{PDOC00383}
{PS00466; ZF_TFIIS_1}
{PS51133; ZF_TFIIS_2}
{BEGIN}
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* Zinc finger TFIIS-type signature and profile *
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In  eukaryotes  the  initiation  of transcription of protein encoding genes by
polymerase  II  (Pol  II)  is  modulated by general and specific transcription
factors.  The  general  transcription factors operate through common promoters
elements  (such  as the TATA box). At least eight different proteins associate
to  form  the  general  transcription  factors: TFIIA, -IIB, -IID, -IIE, -IIF,
-IIG, -IIH and -IIS [1].

During  mRNA elongation, Pol II can encounter DNA sequences that cause reverse
movement  of  the  enzyme.  Such  'backtracking' involved extrusion of the RNA
3'-end  into  the  pore,  and  can lead to transcriptional arrest. Escape from
arrest requires cleavage of the extruded RNA with the help of TFIIS [2]. TFIIS
is  a  protein  of about 300 amino acids. It contains two conserved regions, a
central  domain  which is required for Pol II binding and a C-terminal C4-type
zinc   finger  essential  for  RNA  cleavage.  The  zinc  finger  folds  in  a
conformation  termed  a  'zinc ribbon' (see <PDB:1TFI>) [3] characterized by a
three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model
for  Pol  II-TFIIS  complex  was obtained from X-ray analysis. It shows that a
beta  hairpin protrudes from the zinc finger and complements the pol II active
site [4].

The TFIIS zinc finger is also found in the following proteins:

 - Eukaryotic  and  archebacterial  RNA  polymerase  subunits of the 15 Kd / M
   family (see <PDOC00790>).
 - Vaccinia virus RNA polymerase 30 Kd subunit (rpo30) [5].
 - African swine fever virus protein I243L [6].

The  pattern  we developed starts at the first cysteine of the zinc finger and
ends  at  the  last  one.  We  also  developed a profile which spans the whole
structural domain.

-Consensus pattern: C-x(2)-C-x(9)-[LIVMQSART]-[QH]-[STQLMI]-[RA]-[SACR]-x-
                    [DE]-[DET]-[PGSEAM]-x(6)-C-x(2,5)-C-x(3)-[FWE]
                    [The 4 C's are zinc ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: April 2006 / Pattern revised.

[ 1] Hirashima S., Hirai H., Nakanishi Y., Natori S.
     "Molecular cloning and characterization of cDNA for eukaryotic
     transcription factor S-II."
     J. Biol. Chem. 263:3858-3863(1988).
     PubMed=3346229
[ 2] Wind M., Reines D.
     "Transcription elongation factor SII."
     Bioessays 22:327-336(2000).
     PubMed=10723030; DOI=10.1002/(SICI)1521-1878(200004)22:4<327::AID-BIES3>3.0.CO;2-4
[ 3] Qian X., Jeon C., Yoon H., Agarwal K., Weiss M.A.
     "Structure of a new nucleic-acid-binding motif in eukaryotic
     transcriptional elongation factor TFIIS."
     Nature 365:277-279(1993).
     PubMed=7626141; DOI=10.1038/365277a0;
[ 4] Kettenberger H., Armache K.J., Cramer P.
     "Architecture of the RNA polymerase II-TFIIS complex and implications
     for mRNA cleavage."
     Cell 114:347-357(2003).
     PubMed=12914699
[ 5] Ahn B.-Y., Gershon P.D., Jones E.V., Moss B.
     "Identification of rpo30, a vaccinia virus RNA polymerase gene with
     structural similarity to a eucaryotic transcription elongation
     factor."
     Mol. Cell. Biol. 10:5433-5441(1990).
     PubMed=2398897
[ 6] Rodriguez J.M., Salas M.L., Vinuela E.
     "Genes homologous to ubiquitin-conjugating proteins and eukaryotic
     transcription factor SII in African swine fever virus."
     Virology 186:40-52(1992).
     PubMed=1309282

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