Pathways & interactions
Zinc finger, DksA/TraR C4-type, bacteria (IPR020460)
Short name: Znf_C4-type_bac
Overlapping homologous superfamilies
- Zinc finger, DksA/TraR C4-type (IPR000962)
- Zinc finger, DksA/TraR C4-type, bacteria (IPR020460)
Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [PMID: 10529348, PMID: 15963892, PMID: 15718139, PMID: 17210253, PMID: 12665246]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [PMID: 11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
This entry represents the zinc fingers identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [PMID: 15294156, PMID: 15294157]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [PMID: 2180916] and deletion [PMID: 8063112] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination [PMID: 8063112]. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production [PMID: 12775693].
The DksA protein is structurally similar to the transcription factor GreA. 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. This entry represents the whole zinc finger.
- PR00618 (DKSAZNFINGER)