1y5o: Difference between revisions

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-{{Seed}}
-[[Image:1y5o.png|left|200px]]
-<!--
+==NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH==
-The line below this paragraph, containing "STRUCTURE_1y5o", creates the "Structure Box" on the page.
+<StructureSection load='1y5o' size='340' side='right'caption='[[1y5o]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1y5o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y5O FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1y5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5o OCA], [https://pdbe.org/1y5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y5o RCSB], [https://www.ebi.ac.uk/pdbsum/1y5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5o ProSAT]</span></td></tr>
-{{STRUCTURE_1y5o|  PDB=1y5o  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TFB1_YEAST TFB1_YEAST] 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5o_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </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/main_output.php?pdb_ID=1y5o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+General transcription factor IIH (TFIIH) is recruited to the preinitiation complex (PIC) through direct interactions between its p62 (Tfb1) subunit and the carboxyl-terminal domain of TFIIEalpha. TFIIH has also been shown to interact with a number of transcriptional activator proteins through interactions with the same p62 (Tfb1) subunit. We have determined the NMR solution structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH (Tfb1(1-115)). Like the corresponding domain from the human p62 protein, Tfb1(1-115) contains a PH domain fold despite a low level of sequence identity between the two functionally homologous proteins. In addition, we have performed in vitro binding studies that demonstrate that the PH domains of Tfb1 and p62 specifically bind to monophosphorylated inositides [PtdIns(5)P and PtdIns(3)P]. NMR chemical shift mapping demonstrated that the PtdIns(5)P binding site on Tfb1 (p62) is located in the basic pocket formed by beta-strands beta5-beta7 of the PH domain fold. Interestingly, the structural composition of the PtdIns(5)P binding site is different from the composition of the binding sites for phosphoinositides on prototypic PH domains. We have also determined that the PH domains from Tfb1 and p62 are sufficient for binding to the activation domain of VP16. NMR chemical shift mapping demonstrated that the VP16 binding site within the PH domain of Tfb1 (p62) overlaps with the PtdIns(5)P binding site on Tfb1 (p62). These results provide new information about the recognition of phosphoinositides by PH domains, and point to a potential role for phosphoinositides in VP16 regulation.
-===NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH===
+NMR structure of the amino-terminal domain from the Tfb1 subunit of TFIIH and characterization of its phosphoinositide and VP16 binding sites.,Di Lello P, Nguyen BD, Jones TN, Potempa K, Kobor MS, Legault P, Omichinski JG Biochemistry. 2005 May 31;44(21):7678-86. PMID:15909982<ref>PMID:15909982</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15909982}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1y5o" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15909982 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15909982}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Y5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5O OCA].
-==Reference==
-NMR structure of the amino-terminal domain from the Tfb1 subunit of TFIIH and characterization of its phosphoinositide and VP16 binding sites., Di Lello P, Nguyen BD, Jones TN, Potempa K, Kobor MS, Legault P, Omichinski JG, Biochemistry. 2005 May 31;44(21):7678-86. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15909982 15909982]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Di Lello P]]
-[[Category: Jones, T N.]]
+[[Category: Jones TN]]
-[[Category: Kobor, M S.]]
+[[Category: Kobor MS]]
-[[Category: Legault, P.]]
+[[Category: Legault P]]
-[[Category: Lello, P Di.]]
+[[Category: Nguyen BD]]
-[[Category: Nguyen, B D.]]
+[[Category: Omichinski JG]]
-[[Category: Omichinski, J G.]]
+[[Category: Potempa K]]
-[[Category: Potempa, K.]]
-[[Category: Ph domain]]
-[[Category: Phosphoinositide]]
-[[Category: Tfb1]]
-[[Category: Tfiih]]
-[[Category: Vp16]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 16:49:18 2008''