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| | ==Crystal structure of the N-terminal domain of resistance protein== | | ==Crystal structure of the N-terminal domain of resistance protein== |
| - | <StructureSection load='3wrw' size='340' side='right' caption='[[3wrw]], [[Resolution|resolution]] 2.71Å' scene=''> | + | <StructureSection load='3wrw' size='340' side='right'caption='[[3wrw]], [[Resolution|resolution]] 2.71Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wrw]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WRW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wrw]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.71Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vkw|3vkw]], [[3wrv|3wrv]], [[3wrx|3wrx]], [[3wry|3wry]]</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=3wrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrw OCA], [https://pdbe.org/3wrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wrw RCSB], [https://www.ebi.ac.uk/pdbsum/3wrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wrw 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=3wrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrw OCA], [http://pdbe.org/3wrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wrw RCSB], [http://www.ebi.ac.uk/pdbsum/3wrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wrw ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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:17238011, PubMed:17699618, PubMed:19423673, PubMed:23415925, PubMed:28107419, PubMed:29582165, PubMed:3686829). 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:23415925, PubMed:23658455). 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| - | Tm-1, an inhibitor protein of Tomato mosaic virus RNA replication, contains two conserved domains: an uncharacterized domain at its N-terminus and a TIM-barrel-like domain at its C-terminus. The N-terminal domain of Tm-1 has an inhibitory activity and its three-dimensional structure has not been determined. Here, the crystallization and preliminary X-ray diffraction of the N-terminal domain of Tm-1 are reported. A three-wavelength MAD data set was collected from a selenomethionine-labelled crystal and processed to 2.7 A resolution. The crystal belonged to the triclinic space group P1, with unit-cell parameters a = 77.97, b = 105.28, c = 110.62 A, alpha = 94.6, beta = 109.3, gamma = 108.0 degrees . | + | 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. |
| | | | |
| - | Crystallization and preliminary X-ray crystallographic analysis of the inhibitory domain of the tomato mosaic virus resistance protein Tm-1.,Kato M, Kezuka Y, Kobayashi C, Ishibashi K, Nonaka T, Ishikawa M, Katoh E Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Dec;69(Pt 12):1411-4. doi:, 10.1107/S1744309113030819. Epub 2013 Nov 29. PMID:24316842<ref>PMID:24316842</ref>
| + | 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> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Katoh, E]] | + | [[Category: Large Structures]] |
| - | [[Category: Kezuka, Y]] | + | [[Category: Solanum lycopersicum]] |
| - | [[Category: Alpha/beta domain]] | + | [[Category: Katoh E]] |
| - | [[Category: Resistance factor]] | + | [[Category: Kezuka Y]] |
| - | [[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:17238011, PubMed:17699618, PubMed:19423673, PubMed:23415925, PubMed:28107419, PubMed:29582165, PubMed:3686829). 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:23415925, PubMed:23658455). Inhibits triphosphatase activity of ToMV replication proteins (PubMed:25092327).[1] [2] [3] [4] [5] [6] [7] [8] [9]
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[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
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
- ↑ 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
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