1y5o: Difference between revisions

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-[[Image:1y5o.gif|left|200px]]
- {{Structure
+==NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH==
-|PDB= 1y5o |SIZE=350|CAPTION= <scene name='initialview01'>1y5o</scene>
+<StructureSection load='1y5o' size='340' side='right'caption='[[1y5o]]' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<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>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-|GENE= TFB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
+<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>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Function ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5o OCA], [http://www.ebi.ac.uk/pdbsum/1y5o PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y5o RCSB]</span>
+[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]]
-'''NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH'''
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5o_consurf.spt"</scriptWhenChecked>
-==Overview==
+    <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.
-==About this Structure==
+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>
-Y5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y5O OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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]
+</div>
+<div class="pdbe-citations 1y5o" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[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 Mar 31 00:59:08 2008''