| | ==Solution structure of the GGQ domain of YaeJ protein from Escherichia coli== | | ==Solution structure of the GGQ domain of YaeJ protein from Escherichia coli== |
| - | <StructureSection load='2rtx' size='340' side='right'caption='[[2rtx]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2rtx' size='340' side='right'caption='[[2rtx]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2rtx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2rtx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTX FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yaeJ, b0191, JW0187 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | </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=2rtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rtx OCA], [https://pdbe.org/2rtx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rtx RCSB], [https://www.ebi.ac.uk/pdbsum/2rtx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rtx ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aminoacyl-tRNA_hydrolase Aminoacyl-tRNA hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.29 3.1.1.29] </span></td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rtx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rtx OCA], [https://pdbe.org/2rtx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rtx RCSB], [https://www.ebi.ac.uk/pdbsum/2rtx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rtx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ARFB_ECOLI ARFB_ECOLI]] Rescues stalled ribosomes. Can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs that contain rare codon clusters. May function as a complementary rescue system when the stalled ribosome can not be rescued by the SsrA(tmRNA)-SmpB quality control system or the alternative ribosome-rescue factor A.<ref>PMID:21418110</ref> <ref>PMID:21051357</ref>
| + | [https://www.uniprot.org/uniprot/ARFB_ECOLI ARFB_ECOLI] Rescues stalled ribosomes. Can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs that contain rare codon clusters. May function as a complementary rescue system when the stalled ribosome can not be rescued by the SsrA(tmRNA)-SmpB quality control system or the alternative ribosome-rescue factor A.<ref>PMID:21418110</ref> <ref>PMID:21051357</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aminoacyl-tRNA hydrolase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Ecoli]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Enomoto, M]] | + | [[Category: Enomoto M]] |
| - | [[Category: Guntert, P]] | + | [[Category: Guntert P]] |
| - | [[Category: Kogure, H]] | + | [[Category: Kogure H]] |
| - | [[Category: Nameki, N]] | + | [[Category: Nameki N]] |
| - | [[Category: Tochio, N]] | + | [[Category: Tochio N]] |
| - | [[Category: Ggc domain]]
| + | |
| - | [[Category: Hydrolase]]
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| Structural highlights
Function
ARFB_ECOLI Rescues stalled ribosomes. Can hydrolyze peptidyl-tRNA on ribosomes stalled by both non-stop mRNAs and mRNAs that contain rare codon clusters. May function as a complementary rescue system when the stalled ribosome can not be rescued by the SsrA(tmRNA)-SmpB quality control system or the alternative ribosome-rescue factor A.[1] [2]
Publication Abstract from PubMed
The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on a non-stop mRNA, and for ribosome-binding efficiency. We focused on residues conserved among bacterial YaeJ proteins. Additionally, we determined the solution structure of the GGQ domain of YaeJ from E. coli using nuclear magnetic resonance spectroscopy. YaeJ and a human homolog, ICT1, had similar levels of PTH activity, despite various differences in sequence and structure. While no YaeJ-specific residues important for PTH activity occur in the structured GGQ domain, Arg118, Leu119, Lys122, Lys129 and Arg132 in the following C-terminal extension were required for PTH activity. All of these residues are completely conserved among bacteria. The equivalent residues were also found in the C-terminal extension of ICT1, allowing an appropriate sequence alignment between YaeJ and ICT1 proteins from various species. Single amino acid substitutions for each of these residues significantly decreased ribosome-binding efficiency. These biochemical findings provide clues to understanding how YaeJ enters the A-site of stalled ribosomes.
Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ.,Kogure H, Handa Y, Nagata M, Kanai N, Guntert P, Kubota K, Nameki N Nucleic Acids Res. 2013 Dec 9. PMID:24322300[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chadani Y, Ono K, Kutsukake K, Abo T. Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways. Mol Microbiol. 2011 May;80(3):772-85. doi: 10.1111/j.1365-2958.2011.07607.x. Epub, 2011 Mar 21. PMID:21418110 doi:http://dx.doi.org/10.1111/j.1365-2958.2011.07607.x
- ↑ Handa Y, Inaho N, Nameki N. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Nucleic Acids Res. 2011 Mar;39(5):1739-48. doi: 10.1093/nar/gkq1097. Epub 2010, Nov 3. PMID:21051357 doi:http://dx.doi.org/10.1093/nar/gkq1097
- ↑ Kogure H, Handa Y, Nagata M, Kanai N, Guntert P, Kubota K, Nameki N. Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. Nucleic Acids Res. 2013 Dec 9. PMID:24322300 doi:http://dx.doi.org/10.1093/nar/gkt1280
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