2oug: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==Crystal structure of the RfaH transcription factor at 2.1A resolution==
==Crystal structure of the RfaH transcription factor at 2.1A resolution==
<StructureSection load='2oug' size='340' side='right' caption='[[2oug]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
<StructureSection load='2oug' size='340' side='right'caption='[[2oug]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2oug]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OUG FirstGlance]. <br>
<table><tr><td colspan='2'>[[2oug]] 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=2OUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OUG FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rfaH, hlyT, sfrB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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]] 2.1&#8491;</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=2oug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oug OCA], [http://pdbe.org/2oug PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oug RCSB], [http://www.ebi.ac.uk/pdbsum/2oug PDBsum]</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=2oug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oug OCA], [https://pdbe.org/2oug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oug RCSB], [https://www.ebi.ac.uk/pdbsum/2oug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oug 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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ou/2oug_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ou/2oug_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2oug ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
RfaH, a paralog of the general transcription factor NusG, is recruited to elongating RNA polymerase at specific regulatory sites. The X-ray structure of Escherichia coli RfaH reported here reveals two domains. The N-terminal domain displays high similarity to that of NusG. In contrast, the alpha-helical coiled-coil C domain, while retaining sequence similarity, is strikingly different from the beta barrel of NusG. To our knowledge, such an all-beta to all-alpha transition of the entire domain is the most extreme example of protein fold evolution known to date. Both N domains possess a vast hydrophobic cavity that is buried by the C domain in RfaH but is exposed in NusG. We propose that this cavity constitutes the RNA polymerase-binding site, which becomes unmasked in RfaH only upon sequence-specific binding to the nontemplate DNA strand that triggers domain dissociation. Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for the initiation sigma factors.
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.,Belogurov GA, Vassylyeva MN, Svetlov V, Klyuyev S, Grishin NV, Vassylyev DG, Artsimovitch I Mol Cell. 2007 Apr 13;26(1):117-29. PMID:17434131<ref>PMID:17434131</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2oug" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Transcriptional activator|Transcriptional activator]]
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Artsimovitch, I]]
[[Category: Large Structures]]
[[Category: Svetlov, V]]
[[Category: Artsimovitch I]]
[[Category: Vassylyev, D G]]
[[Category: Svetlov V]]
[[Category: Vassylyeva, M N]]
[[Category: Vassylyev DG]]
[[Category: Transcription]]
[[Category: Vassylyeva MN]]
[[Category: Transcription elongation]]
[[Category: Transcription factor]]
[[Category: Transcription pausing]]
[[Category: Virulence]]

Latest revision as of 12:06, 21 February 2024

Crystal structure of the RfaH transcription factor at 2.1A resolutionCrystal structure of the RfaH transcription factor at 2.1A resolution

Structural highlights

2oug is a 4 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:X-ray diffraction, Resolution 2.1Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ 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
  2. ↑ Leeds JA, Welch RA. RfaH enhances elongation of Escherichia coli hlyCABD mRNA. J Bacteriol. 1996 Apr;178(7):1850-7. PMID:8606157
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ Santangelo TJ, Roberts JW. RfaH, a bacterial transcription antiterminator. Mol Cell. 2002 Apr;9(4):698-700. PMID:11983161
  9. ↑ 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

2oug, resolution 2.10Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2oug&oldid=4062192"