1lvb: Difference between revisions

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-{{Seed}}
-[[Image:1lvb.png|left|200px]]
-<!--
+==CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE==
-The line below this paragraph, containing "STRUCTURE_1lvb", creates the "Structure Box" on the page.
+<StructureSection load='1lvb' size='340' side='right'caption='[[1lvb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1lvb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tobacco_etch_virus Tobacco etch virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LVB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_1lvb|  PDB=1lvb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lvb OCA], [https://pdbe.org/1lvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lvb RCSB], [https://www.ebi.ac.uk/pdbsum/1lvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lvb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_TEV POLG_TEV] Capsid protein: involved in aphid transmission, cell-to-cell and systemis movement, encapsidation of the viral RNA and in the regulation of viral RNA amplification.<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>   Nuclear inclusion protein B: an RNA-dependent RNA polymerase that plays an essential role in the virus replication.<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>   Helper component proteinase: required for aphid transmission and also has proteolytic activity. Only cleaves a Gly-Gly dipeptide at its own C-terminus. Interacts with virions and aphid stylets. 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 have RNA-binding activity.<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>   Cytoplasmic inclusion protein: has helicase activity. It may be involved in replication.<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>   Both 6K peptides are indispensable for virus replication (By similarity).<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>   Nuclear inclusion protein A: has RNA-binding and proteolytic activities.<ref>PMID:9880030</ref> <ref>PMID:11414807</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lv/1lvb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1lvb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.
-===CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE===
+Structural basis for the substrate specificity of tobacco etch virus protease.,Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK 3rd, Kapust RB, Li M, Wlodawer A, Waugh DS J Biol Chem. 2002 Dec 27;277(52):50564-72. Epub 2002 Oct 10. PMID:12377789<ref>PMID:12377789</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1lvb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12377789}}, adds the Publication Abstract to the page
+*[[Tobacco Etch Virus (TEV) Protease|Tobacco Etch Virus (TEV) Protease]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12377789 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12377789}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LVB is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Tobacco_etch_virus Tobacco etch virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LVB OCA].
-==Reference==
-Structural basis for the substrate specificity of tobacco etch virus protease., Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK 3rd, Kapust RB, Li M, Wlodawer A, Waugh DS, J Biol Chem. 2002 Dec 27;277(52):50564-72. Epub 2002 Oct 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12377789 12377789]
-[[Category: Protein complex]]
 [[Category: Tobacco etch virus]]
-[[Category: Evdokimov, A G.]]
+[[Category: Evdokimov AG]]
-[[Category: III, H K.Peters.]]
+[[Category: Kapust RB]]
-[[Category: Kapust, R B.]]
+[[Category: Li M]]
-[[Category: Li, M.]]
+[[Category: Peters III HK]]
-[[Category: Phan, J.]]
+[[Category: Phan J]]
-[[Category: Tropea, J E.]]
+[[Category: Tropea JE]]
-[[Category: Waugh, D S.]]
+[[Category: Waugh DS]]
-[[Category: Wlodawer, A.]]
+[[Category: Wlodawer A]]
-[[Category: Zdanov, A.]]
+[[Category: Zdanov A]]
-[[Category: Beta barrel]]
-[[Category: Chymotrypsin-like cystein protease]]
-[[Category: Protein-peptide complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 22:25:00 2008''