Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
29  structures 101  species 1  interaction 872  sequences 6  architectures

Family: IRF (PF00605)

Summary: Interferon regulatory factor transcription factor

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Interferon regulatory factors". More...

Interferon regulatory factors Edit Wikipedia article

Interferon regulatory factor transcription factor
PDB 1irf EBI.jpg
interferon regulatory factor-2 dna binding domain, nmr, minimized average structure
Identifiers
Symbol IRF
Pfam PF00605
InterPro IPR001346
SCOP 1if1
SUPERFAMILY 1if1

Interferon regulatory factors are proteins which regulate transcription of interferons (see regulation of gene expression).[1]

They are used in the JAK-STAT signaling pathway.[2]

Interferon regulatory factors contain a conserved N-terminal region of about 120 amino acids, which folds into a structure that binds specifically to the interferon consensus sequence (ICS), which is located upstream of the interferon genes.[3] The remaining parts of the interferon regulatory factor sequence vary depending on the precise function of the protein.[3]

Genes[edit]

See also[edit]

References[edit]

  1. ^ Paun A, Pitha PM (2007). "The IRF family, revisited". Biochimie 89 (6–7): 744–53. doi:10.1016/j.biochi.2007.01.014. PMC 2139905. PMID 17399883. 
  2. ^ Tsuneya Ikezu; Howard E. Gendelman (2008). Neuroimmune Pharmacology. Springer. pp. 213–. ISBN 978-0-387-72572-7. Retrieved 28 November 2010. 
  3. ^ a b Weisz A, Marx P, Sharf R, Appella E, Driggers PH, Ozato K, Levi BZ (December 1992). "Human interferon consensus sequence binding protein is a negative regulator of enhancer elements common to interferon-inducible genes". J. Biol. Chem. 267 (35): 25589–96. PMID 1460054. 

External links[edit]


This article incorporates text from the public domain Pfam and InterPro IPR001346

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.

Interferon regulatory factor transcription factor Provide feedback

This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA.

Literature references

  1. Escalante CR, Yie J, Thanos D, Aggarwal AK; , Nature 1998;1:103-106.: Structure of IRF-1 with bound DNA reveals determinants of interfereon regulation. PUBMED:9422515 EPMC:9422515


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001346

Viral infections induce the expression of type I interferons (IFN-alpha and IFN-beta) genes. The induction is due to the transcriptional activation of the IFN genes. Interferon regulatory factor I (IRF-1) is one of the transcription factors responsible for that activation. IRF-1 binds to an upstream regulatory cis element, known as the interferon consensus sequence (ICS), which is found in the promoters of type I IFN and IFN-inducible MHC class I genes. Interferon regulatory factor 2 (IRF-2) is a protein that also interacts with the ICS, but that does not function as an activator; rather, it suppresses the function of IRF-1 under certain circumstances [PUBMED:2691585].

These proteins share a highly conserved N-terminal domain of about 100 amino acid residues which is involved in DNA-binding and which contain five conserved tryptophans. This domain is known as a 'tryptophan pentad repeat' or a 'tryptophan cluster' and is also present in:

  • Interferon consensus sequence binding protein (ICSBP) [PUBMED:2111015], a transcription factor expressed predominantly in lymphoid tissues and induced by IFN-gamma that also binds to the ICS.
  • Transcriptional regulator ISGF3 gamma subunit [PUBMED:1630447]. ISGF3 is responsible for the initial stimulation of interferon-alpha-responsive genes. It recognises and binds to the interferon-stimulated response element (ISRE) within the regulatory sequences of target genes.
  • Interferon regulatory factor 3 (IRF-3).
  • Interferon regulatory factor 4 (IRF-4) which binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter.
  • Interferon regulatory factor 5 (IRF-5).
  • Interferon regulatory factor 6 (IRF-6).
  • Interferon regulatory factor 7 (IRF-7).
  • Gamma Herpesviruses vIRF-1, -2 and -3, proteins with homology to the cellular transcription factors of the IRF family [PUBMED:10933732]. Neither vIRF-1 nor vIRF-2 bind to DNA with the same specificity as cellular IRFs, indicating that if vIRFs are DNA-binding proteins, their binding has a pattern distinct from that of the cellular IRFs. Whether vIRF-3 can bind DNA with the same specificity as cellular IRFs is not known.

The IRF tryptophan pentad repeat DNA-binding domain has an alpha/beta architecture comprising a cluster of three alpha-helices (alpha1-alpha3) flanked on one side by a mixed four-stranded beta-sheet (beta1-beta4). It forms a helix-turn-helix motif that binds to ISRE consensus sequences found in target promoters. Three of the tryptophan residues contact DNA by recognising a GAAA sequence [PUBMED:9422515].

This entry represents the IRF tryptophan pentad repeat DNA-binding domain.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(26)
Full
(872)
Representative proteomes NCBI
(642)
Meta
(0)
RP15
(43)
RP35
(68)
RP55
(158)
RP75
(310)
Jalview View  View  View  View  View  View  View   
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(26)
Full
(872)
Representative proteomes NCBI
(642)
Meta
(0)
RP15
(43)
RP35
(68)
RP55
(158)
RP75
(310)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(26)
Full
(872)
Representative proteomes NCBI
(642)
Meta
(0)
RP15
(43)
RP35
(68)
RP55
(158)
RP75
(310)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 26
Number in full: 872
Average length of the domain: 105.30 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 28.65 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.1 21.8
Noise cut-off 20.9 20.8
Model length: 110
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

IRF

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 IRF domain has been found. There are 29 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.

Loading structure mapping...