This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3wrw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (05:47, 3 August 2022) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==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]] 2.71&Aring;' scene=''>
+
<StructureSection load='3wrw' size='340' side='right'caption='[[3wrw]], [[Resolution|resolution]] 2.71&Aring;' 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/Lycopersicon_esculentum Lycopersicon esculentum]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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='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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vkw|3vkw]], [[3wrv|3wrv]], [[3wrx|3wrx]], [[3wry|3wry]]</div></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://www.rcsb.org/pdb/explore.do?structureId=3wrw RCSB], [http://www.ebi.ac.uk/pdbsum/3wrw PDBsum]</span></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=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>
</table>
</table>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
-
Tm-1, the protein product of Tm-1, a semidominant resistance gene of tomato, inhibits tomato mosaic virus (ToMV) replication by binding to ToMV replication proteins. Previous studies suggested the importance of the Tm-1 N-terminal region for its inhibitory activity; however, it has not been determined if the N-terminal region is sufficient for inhibition. Furthermore, the three-dimensional structure of Tm-1 has not been determined. In this study, an N-terminal fragment of Tm-1 (residues 1-431) as a fusion protein containing an upstream maltose-binding protein was expressed in E. coli Rosetta (DE3) cells at 30 degrees C and then purified. The solubility of the fusion protein was greater when the cells were cultured at 30 degrees C than when cultured at lower or higher temperatures. The purified N-terminal Tm-1 fragment from which the maltose-binding protein tag had been removed has inhibitory activity against ToMV RNA replication.
+
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.
-
Expression, purification, and functional characterization of an N-terminal fragment of the tomato mosaic virus resistance protein Tm-1.,Kato M, Ishibashi K, Kobayashi C, Ishikawa M, Katoh E Protein Expr Purif. 2013 May;89(1):1-6. doi: 10.1016/j.pep.2013.02.001. Epub 2013, Feb 13. PMID:23415925<ref>PMID:23415925</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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 +
<div class="pdbe-citations 3wrw" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Lycopersicon esculentum]]
[[Category: Katoh, E]]
[[Category: Katoh, E]]
[[Category: Kezuka, Y]]
[[Category: Kezuka, Y]]

Current revision

Crystal structure of the N-terminal domain of resistance protein

PDB ID 3wrw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3wrw"
Personal tools