{PDOC00846}
{PS01102; ZF_DKSA_1}
{PS51128; ZF_DKSA_2}
{BEGIN}
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* Prokaryotic dksA C4-type zinc finger signature and profile *
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Guanosine tetraphosphate (ppGpp) or alarmone is a key nucleotide that triggers
various  regulatory  events  in bacterial cells starved for amino acids. ppGpp
specifically   inhibits  the  initiation  of  transcription  from  stable  RNA
promoters.  It  directly  binds  near the catalytic site of RNA polymerase and
modulates  its activity. Dksa augments ppGpp regulatory signal through binding
to  RNA  polymerase  [1].  ppGpp  and  dksa  also have an activation effect on
promoters of enzymes involved in amino acid biosynthesis [2].

The  crystal  structure  of  E.  coli  dksA  protein  has been determined (see
<PDB:1TJL>)  [3].  It is structurally similar to the transcription factor greA
(see  <PDOC00651>).  Both are comprised of a coiled-coil region and a globular
domain.  The  dksa zinc finger (C4-type) starts in the coiled-coil and ends in
the  globular domain. The coiled-coil region binds the RNA polymerase near the
ppGpp  binding  site  and  could  contribute  to  the  stability  of  the  RNA
polymerase-ppGpp complex.

Some proteins known to contain a dksa zinc finger:

 - Escherichia coli and Haemophilus influenzae protein dksA.
 - Escherichia coli plasmid F protein traR.
 - Bacteriophage p2 orf82.
 - Bacteriophage 186 cp80.
 - Escherichia coli hypothetical protein ybiI.
 - Haemophilus influenzae hypothetical protein HI1497.

The  pattern  we  developed  covers  the  whole  C4-type  zinc finger. We also
developed  a  profile that starts at the N-terminus of the second helice of the
coiled-coil and ends at the C-terminal extremity of the globular domain.

-Consensus pattern: C-[DESN]-x-[CTS]-x(3)-I-x(3)-[RK]-x(4)-P-x(4)-[CSLAT]-
                    x(2)-[CAYF]
-Sequences known to belong to this class detected by the profile: 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] de Lange F.J., Moorman A.F., Anderson R.H., Manner J., Soufan A.T.,
     de Gier-de Vries C., Schneider M.D., Webb S., van den Hoff M.J.,
     Christoffels V.M.
     "Lineage and morphogenetic analysis of the cardiac valves."
     Circ. Res. 95:645-654(2004).
     PubMed=15297379; DOI=10.1161/01.RES.0000141429.13560.cb
[ 2] Paul B.J., Berkmen M.B., Gourse R.L.
     "From the Cover: DksA potentiates direct activation of amino acid
     promoters by ppGpp."
     Proc. Natl. Acad. Sci. U.S.A. 102:7823-7828(2005).
     PubMed=15899978; DOI=10.1073/pnas.0501170102
[ 3] Perederina A., Svetlov V., Vassylyeva M.N., Tahirov T.H., Yokoyama S.,
     Artsimovitch I., Vassylyev D.G.
     "Regulation through the secondary channel-structural framework for
     ppGpp-DksA synergism during transcription."
     Cell 118:297-309(2004).
     PubMed=15294156; DOI=10.1016/j.cell.2004.06.030

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