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PDBsum entry 1d8j

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protein links
Gene regulation PDB id
1d8j
Jmol
Contents
Protein chain
81 a.a. *
* Residue conservation analysis
PDB id:
1d8j
Name: Gene regulation
Title: Solution structure of the central core domain of tfiie beta
Structure: General transcription factor tfiie-beta. Chain: a. Fragment: central core domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: M.Okuda,Y.Watanabe,H.Okamura,F.Hanaoka,Y.Ohkuma,Y.Nishimura, Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
M.Okuda et al. (2000). Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface. EMBO J, 19, 1346-1356. PubMed id: 10716934 DOI: 10.1093/emboj/19.6.1346
Date:
25-Oct-99     Release date:   26-Apr-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29084  (T2EB_HUMAN) -  Transcription initiation factor IIE subunit beta
Seq:
Struc:
291 a.a.
81 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     transcription factor TFIIE complex   1 term 
  Biological process     transcription initiation from RNA polymerase II promoter   1 term 

 

 
DOI no: 10.1093/emboj/19.6.1346 EMBO J 19:1346-1356 (2000)
PubMed id: 10716934  
 
 
Structure of the central core domain of TFIIEbeta with a novel double-stranded DNA-binding surface.
M.Okuda, Y.Watanabe, H.Okamura, F.Hanaoka, Y.Ohkuma, Y.Nishimura.
 
