8pib

From Proteopedia

(Difference between revisions)

Current revision

autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)

Structural highlights

8pib is a 9 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RFAH_ECOLI Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an alpha-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a beta-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.

Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.,Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH Nat Commun. 2024 Apr 8;15(1):3040. doi: 10.1038/s41467-024-47368-4. PMID:38589445^[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bailey MJ, Koronakis V, Schmoll T, Hughes C. Escherichia coli HlyT protein, a transcriptional activator of haemolysin synthesis and secretion, is encoded by the rfaH (sfrB) locus required for expression of sex factor and lipopolysaccharide genes. Mol Microbiol. 1992 Apr;6(8):1003-12. PMID:1584020
↑ Leeds JA, Welch RA. RfaH enhances elongation of Escherichia coli hlyCABD mRNA. J Bacteriol. 1996 Apr;178(7):1850-7. PMID:8606157
↑ Bailey MJ, Hughes C, Koronakis V. Increased distal gene transcription by the elongation factor RfaH, a specialized homologue of NusG. Mol Microbiol. 1996 Nov;22(4):729-37. PMID:8951819
↑ Leeds JA, Welch RA. Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream JUMPStart DNA sequences function together via a postinitiation mechanism. J Bacteriol. 1997 Jun;179(11):3519-27. PMID:9171395
↑ Bailey MJ, Hughes C, Koronakis V. RfaH and the ops element, components of a novel system controlling bacterial transcription elongation. Mol Microbiol. 1997 Dec;26(5):845-51. PMID:9426123
↑ Bailey MJ, Hughes C, Koronakis V. In vitro recruitment of the RfaH regulatory protein into a specialised transcription complex, directed by the nucleic acid ops element. Mol Gen Genet. 2000 Jan;262(6):1052-9. PMID:10660066
↑ Artsimovitch I, Landick R. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell. 2002 Apr 19;109(2):193-203. PMID:12007406
↑ Santangelo TJ, Roberts JW. RfaH, a bacterial transcription antiterminator. Mol Cell. 2002 Apr;9(4):698-700. PMID:11983161
↑ Beloin C, Michaelis K, Lindner K, Landini P, Hacker J, Ghigo JM, Dobrindt U. The transcriptional antiterminator RfaH represses biofilm formation in Escherichia coli. J Bacteriol. 2006 Feb;188(4):1316-31. PMID:16452414 doi:http://dx.doi.org/10.1128/JB.188.4.1316-1331.2006
↑ Zuber PK, Said N, Hilal T, Wang B, Loll B, González-Higueras J, Ramírez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH. Concerted transformation of a hyper-paused transcription complex and its reinforcing protein. Nat Commun. 2024 Apr 8;15(1):3040. PMID:38589445 doi:10.1038/s41467-024-47368-4

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8pib"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8pib is ON HOLD
+==autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)==
+<StructureSection load='8pib' size='340' side='right'caption='[[8pib]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8pib]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PIB 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]] 2.6&#8491;</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=8pib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pib OCA], [https://pdbe.org/8pib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pib RCSB], [https://www.ebi.ac.uk/pdbsum/8pib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pib ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RFAH_ECOLI RFAH_ECOLI] Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.<ref>PMID:1584020</ref> <ref>PMID:8606157</ref> <ref>PMID:8951819</ref> <ref>PMID:9171395</ref> <ref>PMID:9426123</ref> <ref>PMID:10660066</ref> <ref>PMID:12007406</ref> <ref>PMID:11983161</ref> <ref>PMID:16452414</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an alpha-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a beta-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
-Authors:
+Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.,Zuber PK, Said N, Hilal T, Wang B, Loll B, Gonzalez-Higueras J, Ramirez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH Nat Commun. 2024 Apr 8;15(1):3040. doi: 10.1038/s41467-024-47368-4. PMID:38589445<ref>PMID:38589445</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8pib" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Hilal T]]
+[[Category: Knauer SH]]
+[[Category: Loll B]]
+[[Category: Said N]]
+[[Category: Wahl MC]]
+[[Category: Zuber PK]]

8pib

From Proteopedia

Current revision

autoinhibited RfaH bound to E. coli transcription complex paused at ops site (encounter complex)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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