Summary: Prokaryotic dksA/traR C4-type zinc finger
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Prokaryotic dksA/traR C4-type zinc finger Provide feedback
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000962
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 [PUBMED:10529348, PUBMED:15963892, PUBMED:15718139, PUBMED:17210253, PUBMED: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 [PUBMED:11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
This entry represents domains 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 [PUBMED:15294156, PUBMED:15294157]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [PUBMED:2180916] and deletion [PUBMED:8063112] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination [PUBMED:8063112]. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production [PUBMED:12775693].
The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include:
- the traR gene products encoded on the E. coli F and R100 plasmids [PUBMED:8021201, PUBMED:12932736]
- the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT
- the dnaK suppressor
- hypothetical proteins from bacteria and bacteriophage
- FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [PUBMED:10049694]
More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].
|Molecular function||zinc ion binding (GO:0008270)|
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A clan of zinc-binding ribbon domains.
The clan contains the following 50 members:A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C DNA_RNApol_7kD DUF1610 DUF1936 DUF2116 DUF2180 DUF2387 DZR Elf1 GATA NinF NOB1_Zn_bind Ogr_Delta OrfB_Zn_ribbon PhnA_Zn_Ribbon Prim_Zn_Ribbon Ribosomal_L32p Ribosomal_L37ae Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD RRN7 Spt4 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 zf-C4_Topoisom zf-CHC2 zf-DHHC zf-dskA_traR zf-FPG_IleRS zf-GRF zf-NADH-PPase zf-RanBP zf-ribbon_3 zf-TFIIB zinc-ribbons_6 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 Zn-ribbon_8 Zn_ribbon_recom Zn_Tnp_IS1 Zn_Tnp_IS1595
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Curation and family details
|Author:||Finn RD, Bateman A|
|Number in seed:||241|
|Number in full:||5127|
|Average length of the domain:||36.80 aa|
|Average identity of full alignment:||38 %|
|Average coverage of the sequence by the domain:||28.18 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the zf-dskA_traR domain has been found. There are 13 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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