6omf: Difference between revisions

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 <SX load='6omf' size='340' side='right' viewer='molstar' caption='[[6omf]], [[Resolution|resolution]] 3.26&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6omf]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OMF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.26&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoS, C2273_13580 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892]), crl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [https://pdbe.org/6omf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [https://www.ebi.ac.uk/pdbsum/6omf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6omf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6omf OCA], [http://pdbe.org/6omf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6omf RCSB], [http://www.ebi.ac.uk/pdbsum/6omf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6omf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A0A0F7J6B7_SALTM A0A0F7J6B7_SALTM]] Binds to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. Stimulates RNA polymerase holoenzyme formation and may bind to several other sigma factors, such as sigma-70 and sigma-32.[HAMAP-Rule:MF_01178] [[http://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] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] 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 (By similarity). [[http://www.uniprot.org/uniprot/S5ZIY8_SALTM S5ZIY8_SALTM]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response.[HAMAP-Rule:MF_00959]
+[https://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In bacteria, a primary sigma-factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative sigma-factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative sigma-factors are negatively regulated by anti-sigma-factors. In Escherichia coli, Salmonella enterica, and many other gamma-proteobacteria, the transcription factor Crl positively regulates the alternative sigma(S)-regulon by promoting the association of sigma(S) with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-sigma(S)-RNAP in an open promoter complex with a sigma(S)-regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of sigma(S) (sigma(S) 2), the structure, along with p-benzoylphenylalanine cross-linking, reveals that Crl interacts with a structural element of the RNAP beta'-subunit that we call the beta'-clamp-toe (beta'CT). Deletion of the beta'CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-beta'CT interaction. We conclude that Crl activates sigma(S)-dependent transcription in part through stabilizing sigma(S)-RNAP by tethering sigma(S) 2 and the beta'CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated sigma-activators.
-Structural basis for transcription activation by Crl through tethering of sigma(S) and RNA polymerase.,Cartagena AJ, Banta AB, Sathyan N, Ross W, Gourse RL, Campbell EA, Darst SA Proc Natl Acad Sci U S A. 2019 Sep 17;116(38):18923-18927. doi:, 10.1073/pnas.1910827116. Epub 2019 Sep 4. PMID:31484766<ref>PMID:31484766</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6omf" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Bacillus typhimurium loeffler 1892]]
-[[Category: DNA-directed RNA polymerase]]
 [[Category: Large Structures]]
-[[Category: Campbell, E A]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Cartagena, A Jaramillo]]
+[[Category: Campbell EA]]
-[[Category: Darst, S A]]
+[[Category: Darst SA]]
-[[Category: Betass']]
+[[Category: Jaramillo Cartagena A]]
-[[Category: Dna/rna]]
-[[Category: Sigma]]
-[[Category: Transcription]]
-[[Category: Transcription-activator]]
-[[Category: Transferase-dna complex]]