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| ==Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome== | | ==Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome== |
| <StructureSection load='5u4j' size='340' side='right'caption='[[5u4j]], [[Resolution|resolution]] 3.70Å' scene=''> | | <SX load='5u4j' size='340' side='right' viewer='molstar' caption='[[5u4j]], [[Resolution|resolution]] 3.70Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[5u4j]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U4J FirstGlance]. <br> | | <table><tr><td colspan='2'>[[5u4j]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U4J FirstGlance]. <br> |
| </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u4i|5u4i]]</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">arfA, yhdL, b4550, JW3253 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), prfB, supK, b2891, JW5847 ([http://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'>[https://proteopedia.org/fgij/fg.htm?mol=5u4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4j OCA], [https://pdbe.org/5u4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u4j RCSB], [https://www.ebi.ac.uk/pdbsum/5u4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4j ProSAT]</span></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=5u4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u4j OCA], [http://pdbe.org/5u4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u4j RCSB], [http://www.ebi.ac.uk/pdbsum/5u4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u4j ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RS3_ECOLI RS3_ECOLI]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity).<ref>PMID:15652481</ref> Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/RF2_ECOLI RF2_ECOLI]] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA.[HAMAP-Rule:MF_00094] [[http://www.uniprot.org/uniprot/RS12_ECOLI RS12_ECOLI]] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] Cryo-EM studies suggest that S12 contacts the EF-Tu bound tRNA in the A-site during codon-recognition. This contact is most likely broken as the aminoacyl-tRNA moves into the peptidyl transferase center in the 50S subunit.[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS4_ECOLI RS4_ECOLI]] One of two assembly initiator proteins for the 30S subunit, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Protein S4 is also a translational repressor protein, it controls the translation of the alpha-operon (which codes for S13, S11, S4, RNA polymerase alpha subunit, and L17) by binding to its mRNA.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> Also functions as a rho-dependent antiterminator of rRNA transcription, increasing the synthesis of rRNA under conditions of excess protein, allowing a more rapid return to homeostasis. Binds directly to RNA polymerase.<ref>PMID:2461734</ref> <ref>PMID:11447122</ref> <ref>PMID:15652481</ref> [[http://www.uniprot.org/uniprot/ARFA_ECOLI ARFA_ECOLI]] Rescues the ribosomes stalled at the 3' end of non-stop mRNAs. May induce hydrolysis of the ribosome-bound peptidyl-tRNA. This activity is crucial when the stalled ribosome cannot be rescued by the SsrA(tmRNA)-SmpB quality control system.<ref>PMID:21062370</ref> <ref>PMID:21435036</ref> [[http://www.uniprot.org/uniprot/RS5_ECOLI RS5_ECOLI]] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:15652481</ref> Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref> The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> | | [https://www.uniprot.org/uniprot/RS3_ECOLI RS3_ECOLI] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity).<ref>PMID:15652481</ref> Plays a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.
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| Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.,Zeng F, Chen Y, Remis J, Shekhar M, Phillips JC, Tajkhorshid E, Jin H Nature. 2017 Jan 11. doi: 10.1038/nature21053. PMID:28077875<ref>PMID:28077875</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 5u4j" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
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| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: Bacillus coli migula 1895]]
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| [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Chen, Y]] | | [[Category: Chen Y]] |
| [[Category: Jin, H]] | | [[Category: Jin H]] |
| [[Category: Phillips, J C]] | | [[Category: Phillips JC]] |
| [[Category: Remis, J]] | | [[Category: Remis J]] |
| [[Category: Shekhar, M]] | | [[Category: Shekhar M]] |
| [[Category: Tajkhorshid, E]] | | [[Category: Tajkhorshid E]] |
| [[Category: Zeng, F]] | | [[Category: Zeng F]] |
| [[Category: Arfa]]
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| [[Category: Nonstop translation]]
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| [[Category: Rf2]]
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| [[Category: Ribosome]]
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