Summary: Transcription factor S-II (TFIIS)
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Transcription factor S-II (TFIIS) Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Baculo_LEF5_C DUF523 Ogr_Delta TF_Zn_Ribbon YjdM_Zn_Ribbon Zn_Tnp_IS1595 |
Similarity to PfamA using HHSearch: | YjdM_Zn_Ribbon zinc_ribbon_13 Zn_Tnp_IS1595 zinc_ribbon_4 |
External database links
HOMSTRAD: | TFIIS |
PROSITE: | PDOC00383 |
SCOP: | 1tfi |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001222
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 zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS [PUBMED:3346229]. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites [PUBMED:10723030]. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre.
TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [PUBMED:7626141] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site [PUBMED:12914699].
Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor [PUBMED:2398897].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | zinc ion binding (GO:0008270) |
nucleic acid binding (GO:0003676) | |
Biological process | transcription, DNA-templated (GO:0006351) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Zn_Beta_Ribbon (CL0167), which has the following description:
A clan of zinc-binding ribbon domains.
The clan contains the following 87 members:
A2L_zn_ribbon Auto_anti-p27 Baculo_LEF5_C CpXC DNA_RNApol_7kD DUF1451 DUF1610 DUF1936 DUF2072 DUF2116 DUF2180 DUF2387 DUF2614 DUF35_N DUF3945 DUF4379 DZR DZR_2 Elf1 GATA Lar_restr_allev LIM Mu-like_Com NinF NOB1_Zn_bind Nudix_N_2 Ogr_Delta OrfB_Zn_ribbon PriA_CRR Prim_Zn_Ribbon RecO_C Ribosomal_L32p Ribosomal_L33 Ribosomal_L37ae Ribosomal_L37e Ribosomal_L40e Ribosomal_L44 Ribosomal_S27 Ribosomal_S27e RNA_POL_M_15KD Rubredoxin_2 Spt4 Stc1 TF_Zn_Ribbon TFIIS_C Tnp_zf-ribbon_2 Topo_Zn_Ribbon Toprim_Crpt Trm112p UPF0547 YjdM_Zn_Ribbon zf-C4 zf-C4_ClpX zf-C4_Topoisom zf-CHC2 zf-CSL zf-dskA_traR zf-FPG_IleRS zf-GRF zf-ISL3 zf-NADH-PPase zf-PARP zf-RanBP zf-ribbon_3 zf-RING_7 zf-RRN7 zf-TFIIB zf-trcl zf-ZPR1 zf_PR_Knuckle zf_Rg 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_ribbon_SprT Zn_Tnp_IS1 Zn_Tnp_IS1595Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (92) |
Full (5635) |
Representative proteomes | UniProt (10690) |
NCBI (11538) |
Meta (290) |
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RP15 (1040) |
RP35 (2440) |
RP55 (4031) |
RP75 (5749) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (92) |
Full (5635) |
Representative proteomes | UniProt (10690) |
NCBI (11538) |
Meta (290) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1040) |
RP35 (2440) |
RP55 (4031) |
RP75 (5749) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Prosite |
Previous IDs: | TFIIS; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 92 |
Number in full: | 5635 |
Average length of the domain: | 39.00 aa |
Average identity of full alignment: | 44 % |
Average coverage of the sequence by the domain: | 19.42 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 39 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 11 interactions for this family. More...
RNA_pol_Rpb1_3 RNA_pol_Rpb2_2 RNA_pol_Rpb1_2 RNA_pol_Rpb2_4 RNA_pol_Rpb1_6 RNA_pol_Rpb1_4 RNA_pol_Rpb2_6 RNA_pol_Rpb1_5 RNA_pol_Rpb2_1 RNA_pol_Rpb2_3 RNA_pol_Rpb2_5Structures
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 TFIIS_C domain has been found. There are 211 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 sequence.
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