6pln: Difference between revisions

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<StructureSection load='6pln' size='340' side='right'caption='[[6pln]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='6pln' size='340' side='right'caption='[[6pln]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6pln]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>
<table><tr><td colspan='2'>[[6pln]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tfe, PF0491 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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]] 2.6&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [http://pdbe.org/6pln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [http://www.ebi.ac.uk/pdbsum/6pln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [https://pdbe.org/6pln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [https://www.ebi.ac.uk/pdbsum/6pln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/TFE_PYRFU TFE_PYRFU]] Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.<ref>PMID:17921145</ref> <ref>PMID:17965161</ref>
[https://www.uniprot.org/uniprot/TFE_PYRFU TFE_PYRFU] Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.<ref>PMID:17921145</ref> <ref>PMID:17965161</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEalpha binary, and RNAP-TFEalpha-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEalpha bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEalpha interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEalpha interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEalpha and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.
 
Direct binding of TFEalpha opens DNA binding cleft of RNA polymerase.,Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS, Murakami KS Nat Commun. 2020 Nov 30;11(1):6123. doi: 10.1038/s41467-020-19998-x. PMID:33257704<ref>PMID:33257704</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6pln" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43587]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Jun, S H]]
[[Category: Pyrococcus furiosus]]
[[Category: Murakami, K S]]
[[Category: Jun SH]]
[[Category: General transcription factor]]
[[Category: Murakami KS]]
[[Category: Tfe]]
[[Category: Transcription]]

Latest revision as of 17:55, 13 March 2024

X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alphaX-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha

Structural highlights

6pln is a 2 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TFE_PYRFU Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.[1] [2]

References

  1. ↑ Grunberg S, Bartlett MS, Naji S, Thomm M. Transcription factor E is a part of transcription elongation complexes. J Biol Chem. 2007 Dec 7;282(49):35482-90. doi: 10.1074/jbc.M707371200. Epub 2007 , Oct 5. PMID:17921145 doi:http://dx.doi.org/10.1074/jbc.M707371200
  2. ↑ Micorescu M, Grunberg S, Franke A, Cramer P, Thomm M, Bartlett M. Archaeal transcription: function of an alternative transcription factor B from Pyrococcus furiosus. J Bacteriol. 2008 Jan;190(1):157-67. doi: 10.1128/JB.01498-07. Epub 2007 Oct 26. PMID:17965161 doi:http://dx.doi.org/10.1128/JB.01498-07

6pln, resolution 2.60Å

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