This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1y5o

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:37, 25 April 2018

NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH

Structural highlights

1y5o is a 1 chain structure with sequence from Atcc 18824. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	TFB1 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.^[1] ^[2]

Evolutionary Conservation

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

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 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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Svejstrup JQ, Feaver WJ, LaPointe J, Kornberg RD. RNA polymerase transcription factor IIH holoenzyme from yeast. J Biol Chem. 1994 Nov 11;269(45):28044-8. PMID:7961739
↑ Sung P, Guzder SN, Prakash L, Prakash S. Reconstitution of TFIIH and requirement of its DNA helicase subunits, Rad3 and Rad25, in the incision step of nucleotide excision repair. J Biol Chem. 1996 May 3;271(18):10821-6. PMID:8631896
↑ Di Lello P, Nguyen BD, Jones TN, Potempa K, Kobor MS, Legault P, Omichinski JG. NMR structure of the amino-terminal domain from the Tfb1 subunit of TFIIH and characterization of its phosphoinositide and VP16 binding sites. Biochemistry. 2005 May 31;44(21):7678-86. PMID:15909982 doi:10.1021/bi050099s

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1y5o"

@@ Line 1: / Line 1: @@
 ==NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH==
 <StructureSection load='1y5o' size='340' side='right' caption='[[1y5o]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
@@ Line 4: / Line 5: @@
 <table><tr><td colspan='2'>[[1y5o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y5O FirstGlance]. <br>
 </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TFB1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=1y5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5o OCA], [http://pdbe.org/1y5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5o RCSB], [http://www.ebi.ac.uk/pdbsum/1y5o PDBsum]</span></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=1y5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y5o OCA], [http://pdbe.org/1y5o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y5o RCSB], [http://www.ebi.ac.uk/pdbsum/1y5o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y5o ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y5/1y5o_consurf.spt"</scriptWhenChecked>
+    <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>

1y5o

From Proteopedia

Revision as of 06:37, 25 April 2018

NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox