1ynn: Difference between revisions

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-[[Image:1ynn.gif|left|200px]]
- {{Structure
+==Taq RNA polymerase-rifampicin complex==
-|PDB= 1ynn |SIZE=350|CAPTION= <scene name='initialview01'>1ynn</scene>, resolution 3.30&Aring;
+<StructureSection load='1ynn' size='340' side='right'caption='[[1ynn]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=RFP:RIFAMPICIN'>RFP</scene>
+<table><tr><td colspan='2'>[[1ynn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YNN FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RFP:RIFAMPICIN'>RFP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1ynn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ynn OCA], [https://pdbe.org/1ynn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ynn RCSB], [https://www.ebi.ac.uk/pdbsum/1ynn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ynn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]
+== 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/yn/1ynn_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ynn ConSurf].
+<div style="clear:both"></div>
-'''Taq RNA polymerase-rifampicin complex'''
+==See Also==
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-A combined structural, functional, and genetic approach was used to investigate inhibition of bacterial RNA polymerase (RNAP) by sorangicin (Sor), a macrolide polyether antibiotic. Sor lacks chemical and structural similarity to the ansamycin rifampicin (Rif), an RNAP inhibitor widely used to treat tuberculosis. Nevertheless, structural analysis revealed Sor binds in the same RNAP beta subunit pocket as Rif, with almost complete overlap of RNAP binding determinants, and functional analysis revealed that both antibiotics inhibit transcription by directly blocking the path of the elongating transcript at a length of 2-3 nucleotides. Genetic analysis indicates that Rif binding is extremely sensitive to mutations expected to change the shape of the antibiotic binding pocket, while Sor is not. We suggest that conformational flexibility of Sor, in contrast to the rigid conformation of Rif, allows Sor to adapt to changes in the binding pocket. This has important implications for drug design against rapidly mutating targets.
+[[Category: Large Structures]]
-==About this Structure==
-YNN is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YNN OCA].
-==Reference==
-Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase., Campbell EA, Pavlova O, Zenkin N, Leon F, Irschik H, Jansen R, Severinov K, Darst SA, EMBO J. 2005 Feb 23;24(4):674-82. Epub 2005 Feb 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15692574 15692574]
-[[Category: DNA-directed RNA polymerase]]
-[[Category: Protein complex]]
 [[Category: Thermus aquaticus]]
-[[Category: Campbell, E A.]]
+[[Category: Campbell EA]]
-[[Category: Darst, S A.]]
+[[Category: Darst SA]]
-[[Category: Irschik, H.]]
+[[Category: Irschik H]]
-[[Category: Jansen, R.]]
+[[Category: Jansen R]]
-[[Category: Leon, F.]]
+[[Category: Leon F]]
-[[Category: Pavlova, O.]]
+[[Category: Pavlova O]]
-[[Category: Severinov, K.]]
+[[Category: Severinov K]]
-[[Category: Zenkin, N.]]
+[[Category: Zenkin N]]
-[[Category: RFP]]
-[[Category: ZN]]
-[[Category: rifampicin]]
-[[Category: rna polymerase]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:25:12 2008''