PROSITE documentation PDOC00846

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.