1doq: Difference between revisions

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-[[Image:1doq.png|left|200px]]
-{{STRUCTURE_1doq|  PDB=1doq  |  SCENE=  }}
+==THE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT FROM THERMUS THERMOPHILUS==
+<StructureSection load='1doq' size='340' side='right'caption='[[1doq]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1doq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DOQ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1doq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1doq OCA], [https://pdbe.org/1doq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1doq RCSB], [https://www.ebi.ac.uk/pdbsum/1doq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1doq ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPOA_THETH RPOA_THETH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
+== 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/do/1doq_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=1doq ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The C-terminal domain of the alpha subunit of the RNA polymerase (alphaCTD) from Escherichia coli (Ec) regulates transcription by interacting with many kinds of proteins and promoter upstream (UP) elements consisting of AT-rich sequences. However, it is unclear how this system is common in all eubacteria. We investigate the structure and properties of alphaCTD from an extremely thermophilic eubacterium, Thermus thermophilus (Tt). The solution structure of Tt alphaCTD (85 amino acids) was determined by NMR, and the interaction between Tt alphaCTD and DNA with different sequences was investigated by means of chemical shift perturbation experiments. The tertiary structure of Tt alphaCTD is almost identical with that of Ec alphaCTD despite 32% sequence homology. However, Tt alphaCTD interacts with the upstream region sequence of the promoter in the Tt 16 S ribosomal protein operon rather than the Ec UP element DNA. The upstream region sequence of Tt is composed of 25 base pairs with 40% AT, unlike the Ec UP element with 80% AT. The DNA binding site in Tt alphaCTD is located on the surface composed of helix 4 and the loop preceding helix 4. The electric charges on this surface are not remarkably localized like those of Ec alphaCTD.
-===THE C-TERMINAL DOMAIN OF THE RNA POLYMERASE ALPHA SUBUNIT FROM THERMUS THERMOPHILUS===
+The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus.,Wada T, Yamazaki T, Kyogoku Y J Biol Chem. 2000 May 26;275(21):16057-63. PMID:10821859<ref>PMID:10821859</ref>
-{{ABSTRACT_PUBMED_10821859}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1doq" style="background-color:#fffaf0;"></div>
-[[1doq]] is a 1 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOQ OCA].
 ==See Also==
-*[[RNA polymerase|RNA polymerase]]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:010821859</ref><references group="xtra"/>
+__TOC__
-[[Category: Thermus thermophilus]]
+</StructureSection>
-[[Category: Kyogoku, Y.]]
+[[Category: Large Structures]]
-[[Category: Wada, T.]]
-[[Category: Yamazaki, T.]]
-[[Category: Rna polymerase]]
 [[Category: Thermus thermophilus]]
-[[Category: Transcription]]
+[[Category: Kyogoku Y]]
-[[Category: Transferase]]
+[[Category: Wada T]]
+[[Category: Yamazaki T]]