8orq: Difference between revisions
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==Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation== | |||
<StructureSection load='8orq' size='340' side='right'caption='[[8orq]], [[Resolution|resolution]] 3.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8orq]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ORQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ORQ FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.2Å</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=8orq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8orq OCA], [https://pdbe.org/8orq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8orq RCSB], [https://www.ebi.ac.uk/pdbsum/8orq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8orq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8U0M3_PYRFU Q8U0M3_PYRFU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation. | |||
Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.,Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D Nucleic Acids Res. 2024 May 6:gkae282. doi: 10.1093/nar/gkae282. PMID:38709902<ref>PMID:38709902</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8orq" style="background-color:#fffaf0;"></div> | ||
[[Category: Engel | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pyrococcus furiosus DSM 3638]] | ||
[[Category: Engel C]] | |||
[[Category: Grohmann D]] | |||
[[Category: Hausner W]] | |||
[[Category: Heiss FB]] | |||
[[Category: Pilsl M]] | |||
[[Category: Reichelt R]] | |||
[[Category: Tarau DM]] | |||
Latest revision as of 09:52, 19 June 2024
Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformationCryo-EM structure of Pyrococcus furiosus apo form RNA polymerase open clamp conformation
Structural highlights
FunctionPublication Abstract from PubMedArchaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation. Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment.,Tarau D, Grunberger F, Pilsl M, Reichelt R, Heiss F, Konig S, Urlaub H, Hausner W, Engel C, Grohmann D Nucleic Acids Res. 2024 May 6:gkae282. doi: 10.1093/nar/gkae282. PMID:38709902[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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