{PDOC00846}
{PS01102; ZF_DKSA_1}
{PS51128; ZF_DKSA_2}
{BEGIN}
**************************************************************
* Prokaryotic dksA C4-type zinc finger signature and profile *
**************************************************************
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
{END}