6yys: Difference between revisions
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==== | ==Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering== | ||
<StructureSection load='6yys' size='340' side='right'caption='[[6yys]]' scene=''> | <StructureSection load='6yys' size='340' side='right'caption='[[6yys]], [[Resolution|resolution]] 3.08Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[6yys]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycolicibacterium_smegmatis_MC2_155 Mycolicibacterium smegmatis MC2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YYS FirstGlance]. <br> | ||
</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=6yys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yys OCA], [https://pdbe.org/6yys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yys RCSB], [https://www.ebi.ac.uk/pdbsum/6yys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yys ProSAT]</span></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]] 3.08Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6yys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yys OCA], [https://pdbe.org/6yys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yys RCSB], [https://www.ebi.ac.uk/pdbsum/6yys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yys ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/RPOA_MYCS2 RPOA_MYCS2] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:19926651</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids. | |||
Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.,Kouba T, Koval' T, Sudzinova P, Pospisil J, Brezovska B, Hnilicova J, Sanderova H, Janouskova M, Sikova M, Halada P, Sykora M, Barvik I, Novacek J, Trundova M, Duskova J, Skalova T, Chon U, Murakami KS, Dohnalek J, Krasny L Nat Commun. 2020 Dec 18;11(1):6419. doi: 10.1038/s41467-020-20158-4. PMID:33339823<ref>PMID:33339823</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6yys" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Mycolicibacterium smegmatis MC2 155]] | ||
[[Category: Dohnalek J]] | |||
[[Category: Kouba T]] | |||
[[Category: Koval T]] | |||
[[Category: Krasny L]] | |||
Latest revision as of 11:53, 14 July 2024
Structure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interferingStructure of Mycobacterium smegmatis HelD protein in complex with RNA polymerase core - State II, primary channel engaged and active site interfering
Structural highlights
FunctionRPOA_MYCS2 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059][1] Publication Abstract from PubMedRNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids. Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.,Kouba T, Koval' T, Sudzinova P, Pospisil J, Brezovska B, Hnilicova J, Sanderova H, Janouskova M, Sikova M, Halada P, Sykora M, Barvik I, Novacek J, Trundova M, Duskova J, Skalova T, Chon U, Murakami KS, Dohnalek J, Krasny L Nat Commun. 2020 Dec 18;11(1):6419. doi: 10.1038/s41467-020-20158-4. PMID:33339823[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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