Summary: Transcription factor S-II (TFIIS), central domain
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Transcription factor S-II (TFIIS), central domain Provide feedback
Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and PF01096 are required for transcription activity .
Morin PE, Awrey DE, Edwards AM, Arrowsmith CH; , Proc Natl Acad Sci U S A 1996;93:10604-10608.: Elongation factor TFIIS contains three structural domains: solution structure of domain II. PUBMED:8855225 EPMC:8855225
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This tab holds annotation information from the InterPro database.
InterPro entry IPR003618
Transcription factor S-II (TFIIS) induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius [PUBMED:8502569]. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [PUBMED:1917889, PUBMED:8566795].
TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III [PUBMED:12914699]. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. 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.
This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.
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|Biological process||transcription, DNA-templated (GO:0006351)|
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|Seed source:||Pfam-B_1373 (release 11.0)|
|Number in seed:||331|
|Number in full:||1902|
|Average length of the domain:||111.80 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||18.11 %|
|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:||10|
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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 TFIIS_M domain has been found. There are 11 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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