5nwt: Difference between revisions

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 ==Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex==
-<StructureSection load='5nwt' size='340' side='right' caption='[[5nwt]], [[Resolution|resolution]] 3.76&Aring;' scene=''>
+<StructureSection load='5nwt' size='340' side='right'caption='[[5nwt]], [[Resolution|resolution]] 3.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nwt]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NWT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NWT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nwt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae_subsp._rhinoscleromatis_SB3432 Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5byh 5byh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NWT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">X-ray diffraction, [[Resolution|Resolution]] 3.76&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></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=MSE:SELENOMETHIONINE'>MSE</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=5nwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nwt OCA], [https://pdbe.org/5nwt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nwt RCSB], [https://www.ebi.ac.uk/pdbsum/5nwt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nwt ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nwt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nwt OCA], [http://pdbe.org/5nwt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nwt RCSB], [http://www.ebi.ac.uk/pdbsum/5nwt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nwt ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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] [[http://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] [[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_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] [[http://www.uniprot.org/uniprot/R4YEY9_KLEPR R4YEY9_KLEPR]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.[PIRNR:PIRNR000774]
+[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 ==
-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.
-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>
+==See Also==
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+*[[Sigma factor 3D structures|Sigma factor 3D structures]]
-</div>
-<div class="pdbe-citations 5nwt" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed RNA polymerase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Buck, M]]
+[[Category: Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]]
-[[Category: Darbari, V C]]
+[[Category: Large Structures]]
-[[Category: Glyde, R]]
+[[Category: Buck M]]
-[[Category: Gourse, R L]]
+[[Category: Darbari VC]]
-[[Category: Lu, D]]
+[[Category: Glyde R]]
-[[Category: Murakami, K S]]
+[[Category: Gourse RL]]
-[[Category: Wang, Y]]
+[[Category: Lu D]]
-[[Category: Winkelman, J]]
+[[Category: Murakami KS]]
-[[Category: Yang, Y]]
+[[Category: Wang Y]]
-[[Category: Zhang, N]]
+[[Category: Winkelman J]]
-[[Category: Zhang, X]]
+[[Category: Yang Y]]
-[[Category: Holoenzyme]]
+[[Category: Zhang N]]
-[[Category: Rna polymerase]]
+[[Category: Zhang X]]
-[[Category: Sigma 54]]
-[[Category: Transcription]]
-[[Category: Transferase]]