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| | ==RfaH from Escherichia coli in complex with ops DNA== | | ==RfaH from Escherichia coli in complex with ops DNA== |
| - | <StructureSection load='5ond' size='340' side='right' caption='[[5ond]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='5ond' size='340' side='right'caption='[[5ond]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OND FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5ond]] is a 4 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=5OND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OND FirstGlance]. <br> |
| - | </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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [http://pdbe.org/5ond PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [http://www.ebi.ac.uk/pdbsum/5ond PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></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]] 2.1Å</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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [https://pdbe.org/5ond PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [https://www.ebi.ac.uk/pdbsum/5ond PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5ond" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5ond" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Artsimovitch, I]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Knauer, S H]] | + | [[Category: Large Structures]] |
| - | [[Category: Roesch, P]] | + | [[Category: Artsimovitch I]] |
| - | [[Category: Zuber, P K]] | + | [[Category: Knauer SH]] |
| - | [[Category: Binding of single stranded dna]] | + | [[Category: Roesch P]] |
| - | [[Category: Operon-specific transcription factor]] | + | [[Category: Zuber PK]] |
| - | [[Category: Transcription]]
| + | |
| - | [[Category: Transformer protein]]
| + | |
| - | [[Category: Translation activation]]
| + | |
| Structural highlights
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 transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.
The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand.,Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rosch P, Knauer SH Elife. 2018 May 9;7. pii: 36349. doi: 10.7554/eLife.36349. PMID:29741479[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
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, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rosch P, Knauer SH. The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. Elife. 2018 May 9;7. pii: 36349. doi: 10.7554/eLife.36349. PMID:29741479 doi:http://dx.doi.org/10.7554/eLife.36349
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