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| | ==Crystal structure of helicase complex 1== | | ==Crystal structure of helicase complex 1== |
| - | <StructureSection load='3wrx' size='340' side='right' caption='[[3wrx]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3wrx' size='340' side='right'caption='[[3wrx]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wrx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum] and [http://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=3WRX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WRX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wrx]] 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=3WRX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WRX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </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=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vkw|3vkw]], [[3wrv|3wrv]], [[3wrw|3wrw]], [[3wry|3wry]]</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]], [[3wry|3wry]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Tm-1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3wrx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrx OCA], [http://pdbe.org/3wrx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wrx RCSB], [http://www.ebi.ac.uk/pdbsum/3wrx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wrx 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=3wrx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wrx OCA], [https://pdbe.org/3wrx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wrx RCSB], [https://www.ebi.ac.uk/pdbsum/3wrx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wrx ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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/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). |
| | <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: Large Structures]] |
| | [[Category: Lycopersicon esculentum]] | | [[Category: Lycopersicon esculentum]] |
| | [[Category: Tmv strain tomato]] | | [[Category: Tmv strain tomato]] |
| Structural highlights
Function
[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).
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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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