Summary: CSL zinc finger
CSL zinc finger Provide feedback
This is a zinc binding motif which contains four cysteine residues which chelate zinc . This domain is often found associated with a PF00226 domain. This domain is named after the conserved motif of the final cysteine.
Sun J, Zhang J, Wu F, Xu C, Li S, Zhao W, Wu Z, Wu J, Zhou CZ, Shi Y; , Biochemistry 2005;44:8801-8809.: Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module. PUBMED:15952786 EPMC:15952786
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007872
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 a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ INTERPRO domain.
Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death [PUBMED:11595641]. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [PUBMED:14527407, PUBMED:15485916]. The function of this motif is unknown.
More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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A clan of zinc-binding ribbon domains.
The clan contains the following 70 members:A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C CpXC DNA_RNApol_7kD DUF1451 DUF1610 DUF1936 DUF2072 DUF2116 DUF2180 DUF2387 DUF2614 DUF35_N DUF4379 DZR Elf1 GATA Lar_restr_allev Mu-like_Com NinF NOB1_Zn_bind Nudix_N_2 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-CSL zf-DHHC zf-dskA_traR zf-FPG_IleRS zf-GRF zf-ISL3 zf-NADH-PPase zf-RanBP zf-ribbon_3 zf-TFIIB zf-trcl zf-ZPR1 zinc-ribbon_6 zinc-ribbons_6 zinc_ribbon_10 zinc_ribbon_11 zinc_ribbon_12 zinc_ribbon_13 zinc_ribbon_15 zinc_ribbon_2 zinc_ribbon_4 zinc_ribbon_5 zinc_ribbon_9 Zn-ribbon_8 Zn_ribbon_recom Zn_Tnp_IS1 Zn_Tnp_IS1595
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_12353 (release 7.7)|
|Author:||Wood V, Bateman A, Mistry J|
|Number in seed:||60|
|Number in full:||1036|
|Average length of the domain:||58.60 aa|
|Average identity of full alignment:||39 %|
|Average coverage of the sequence by the domain:||40.30 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|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-CSL domain has been found. There are 5 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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