2eyq: Difference between revisions

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 ==Crystal structure of Escherichia coli transcription-repair coupling factor==
-<StructureSection load='2eyq' size='340' side='right' caption='[[2eyq]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='2eyq' size='340' side='right'caption='[[2eyq]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2eyq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EYQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EYQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2eyq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EYQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EYQ FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mfd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2eyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eyq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eyq RCSB], [http://www.ebi.ac.uk/pdbsum/2eyq PDBsum]</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=2eyq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eyq OCA], [https://pdbe.org/2eyq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eyq RCSB], [https://www.ebi.ac.uk/pdbsum/2eyq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eyq ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MFD_ECOLI MFD_ECOLI] Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site. Can also dissociate RNAP that is blocked by low concentration of nucleoside triphosphates or by physical obstruction, such as bound proteins. In addition, can rescue arrested complexes by promoting forward translocation. Has ATPase activity, which is required for removal of stalled RNAP, but seems to lack helicase activity. May act through a translocase activity that rewinds upstream DNA, leading either to translocation or to release of RNAP when the enzyme active site can not continue elongation.<ref>PMID:8465200</ref> <ref>PMID:7876261</ref> <ref>PMID:7876262</ref> <ref>PMID:12086674</ref> <ref>PMID:19700770</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/ey/2eyq_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/2eyq_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2eyq ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Coupling of transcription and DNA repair in bacteria is mediated by transcription-repair coupling factor (TRCF, the product of the mfd gene), which removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair machinery to the site. Here we describe the 3.2 A-resolution X-ray crystal structure of Escherichia coli TRCF. The structure consists of a compact arrangement of eight domains, including a translocation module similar to the SF2 ATPase RecG, and a region of structural similarity to UvrB. Biochemical and genetic experiments establish that another domain with structural similarity to the Tudor-like domain of the transcription elongation factor NusG plays a critical role in TRCF/RNA polymerase interactions. Comparison with the translocation module of RecG as well as other structural features indicate that TRCF function involves large-scale conformational changes. These data, along with a structural model for the interaction of TRCF with the transcription elongation complex, provide mechanistic insights into TRCF function.
-Structural basis for bacterial transcription-coupled DNA repair.,Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA Cell. 2006 Feb 10;124(3):507-20. PMID:16469698<ref>PMID:16469698</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[RapA%2C a Swi2/Snf2 protein|RapA%2C a Swi2/Snf2 protein]]
+*[[Transcription-repair coupling factor 3D structures|Transcription-repair coupling factor 3D structures]]
-*[[Transcription-repair coupling factor|Transcription-repair coupling factor]]
 == References ==
 <references/>
@@ Line 34: / Line 28: @@
 </StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Darst, S A.]]
+[[Category: Large Structures]]
-[[Category: Deaconescu, A M.]]
+[[Category: Darst SA]]
-[[Category: Hydrolase]]
+[[Category: Deaconescu AM]]
-[[Category: Mfd]]
-[[Category: Sf2 atpase]]