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13  structures 626  species 1  interaction 697  sequences 17  architectures

Family: Tfb5 (PF06331)

Summary: Transcription factor TFIIH complex subunit Tfb5

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This is the Wikipedia entry entitled "Tbf5 protein domain". More...

Tbf5 protein domain Edit Wikipedia article

Tbf5
PDB 1ydl EBI.jpg
Crystal structure of the human TFIIH.
Identifiers
Symbol Tbf5
Pfam PF06331
InterPro IPR009400

In molecular biology, this protein domain represents Tbf5 which stands for TTDA subunit of TFIIH basal transcription factor complex (also known as subunit 5 of RNA polymerase II transcription factor B), and Rex1 a type of nucleotide excision repair (NER) proteins. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms. The function of this protein is to aid transcription.

Structure

These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology.

TFIIH

Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH complex consists of ten subunits:

  • ERCC2,
  • ERCC3,
  • GTF2H1,
  • GTF2H2,
  • GTF2H3,
  • GTF2H4,
  • GTF2H5,
  • MNAT1,
  • CDK7 and
  • CCNH.

TTDA is also required for the stability of the TFIIH complex and for the presence of normal levels of TFIIH in the cell. TFIIH is one of five general transcription factors (GTFs) that assemble with RNA polymerase IIat a promoter site prior to the initiation of transcription. It is one of ten subunits that complete part of the 10 subunit protein complex (holoTFIIH) and part of a six-subunit complex of Rad3, Tfb1, Tfb2, Tfb4, Tfb5, and Ssl1 (referred to as core) [1]

Function

In humans, the function of Tbf5 is clear, as loss of it leads to trichothiosystropy. Defects in GTF2H5 cause the disease trichothiodystrophy (TTD), therefore GTF2H5 (general transcription factor 2H subunit 5) is also known as the TTD group A (TTDA) subunit (and as Tfb5).[2] The TTDA subunit is responsible for the DNA repair function of the complex. TTDA is present both bound to TFIIH, and as a free fraction that shuffles between the cytoplasm and nucleus; induction of NER-type DNA lesions shifts the balance towards TTDA's more stable association with TFIIH.[3]

REX1, which is short for, required for excision 1, is required for DNA repair in the single-celled, photosynthetic algae Chlamydomonas reinhardtii,[4] and has homologues in other eukaryotes.

References

  1. ^ Gibbons BJ, Brignole EJ, Azubel M, Murakami K, Voss NR, Bushnell DA, et al. (2012). "Subunit architecture of general transcription factor TFIIH.". Proc Natl Acad Sci U S A. 109 (6): 1949–54. doi:10.1073/pnas.1105266109. PMC 3277522Freely accessible. PMID 22308316. 
  2. ^ Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ, Botta E, Stefanini M, Egly JM, Aebersold R, Hoeijmakers JH, Vermeulen W (July 2004). "A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A". Nat. Genet. 36 (7): 714–9. doi:10.1038/ng1387. PMID 15220921. 
  3. ^ Giglia-Mari G, Miquel C, Theil AF, Mari PO, Hoogstraten D, Ng JM, Dinant C, Hoeijmakers JH, Vermeulen W (June 2006). "Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells". PLoS Biol. 4 (6): e156. doi:10.1371/journal.pbio.0040156. PMC 1457016Freely accessible. PMID 16669699. 
  4. ^ Cenkci B, Petersen JL, Small GD (June 2003). "REX1, a novel gene required for DNA repair". J. Biol. Chem. 278 (25): 22574–7. doi:10.1074/jbc.M303249200. PMID 12697762. 

This article incorporates text from the public domain Pfam and InterPro IPR009400

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Transcription factor TFIIH complex subunit Tfb5 Provide feedback

This family is a component of the general transcription and DNA repair factor IIH. TFB5 has been shown to be required for efficient recruitment of TFIIH to a promoter [3].

Literature references

  1. Blandin G, Durrens P, Tekaia F, Aigle M, Bolotin-Fukuhara M, Bon E, Casaregola S, de Montigny J, Gaillardin C, Lepingle A, Llorente B, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Perrin A, Potier S, Souciet J, Talla E, Toffano-Nioche C, Wesolowski-, FEBS Lett 2000;487:31-36.: Genomic exploration of the hemiascomycetous yeasts: 4. The genome of Saccharomyces cerevisiae revisited. PUBMED:11152879 EPMC:11152879

  2. Cenkci B, Petersen JL, Small GD; , 0;0:0-0.: REX1, a novel gene required for DNA repair. PUBMED:12697762 EPMC:12697762

  3. Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R; , Nat Genet. 2004;36:707-713.: Identification of TFB5, a new component of general transcription and DNA repair factor IIH. PUBMED:15220919 EPMC:15220919


This tab holds annotation information from the InterPro database.

InterPro entry IPR009400

This entry represents TTDA/Tfb5 subunit of TFIIH basal transcription factor complex. These proteins have a structural motif consisting of a 2-layer sandwich structure with an alpha/beta plait topology. Nucleotide excision repair is a major pathway for repairing UV light-induced DNA damage in most organisms.

Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair. The TFIIH multiprotein complex consists of a 7-subunit core (XPB, p62, p52, p44, p34, and TTDA) that is associated with a 3-subunit CDK-activating kinase module (MAT1, cyclin H and Cdk7) [PUBMED:21592869].

In humans, defects in TTDA cause the trichothiodystrophy photosensitive (TTDP), an autosomal recessive disease characterised by sulfur-deficient brittle hair and nails, ichthyosis, mental retardation, impaired sexual development, abnormal facies and cutaneous photosensitivity correlated with a nucleotide excision repair (NER) defect [PUBMED:15220921].

Gene Ontology

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Domain organisation

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Alignments

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(90)
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(965)
NCBI
(862)
Meta
(4)
RP15
(167)
RP35
(358)
RP55
(546)
RP75
(704)
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  Seed
(90)
Full
(697)
Representative proteomes UniProt
(965)
NCBI
(862)
Meta
(4)
RP15
(167)
RP35
(358)
RP55
(546)
RP75
(704)
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  Seed
(90)
Full
(697)
Representative proteomes UniProt
(965)
NCBI
(862)
Meta
(4)
RP15
(167)
RP35
(358)
RP55
(546)
RP75
(704)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: SWISS-PROT
Previous IDs: REX1; Tbf5;
Type: Family
Author: Studholme DJ, Wood V
Number in seed: 90
Number in full: 697
Average length of the domain: 64.10 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 66.31 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 23.3 23.4
Model length: 67
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

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Tfb5

Structures

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 Tfb5 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 sequence.

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