  ABSTRACT  
 
Human general transcription factor TFIIE consists of two subunits, TFIIEalpha and TFIIEbeta. Recently, TFIIEbeta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. Here, the central core domain of human TFIIEbeta (TFIIEbetac) has been identified by a limited proteolysis. This solution structure has been determined by NMR. It consists of three helices with a beta hairpin at the C-terminus, resembling the winged helix proteins. However, TFIIEbetac shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow. A model will be proposed that TFIIE stabilizes the preinitiation complex by binding not only to the general transcription factors together with RNA polymerase II but also to the promoter DNA, where double-stranded DNA starts to open to be single-stranded upon activation of the preinitiation complex.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Stereo view of the solution structure of human TFIIE c. (A) Best-fit superposition of the ensemble of the final 20 NMR structures of human TFIIE c. (B) The averaged structure of human TFIIE c. The averaged structure over the final 20 NMR structures of human TFIIE c is shown in a ribbon representation. These figures were made using the program MOLMOL (Koradi et al., 1996).
Figure 3.
Figure 3 The hydrophobic core of TFIIE c. The side chains of amino acids that form the hydrophobic core of TFIIE c are shown. The hydrophobic side chains from the -helices, the -sheet and the helical turn are shown in cyan, light-green and yellow, respectively. This figure was made using the program MOLMOL (Koradi et al., 1996).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 1346-1356) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22751016 S.Grünberg, L.Warfield, and S.Hahn (2012).
Architecture of the RNA polymerase II preinitiation complex and mechanism of ATP-dependent promoter opening.
  Nat Struct Mol Biol, 19, 788-796.  
21358628 S.Lefèvre, H.Dumay-Odelot, L.El-Ayoubi, A.Budd, P.Legrand, N.Pinaud, M.Teichmann, and S.Fribourg (2011).
Structure-function analysis of hRPC62 provides insights into RNA polymerase III transcription initiation.
  Nat Struct Mol Biol, 18, 352-358.
PDB codes: 2xub 2xv4
20797630 S.R.Geiger, K.Lorenzen, A.Schreieck, P.Hanecker, D.Kostrewa, A.J.Heck, and P.Cramer (2010).
RNA polymerase I contains a TFIIF-related DNA-binding subcomplex.
  Mol Cell, 39, 583-594.
PDB codes: 3nff 3nfg 3nfh 3nfi
19210545 A.Tanaka, T.Watanabe, Y.Iida, F.Hanaoka, and Y.Ohkuma (2009).
Central forkhead domain of human TFIIE beta plays a primary role in binding double-stranded DNA at transcription initiation.
  Genes Cells, 14, 395-405.  
19359364 J.Zhang, E.Li, and G.J.Olsen (2009).
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.
  Nucleic Acids Res, 37, 3588-3601.  
18354501 M.Okuda, A.Tanaka, M.Satoh, S.Mizuta, M.Takazawa, Y.Ohkuma, and Y.Nishimura (2008).
Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH.
  EMBO J, 27, 1161-1171.
PDB codes: 2rnq 2rnr
18218714 S.Akashi, S.Nagakura, S.Yamamoto, M.Okuda, Y.Ohkuma, and Y.Nishimura (2008).
Structural characterization of human general transcription factor TFIIF in solution.
  Protein Sci, 17, 389-400.  
16547462 A.Jawhari, M.Uhring, S.De Carlo, C.Crucifix, G.Tocchini-Valentini, D.Moras, P.Schultz, and A.Poterszman (2006).
Structure and oligomeric state of human transcription factor TFIIE.
  EMBO Rep, 7, 500-505.  
17016021 S.Akashi (2006).
[Structural and functional characterization of biological macromolecules by mass spectrometry]
  Yakugaku Zasshi, 126, 915-929.  
15743411 K.Hayashi, T.Watanabe, A.Tanaka, T.Furumoto, C.Sato-Tsuchiya, M.Kimura, M.Yokoi, A.Ishihama, F.Hanaoka, and Y.Ohkuma (2005).
Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiation.
  Genes Cells, 10, 207-224.  
15508143 R.Sankararamakrishnan, S.Verma, and S.Kumar (2005).
ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis.
  Proteins, 58, 211-221.  
16184598 Y.Itoh, S.Unzai, M.Sato, A.Nagadoi, M.Okuda, Y.Nishimura, and S.Akashi (2005).
Investigation of molecular size of transcription factor TFIIE in solution.
  Proteins, 61, 633-641.  
15004549 C.Alfano, D.Sanfelice, J.Babon, G.Kelly, A.Jacks, S.Curry, and M.R.Conte (2004).
Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein.
  Nat Struct Mol Biol, 11, 323-329.
PDB codes: 1s79 1s7a
15479635 H.T.Chen, and S.Hahn (2004).
Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC.
  Cell, 119, 169-180.  
15385556 M.Okuda, A.Tanaka, Y.Arai, M.Satoh, H.Okamura, A.Nagadoi, F.Hanaoka, Y.Ohkuma, and Y.Nishimura (2004).
A novel zinc finger structure in the large subunit of human general transcription factor TFIIE.
  J Biol Chem, 279, 51395-51403.
PDB code: 1vd4
15196470 P.Cramer (2004).
RNA polymerase II structure: from core to functional complexes.
  Curr Opin Genet Dev, 14, 218-226.  
15114340 S.Hahn (2004).
Structure and mechanism of the RNA polymerase II transcription machinery.
  Nat Struct Mol Biol, 11, 394-403.  
13679366 A.Meinhart, J.Blobel, and P.Cramer (2003).
An extended winged helix domain in general transcription factor E/IIE alpha.
  J Biol Chem, 278, 48267-48274.
PDB code: 1q1h
12665589 T.Watanabe, K.Hayashi, A.Tanaka, T.Furumoto, F.Hanaoka, and Y.Ohkuma (2003).
The carboxy terminus of the small subunit of TFIIE regulates the transition from transcription initiation to elongation by RNA polymerase II.
  Mol Cell Biol, 23, 2914-2926.  
11250146 A.Dvir, J.W.Conaway, and R.C.Conaway (2001).
Mechanism of transcription initiation and promoter escape by RNA polymerase II.
  Curr Opin Genet Dev, 11, 209-214.  
11179888 C.W.Müller (2001).
Transcription factors: global and detailed views.
  Curr Opin Struct Biol, 11, 26-32.  
11248041 K.Kamada, J.De Angelis, R.G.Roeder, and S.K.Burley (2001).
Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF.
  Proc Natl Acad Sci U S A, 98, 3115-3120.
PDB code: 1i27
11331764 L.Spangler, X.Wang, J.W.Conaway, R.C.Conaway, and A.Dvir (2001).
TFIIH action in transcription initiation and promoter escape requires distinct regions of downstream promoter DNA.
  Proc Natl Acad Sci U S A, 98, 5544-5549.  
11113176 S.Yamamoto, Y.Watanabe, P.J.van der Spek, T.Watanabe, H.Fujimoto, F.Hanaoka, and Y.Ohkuma (2001).
Studies of nematode TFIIE function reveal a link between Ser-5 phosphorylation of RNA polymerase II and the transition from transcription initiation to elongation.
  Mol Cell Biol, 21, 1.  
11027286 M.Douziech, F.Coin, J.M.Chipoulet, Y.Arai, Y.Ohkuma, J.M.Egly, and B.Coulombe (2000).
Mechanism of promoter melting by the xeroderma pigmentosum complementation group B helicase of transcription factor IIH revealed by protein-DNA photo-cross-linking.
  Mol Cell Biol, 20, 8168-8177.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.