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| | <StructureSection load='3wry' size='340' side='right'caption='[[3wry]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3wry' size='340' side='right'caption='[[3wry]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wry]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum] and [https://en.wikipedia.org/wiki/Tmv_strain_tomato Tmv strain tomato]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wry]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum] and [https://en.wikipedia.org/wiki/Tobacco_mosaic_virus_strain_tomato/L Tobacco mosaic virus strain tomato/L]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vkw|3vkw]], [[3wrv|3wrv]], [[3wrw|3wrw]], [[3wrx|3wrx]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tm-1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=3wry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wry OCA], [https://pdbe.org/3wry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wry RCSB], [https://www.ebi.ac.uk/pdbsum/3wry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wry 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=3wry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wry OCA], [https://pdbe.org/3wry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wry RCSB], [https://www.ebi.ac.uk/pdbsum/3wry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wry ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RDRP_TOML RDRP_TOML]] Replicase large subunit: is an RNA-dependent RNA polymerase active in viral RNA replication. Replicase small subunit: is a methyltransferase active in RNA capping and an RNA helicase. Methyltransferase displays a cytoplasmic capping enzyme activity. This function is necessary since all viral RNAs are synthesized in the cytoplasm, and host capping enzymes are restricted to the nucleus. Helicase region probably exhibits NTPase and RNA unwinding activities (Potential). It also acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. May mediate silencing suppression through either inhibition of HEN1-mediated siRNA or siRNA demethylation (By similarity).
| + | [https://www.uniprot.org/uniprot/TM1R_SOLLC TM1R_SOLLC] Inhibitor of viral RNA replication which confers resistance to some tobamoviruses including tomato mosaic virus (ToMV) (e.g. isolate L), tobacco mosaic virus (TMV), tobacco mild green mosaic virus (TMGMV) and pepper mild mottle virus (PMMoV), but not to resistance-breaking isolates of ToMV (e.g. LT1, SL-1 and ToMV1-2) and tomato brown rugose fruit virus (ToBRFV) (PubMed:17699618, PubMed:3686829, PubMed:17238011, PubMed:19423673, PubMed:23415925, PubMed:29582165, PubMed:28107419). Prevents tobamoviruses RNA replication by affecting the association of tobamoviruses replication proteins (large and small subunits) with host membrane-associated proteins (e.g. TOM1, TOM2A and ARL8), thus inhibiting the replication complex formation on the membranes and avoiding viral negative-strand RNA synthesis (PubMed:17699618, PubMed:19423673, PubMed:23658455, PubMed:23415925). Inhibits triphosphatase activity of ToMV replication proteins (PubMed:25092327).<ref>PMID:17238011</ref> <ref>PMID:17699618</ref> <ref>PMID:19423673</ref> <ref>PMID:23415925</ref> <ref>PMID:23658455</ref> <ref>PMID:25092327</ref> <ref>PMID:28107419</ref> <ref>PMID:29582165</ref> <ref>PMID:3686829</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The tomato mosaic virus (ToMV) resistance gene Tm-1 encodes a protein that shows no sequence homology to functionally characterized proteins. Tm-1 binds ToMV replication proteins and thereby inhibits replication complex formation. ToMV mutants that overcome this resistance have amino acid substitutions in the helicase domain of the replication proteins (ToMV-Hel). A small region of Tm-1 in the genome of the wild tomato Solanum habrochaites has been under positive selection during its antagonistic coevolution with ToMV. Here we report crystal structures for the N-terminal inhibitory domains of Tm-1 and a natural Tm-1 variant with an I91-to-T substitution that has a greater ability to inhibit ToMV RNA replication and their complexes with ToMV-Hel. Each complex contains a Tm-1 dimer and two ToMV-Hel monomers with the interfaces between Tm-1 and ToMV-Hel bridged by ATP. Residues in ToMV-Hel and Tm-1 involved in antagonistic coevolution are found at the interface. The structural differences between ToMV-Hel in its free form and in complex with Tm-1 suggest that Tm-1 affects nucleoside triphosphatase activity of ToMV-Hel, and this effect was confirmed experimentally. Molecular dynamics simulations of complexes formed by Tm-1 with ToMV-Hel variants showed how the amino acid changes in ToMV-Hel impair the interaction with Tm-1 to overcome the resistance. With these findings, together with the biochemical properties of the interactions between ToMV-Hel and Tm-1 variants and effects of the mutations in the polymorphic residues of Tm-1, an atomic view of a step-by-step coevolutionary arms race between a plant resistance protein and a viral protein emerges.
| + | |
| - | | + | |
| - | Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1.,Ishibashi K, Kezuka Y, Kobayashi C, Kato M, Inoue T, Nonaka T, Ishikawa M, Matsumura H, Katoh E Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3486-95. doi:, 10.1073/pnas.1407888111. Epub 2014 Aug 4. PMID:25092327<ref>PMID:25092327</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div> | + | |
| - | <div class="pdbe-citations 3wry" style="background-color:#fffaf0;"></div> | + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lycopersicon esculentum]] | + | [[Category: Solanum lycopersicum]] |
| - | [[Category: Tmv strain tomato]] | + | [[Category: Tobacco mosaic virus strain tomato/L]] |
| - | [[Category: Katoh, E]] | + | [[Category: Katoh E]] |
| - | [[Category: Matsumura, H]] | + | [[Category: Matsumura H]] |
| - | [[Category: Alpha/beta domain]]
| + | |
| - | [[Category: Helicase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
TM1R_SOLLC Inhibitor of viral RNA replication which confers resistance to some tobamoviruses including tomato mosaic virus (ToMV) (e.g. isolate L), tobacco mosaic virus (TMV), tobacco mild green mosaic virus (TMGMV) and pepper mild mottle virus (PMMoV), but not to resistance-breaking isolates of ToMV (e.g. LT1, SL-1 and ToMV1-2) and tomato brown rugose fruit virus (ToBRFV) (PubMed:17699618, PubMed:3686829, PubMed:17238011, PubMed:19423673, PubMed:23415925, PubMed:29582165, PubMed:28107419). Prevents tobamoviruses RNA replication by affecting the association of tobamoviruses replication proteins (large and small subunits) with host membrane-associated proteins (e.g. TOM1, TOM2A and ARL8), thus inhibiting the replication complex formation on the membranes and avoiding viral negative-strand RNA synthesis (PubMed:17699618, PubMed:19423673, PubMed:23658455, PubMed:23415925). Inhibits triphosphatase activity of ToMV replication proteins (PubMed:25092327).[1] [2] [3] [4] [5] [6] [7] [8] [9]
References
- ↑ Strasser M, Pfitzner AJ. The double-resistance-breaking Tomato mosaic virus strain ToMV1-2 contains two independent single resistance-breaking domains. Arch Virol. 2007;152(5):903-14. PMID:17238011 doi:10.1007/s00705-006-0915-8
- ↑ Ishibashi K, Masuda K, Naito S, Meshi T, Ishikawa M. An inhibitor of viral RNA replication is encoded by a plant resistance gene. Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13833-8. PMID:17699618 doi:10.1073/pnas.0703203104
- ↑ Ishibashi K, Naito S, Meshi T, Ishikawa M. An inhibitory interaction between viral and cellular proteins underlies the resistance of tomato to nonadapted tobamoviruses. Proc Natl Acad Sci U S A. 2009 May 26;106(21):8778-83. PMID:19423673 doi:10.1073/pnas.0809105106
- ↑ Kato M, Ishibashi K, Kobayashi C, Ishikawa M, Katoh E. Expression, purification, and functional characterization of an N-terminal fragment of the tomato mosaic virus resistance protein Tm-1. Protein Expr Purif. 2013 May;89(1):1-6. doi: 10.1016/j.pep.2013.02.001. Epub 2013, Feb 13. PMID:23415925 doi:http://dx.doi.org/10.1016/j.pep.2013.02.001
- ↑ Ishibashi K, Ishikawa M. The resistance protein Tm-1 inhibits formation of a Tomato mosaic virus replication protein-host membrane protein complex. J Virol. 2013 Jul;87(14):7933-9. PMID:23658455 doi:10.1128/JVI.00743-13
- ↑ Ishibashi K, Kezuka Y, Kobayashi C, Kato M, Inoue T, Nonaka T, Ishikawa M, Matsumura H, Katoh E. Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3486-95. doi:, 10.1073/pnas.1407888111. Epub 2014 Aug 4. PMID:25092327 doi:http://dx.doi.org/10.1073/pnas.1407888111
- ↑ Luria N, Smith E, Reingold V, Bekelman I, Lapidot M, Levin I, Elad N, Tam Y, Sela N, Abu-Ras A, Ezra N, Haberman A, Yitzhak L, Lachman O, Dombrovsky A. A New Israeli Tobamovirus Isolate Infects Tomato Plants Harboring Tm-22 Resistance Genes. PLoS One. 2017 Jan 20;12(1):e0170429. PMID:28107419 doi:10.1371/journal.pone.0170429
- ↑ Maayan Y, Pandaranayaka EPJ, Srivastava DA, Lapidot M, Levin I, Dombrovsky A, Harel A. Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus. Arch Virol. 2018 Jul;163(7):1863-1875. PMID:29582165 doi:10.1007/s00705-018-3819-5
- ↑ Watanabe Y, Kishibayashi N, Motoyoshi F, Okada Y. Characterization of Tm-1 gene action on replication of common isolates and a resistance-breaking isolate of TMV. Virology. 1987 Dec;161(2):527-32. PMID:3686829 doi:10.1016/0042-6822(87)90147-4
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