5byh

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#REDIRECT [[5nwt]] This PDB entry is obsolete and replaced by 5nwt
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==Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex==
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<StructureSection load='5byh' size='340' side='right'caption='[[5byh]], [[Resolution|resolution]] 3.76&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5byh]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BYH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BYH FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4yg2|4yg2]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, FAZ83_23195 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, b3649, JW3624 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoN, AM386_06570, AM447_14830, B4U21_26550, B4U61_10775, B5L96_24890, BANRA_01956, BANRA_03272, BL124_00020515, BN49_0508, BVX91_19500, C3F39_17700, C4Y50_018355, CK508_022735, DD581_18145, DD583_08830, DM059_27505, DM060_25975, DM062_31185, EAO17_11045, EPB11_01460, FXN67_08250, G5637_17550, G7Z27_02650, GF489_02505, GJI97_002620, GJI97_00400, GJJ08_002620, GJJ08_00400, GNE24_14685, GNG14_08115, GQY16_02610, HJW74_02545, NCTC13465_03419, NCTC1936_05187, NCTC3279_03959, NCTC5047_03164, SAMEA24002668_02395, SAMEA3499901_03507, SAMEA3515094_02864, SAMEA3538546_01627, SAMEA3538560_01627, SAMEA3649435_03395, SAMEA3649466_03329, SAMEA3649630_02927, SAMEA3649650_00080, SAMEA3649733_03935, SAMEA3649758_00080, SAMEA3673026_02122, SAMEA3673122_02180, SAMEA3720909_03353, SAMEA3721038_02488, SAMEA3727579_03145, SAMEA3727651_01748, SAMEA3727679_00080, SAMEA4364603_00630, SAMEA4370540_02816, SAMEA4370542_01833, SAMEA4873581_03318, WP4S18C04_05100 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5byh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5byh OCA], [https://pdbe.org/5byh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5byh RCSB], [https://www.ebi.ac.uk/pdbsum/5byh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5byh ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/RPOZ_ECOLI RPOZ_ECOLI]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.[HAMAP-Rule:MF_00366] [[https://www.uniprot.org/uniprot/A0A4S5AL01_ECOLI A0A4S5AL01_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059] [[https://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[https://www.uniprot.org/uniprot/RPOB_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[https://www.uniprot.org/uniprot/A0A0N9UTC1_KLEPN A0A0N9UTC1_KLEPN]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Transcription by RNA polymerase (RNAP) in bacteria requires specific promoter recognition by sigma factors. The major variant sigma factor (sigma(54)) initially forms a transcriptionally silent complex requiring specialized adenosine triphosphate-dependent activators for initiation. Our crystal structure of the 450-kilodalton RNAP-sigma(54) holoenzyme at 3.8 angstroms reveals molecular details of sigma(54) and its interactions with RNAP. The structure explains how sigma(54) targets different regions in RNAP to exert its inhibitory function. Although sigma(54) and the major sigma factor, sigma(70), have similar functional domains and contact similar regions of RNAP, unanticipated differences are observed in their domain arrangement and interactions with RNAP, explaining their distinct properties. Furthermore, we observe evolutionarily conserved regulatory hotspots in RNAPs that can be targeted by a diverse range of mechanisms to fine tune transcription.
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TRANSCRIPTION. Structures of the RNA polymerase-sigma54 reveal new and conserved regulatory strategies.,Yang Y, Darbari VC, Zhang N, Lu D, Glyde R, Wang YP, Winkelman JT, Gourse RL, Murakami KS, Buck M, Zhang X Science. 2015 Aug 21;349(6250):882-5. doi: 10.1126/science.aab1478. PMID:26293966<ref>PMID:26293966</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5byh" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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*[[Sigma factor 3D structures|Sigma factor 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Buck, M]]
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[[Category: Darbari, V C]]
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[[Category: Glyde, R]]
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[[Category: Gourse, R L]]
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[[Category: Lu, D]]
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[[Category: Murakami, K S]]
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[[Category: Wang, Y]]
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[[Category: Winkelman, J]]
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[[Category: Yang, Y]]
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[[Category: Zhang, N]]
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[[Category: Zhang, X]]
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[[Category: Holoenzyme]]
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[[Category: Rna polymerase]]
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[[Category: Sigma 54]]
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[[Category: Transcription]]
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[[Category: Transferase]]
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Current revision

  1. REDIRECT 5nwt This PDB entry is obsolete and replaced by 5nwt

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