{PDOC51344}
{PS51344; HTH_TFE_IIE}
{BEGIN}
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* TFE/IIEalpha-type HTH domain profile *
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Initiation of  eukaryotic  mRNA transcription requires melting of promoter DNA
with the  help  of  the  general  transcription factors TFIIE and TFIIH. TFIIE
consists of  a  large  and  a  small  subunit,  referred to as alpha and beta,
respectively, in  higher  eukaryotes.  Archaea contain a TFIIE homolog, called
TFE, that  corresponds  to  the N-terminal half of TFIIEalpha. It appears that
archaeal TFE   corresponds   to  the  minimal  essential  region  of  eukaryal
TFIIEalpha. In  archaea  TFE  contains an N-terminal, weakly conserved, helix-
turn-helix (HTH)  motif  within  a  leucine-rich  region and a C-terminal zinc
ribbon [1-3].  It has been proposed that the TFE/IIEalpha-type HTH domain acts
as a  bridging  factor  or  adapter  between the TATA box-binding protein, the
polymerase, and possibly promoter DNA [4].

The TFE/IIEalpha-type  HTH domain adopts a winged HTH (winged helix) fold (see
<PDB:1Q1H>), comprising  three  alpha-helices  and  three  beta-strands in the
canonical order   alpha1-beta1-alpha2-alpha3-beta2-beta3.  Conserved  residues
within helices  alpha1-alpha3  form the tightly packed hydrophobic core of the
winged helix  domain.  A specific feature of the structure is the extension of
the canonical  winged  helix  fold  at  the  N and C termini by the additional
helices alpha0   and  alpha4,  respectively.  Hydrophobic  residues  from  the
additional helix  alpha0  extend  the  hydrophobic  core  of  the winged helix
domain, and  helix alpha0 is tightly packed against the canonical winged helix
fold. Helix alpha4 comprises only one turn [4].

The profile we developed covers the entire TFE/IIEalpha-type HTH domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: December 2007 / First entry.

[ 1] Kuldell N.H., Buratowski S.
     "Genetic analysis of the large subunit of yeast transcription factor
     IIE reveals two regions with distinct functions."
     Mol. Cell. Biol. 17:5288-5298(1997).
     PubMed=9271406
[ 2] Bell S.D., Brinkman A.B., van der Oost J., Jackson S.P.
     "The archaeal TFIIEalpha homologue facilitates transcription
     initiation by enhancing TATA-box recognition."
     EMBO Rep. 2:133-138(2001).
     PubMed=11258705; DOI=10.1093/embo-reports/kve021
[ 3] Hanzelka B.L., Darcy T.J., Reeve J.N.
     "TFE, an archaeal transcription factor in Methanobacterium
     thermoautotrophicum related to eucaryal transcription factor
     TFIIEalpha."
     J. Bacteriol. 183:1813-1818(2001).
     PubMed=11160119; DOI=10.1128/JB.183.5.1813-1818.2001
[ 4] Meinhart A., Blobel J., Cramer P.
     "An extended winged helix domain in general transcription factor E/IIE
     alpha."
     J. Biol. Chem. 278:48267-48274(2003).
     PubMed=13679366; DOI=10.1074/jbc.M307874200

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