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| | ==Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex== | | ==Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex== |
| - | <StructureSection load='5nsr' size='340' side='right' caption='[[5nsr]], [[Resolution|resolution]] 3.80Å' scene=''> | + | <SX load='5nsr' size='340' side='right' viewer='molstar' caption='[[5nsr]], [[Resolution|resolution]] 3.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5nsr]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NSR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NSR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nsr]] is a 8 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 Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NSR FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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]] 3.8Å</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=5nsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nsr OCA], [https://pdbe.org/5nsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nsr RCSB], [https://www.ebi.ac.uk/pdbsum/5nsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nsr 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=5nsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nsr OCA], [http://pdbe.org/5nsr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nsr RCSB], [http://www.ebi.ac.uk/pdbsum/5nsr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nsr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[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/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/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/A0A0J4U551_KLEPN A0A0J4U551_KLEPN]] 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5nsr" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5nsr" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | + | *[[Sigma factor 3D structures|Sigma factor 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| - | [[Category: DNA-directed RNA polymerase]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Buck, M]] | + | [[Category: Klebsiella pneumoniae]] |
| - | [[Category: Darbari, V C]] | + | [[Category: Large Structures]] |
| - | [[Category: Glyde, R]] | + | [[Category: Buck M]] |
| - | [[Category: Ye, F Z]] | + | [[Category: Darbari VC]] |
| - | [[Category: Zhang, N]] | + | [[Category: Glyde R]] |
| - | [[Category: Zhang, X D]] | + | [[Category: Ye FZ]] |
| - | [[Category: Rna polymerase]] | + | [[Category: Zhang N]] |
| - | [[Category: Sigma54]] | + | [[Category: Zhang XD]] |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transcription initiation]]
| + | |
| Structural highlights
Function
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]
Publication Abstract from PubMed
Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative sigma54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 A. Our structures show how RNAP-sigma54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and sigma54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo.
Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.,Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X Mol Cell. 2017 Jul 6;67(1):106-116.e4. doi: 10.1016/j.molcel.2017.05.010. Epub, 2017 Jun 1. PMID:28579332[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X. Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell. 2017 Jul 6;67(1):106-116.e4. doi: 10.1016/j.molcel.2017.05.010. Epub, 2017 Jun 1. PMID:28579332 doi:http://dx.doi.org/10.1016/j.molcel.2017.05.010
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