3vkw

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Current revision (08:40, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vkw' size='340' side='right'caption='[[3vkw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3vkw' size='340' side='right'caption='[[3vkw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vkw]] is a 1 chain structure with sequence from [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=3VKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VKW FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vkw]] is a 1 chain structure with sequence from [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=3VKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VKW FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3vkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vkw OCA], [https://pdbe.org/3vkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vkw RCSB], [https://www.ebi.ac.uk/pdbsum/3vkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vkw 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=3vkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vkw OCA], [https://pdbe.org/3vkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vkw RCSB], [https://www.ebi.ac.uk/pdbsum/3vkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vkw ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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).
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[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).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The genomes of the Tomato mosaic virus and many other plant and animal positive-strand RNA viruses of agronomic and medical importance encode superfamily 1 helicases. Although helicases play important roles in viral replication, the crystal structures of viral superfamily 1 helicases have not been determined. Here, we report the crystal structure of a fragment (S666 to Q1116) of the replication protein from Tomato mosaic virus. The structure reveals a novel N-terminal domain tightly associated with a helicase core. The helicase core contains two RecA-like alpha/beta domains without any of the accessory domain insertions that are found in other superfamily 1 helicases. The N-terminal domain contains a flexible loop, a long alpha-helix, and an antiparallel six-stranded beta-sheet. On the basis of the structure, we constructed deletion mutants of the S666-to-Q1116 fragment and performed split-ubiquitin-based interaction assays in Saccharomyces cerevisiae with TOM1 and ARL8, host proteins that are essential for tomato mosaic virus RNA replication. The results suggested that both TOM1 and ARL8 interact with the long alpha-helix in the N-terminal domain and that TOM1 also interacts with the helicase core. Prediction of secondary structures in other viral superfamily 1 helicases and comparison of those structures with the S666-to-Q1116 structure suggested that these helicases have a similar fold. Our results provide a structural basis of viral superfamily 1 helicases.
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Crystal structure of the superfamily 1 helicase from tomato mosaic virus.,Nishikiori M, Sugiyama S, Xiang H, Niiyama M, Ishibashi K, Inoue T, Ishikawa M, Matsumura H, Katoh E J Virol. 2012 Jul;86(14):7565-76. Epub 2012 May 9. PMID:22573863<ref>PMID:22573863</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vkw" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Tmv strain tomato]]
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[[Category: Tobacco mosaic virus strain tomato/L]]
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[[Category: Inoue, T]]
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[[Category: Inoue T]]
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[[Category: Ishibashi, K]]
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[[Category: Ishibashi K]]
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[[Category: Ishikawa, M]]
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[[Category: Ishikawa M]]
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[[Category: Katoh, E]]
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[[Category: Katoh E]]
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[[Category: Matsumura, H]]
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[[Category: Matsumura H]]
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[[Category: Niiyama, M]]
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[[Category: Niiyama M]]
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[[Category: Nishikiori, M]]
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[[Category: Nishikiori M]]
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[[Category: Sugiyama, S]]
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[[Category: Sugiyama S]]
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[[Category: Xiang, H]]
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[[Category: Xiang H]]
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[[Category: Alpha/beta domain]]
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[[Category: Helicase]]
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[[Category: Transferase]]
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Current revision

Crystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus

PDB ID 3vkw

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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