View source for 8uot


==Composite map of PICdeltaTFIIK form1==
<StructureSection load='8uot' size='340' side='right'caption='[[8uot]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8uot]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8UOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8UOT 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]] 3.7&#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=8uot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8uot OCA], [https://pdbe.org/8uot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8uot RCSB], [https://www.ebi.ac.uk/pdbsum/8uot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8uot ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RAD3_YEAST RAD3_YEAST] ATP-dependent DNA helicase involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Necessary for excision of pyrimidine dimers. Also unwinds DNA/RNA duplexes. Plays an essential role in the cell viability. Involved in the maintenance of the fidelity of DNA replication. Acts as component of the general transcription and DNA repair factor IIH (TFIIH) core, which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activity, and is essential for polymerase II transcription in vitro.<ref>PMID:7961739</ref> <ref>PMID:8631896</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
RNA polymerase II (pol II) initiates transcription from transcription start sites (TSSs) located approximately 30-35 bp downstream of the TATA box in metazoans, whereas in the yeast Saccharomyces cerevisiae, pol II scans further downstream TSSs located approximately 40-120 bp downstream of the TATA box. Previously, we found that removal of the kinase module TFIIK (Kin28-Ccl1-Tfb3) from TFIIH shifts the TSS in a yeast in vitro system upstream to the location observed in metazoans and that addition of recombinant Tfb3 back to TFIIH-DeltaTFIIK restores the downstream TSS usage. Here, we report that this biochemical activity of yeast TFIIK in TSS scanning is attributable to the Tfb3 RING domain at the interface with pol II in the pre-initiation complex (PIC): especially, swapping Tfb3 Pro51-a residue conserved among all fungi-with Ala or Ser as in MAT1, the metazoan homolog of Tfb3, confers an upstream TSS shift in vitro in a similar manner to the removal of TFIIK. Yeast genetic analysis suggests that both Pro51 and Arg64 of Tfb3 are required to maintain the stability of the Tfb3-pol II interface in the PIC. Cryo-electron microscopy analysis of a yeast PIC lacking TFIIK reveals considerable variability in the orientation of TFIIH, which impairs TSS scanning after promoter opening.

Transcription start site scanning requires the fungi-specific hydrophobic loop of Tfb3.,Yang C, Basnet P, Sharmin S, Shen H, Kaplan CD, Murakami K Nucleic Acids Res. 2024 Sep 17:gkae805. doi: 10.1093/nar/gkae805. PMID:39287137<ref>PMID:39287137</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8uot" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Murakami K]]
[[Category: Yang C]]