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PDBsum entry 1vd4

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protein metals links
Transcription PDB id
1vd4
Jmol
Contents
Protein chain
62 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1vd4
Name: Transcription
Title: Solution structure of the zinc finger domain of tfiie alpha
Structure: Transcription initiation factor iie, alpha subunit. Chain: a. Fragment: zinc finger domain. Synonym: tfiie-alpha, general transcription factor iie 56 kda subunit, general transcription factor tfiie alpha. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: gtf2e1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: M.Okuda,A.Tanaka,Y.Arai,M.Satoh,H.Okamura,A.Nagadoi, F.Hanaoka,Y.Ohkuma,Y.Nishimura
Key ref:
M.Okuda et al. (2004). A novel zinc finger structure in the large subunit of human general transcription factor TFIIE. J Biol Chem, 279, 51395-51403. PubMed id: 15385556 DOI: 10.1074/jbc.M404722200
Date:
18-Mar-04     Release date:   05-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29083  (T2EA_HUMAN) -  General transcription factor IIE subunit 1
Seq:
Struc:
439 a.a.
62 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1074/jbc.M404722200 J Biol Chem 279:51395-51403 (2004)
PubMed id: 15385556  
 
 
A novel zinc finger structure in the large subunit of human general transcription factor TFIIE.
M.Okuda, A.Tanaka, Y.Arai, M.Satoh, H.Okamura, A.Nagadoi, F.Hanaoka, Y.Ohkuma, Y.Nishimura.
 
  ABSTRACT  
 
The zinc finger domain in the large subunit of TFIIE (TFIIEalpha) is phylogenetically conserved and is essential for transcription. Here, we determined the solution structure of this domain by using NMR. It consisted of one alpha-helix and five beta-strands, showing novel features distinct from previously determined zinc-binding structures. We created point mutants of TFIIEalpha in this domain and examined their binding abilities to other general transcription factors as well as their transcription activities. Four Zn(2+)-ligand mutants, in which each of cysteine residues at positions 129, 132, 154, and 157 was replaced by alanine, possessed no transcription activities on a linearized template, whereas, on a supercoiled template, interesting functional asymmetry was observed: although the C-terminal two mutants abolished transcription activity (<5%), the N-terminal two mutants retained about 20% activities. The N-terminal two mutants bound stronger to the small subunit of TFIIF than the wild type and the C-terminal two mutants were impaired in their binding abilities to the XPB subunits of TFIIH. These suggest that the structural integrity of the zinc finger domain is essential for the TFIIE function, particularly in the transition from the transcription initiation to elongation and the conformational tuning of this domain for appropriate positioning of TFIIF, TFIIH, and polymerase II would be needed depending on the situation and timing.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Sequence alignment of the TFIIE c. Conserved amino acids are shown in bold.Zn2+-coordinating cysteines are boxed in red. Residues that contribute to the formation of the hydrophobic core are boxed in yellow. Mutated residues in the mutation analyses are boxed and numbered. The secondary structure of the hTFIIE c is shown above the aligned sequence. Arrows and a cylinder indicate -strands and an -helix, respectively. Xenop, Xenopus; Droso, Drosophila; C.ele, Caenorhabditis elegans; S.pom, Schizosaccharomyces pombe; S.cer, Saccharomyces cerevisiae; A.per, Aeropyrum pernix; M.jan, Methanococcus jannaschii; M.the, Methanobacterium thermoautotrophicum; S.sol, Sulfolobus solfataricus; (GenBankTM accession numbers: human, CAA45068 [GenBank] mouse, BAB27686 [GenBank] Xenopus, CAA78505 [GenBank] Drosophila, AAD00187 [GenBank] C. elegans, CAA70050 [GenBank] S. pombe, CAB66310 [GenBank] S. cerevisiae, AAA62665 [GenBank] A. pernix, BAA81014 [GenBank] M. jannaschii, AAB98767 [GenBank] M. thermoautotrophicum, AAB86141 [GenBank] and S. solfataricus, AAK40605 [GenBank] .
Figure 4.
Structural comparison of the hTFIIE {alpha} c with the zinc-ribbon domains. A, ribbon structures of the zinc-coordinating domains. hTFIIE {alpha} c; the core domain of the human TFIIE {alpha} , hTFIISc; the C-terminal domain of the transcription elongation factor TFIIS from human, aTFIIBn; the N-terminal domain of the general transcription factor TFIIB from archaea, yRPB9c; the C-terminal domain of the RPB9 subunit of pol II from S. cerevisiae.Zn2+ are indicated as pink spheres. B, superposition of the zinc-binding sites. Two turns are shown by superposing with the minimum root mean square deviation. Red, hTFIIE {alpha} c; cyan, hTFIISc; green, aTFIIBn; and orange, yRPB9c.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 51395-51403) copyright 2004.  
  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.  
18156466 B.K.Benson, G.Meades, A.Grove, and G.L.Waldrop (2008).
DNA inhibits catalysis by the carboxyltransferase subunit of acetyl-CoA carboxylase: implications for active site communication.
  Protein Sci, 17, 34-42.  
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.  
16042788 I.Callebaut, K.Prat, E.Meurice, J.P.Mornon, and S.Tomavo (2005).
Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes.
  BMC Genomics, 6, 100.  
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.  
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.