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189  structures 348  species 3  interactions 1889  sequences 35  architectures

Family: BIR (PF00653)

Summary: Inhibitor of Apoptosis domain

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Inhibitor of apoptosis domain Edit Wikipedia article

Inhibitor of Apoptosis domain
1QBH BIRC2.png
NMR solution structure of the BIR domain of human BIRC2 protein.[1] The protein is rainbow colored cartoon diagram (N-terminus = blue, C-terminus = red) while the coordinated zinc is represented by a grey sphere.
Identifiers
Symbol BIR
Pfam PF00653
InterPro IPR001370
PROSITE PS50143
SCOP 1qbh
SUPERFAMILY 1qbh

The inhibitor of apoptosis domain -- also known as IAP repeat, Baculovirus Inhibitor of apoptosis protein Repeat, or BIR -- is a structural motif found in proteins with roles in apoptosis, cytokine production, and chromosome segregation.[2] Proteins containing BIR are known as inhibitor of apoptosis proteins (IAPs), or BIR-containing proteins (BIRPs or BIRCs), and include BIRC1 (NAIP), BIRC2 (cIAP1), BIRC3 (cIAP2), BIRC4 (xIAP), BIRC5 (survivin) and BIRC6.[2][3]

BIR domains belong to the zinc-finger domain family and characteristically have a number of invariant amino acid residues, including 3 conserved cysteines and one conserved histidine, which coordinate a zinc ion.[4] They are typically composed of 4-5 alpha helices and a three-stranded beta sheet.

External links[edit]

References[edit]

  1. ^ PDB 1QBH;Hinds MG, Norton RS, Vaux DL, Day CL (July 1999). "Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat". Nat. Struct. Biol. 6 (7): 648–51. doi:10.1038/10701. PMID 10404221. 
  2. ^ a b Silke J, Vaux DL (May 2001). "Two kinds of BIR-containing protein - inhibitors of apoptosis, or required for mitosis". J. Cell. Sci. 114 (Pt 10): 1821–7. PMID 11329368. 
  3. ^ Verhagen AM, Coulson EJ, Vaux DL (2001). "Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs". Genome Biol. 2 (7): REVIEWS3009. doi:10.1186/gb-2001-2-7-reviews3009. PMC 139420. PMID 11516343. 
  4. ^ Birnbaum MJ, Clem RJ, Miller LK (April 1994). "An apoptosis-inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs". J. Virol. 68 (4): 2521–8. PMC 236730. PMID 8139034. 

This article incorporates text from the public domain Pfam and InterPro IPR001370

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.

Inhibitor of Apoptosis domain Provide feedback

BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are usually made up of 4-5 alpha helices and a three-stranded beta-sheet. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin (O15392) [2].

Literature references

  1. Birnbaum MJ, Clem RJ, Miller LK; , J Virol 1994;68:2521-2528.: An apoptosis-inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs. PUBMED:8139034 EPMC:8139034

  2. Verhagen AM, Coulson EJ, Vaux DL; , Genome Biol 2001;2:REVIEWS3009.: Inhibitor of apoptosis proteins and their relatives: IAPs and other BIRPs. PUBMED:11516343 EPMC:11516343


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001370

The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [PUBMED:8139034, PUBMED:8552191]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, INTERPRO).

The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [PUBMED:8445726] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) [PUBMED:8139034]. Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have since been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7 [PUBMED:18992220].

This entry represents the BIR domain, found in inhibitor of apoptosis proteins (IAPs) and also known as IAP repeat. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin [PUBMED:11516343].

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...

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Pfam Clan

This family is a member of clan BIR-like (CL0417), which has the following description:

Clan of domains all involved in binding nucleic acid and sharing the sequence motif C3HC.

The clan contains the following 3 members:

BIR Rsm1 zf-C3HC

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...

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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
(184)
Full
(1889)
Representative proteomes NCBI
(1890)
Meta
(5)
RP15
(236)
RP35
(332)
RP55
(623)
RP75
(901)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(184)
Full
(1889)
Representative proteomes NCBI
(1890)
Meta
(5)
RP15
(236)
RP35
(332)
RP55
(623)
RP75
(901)
Alignment:
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Sequence:
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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
(184)
Full
(1889)
Representative proteomes NCBI
(1890)
Meta
(5)
RP15
(236)
RP35
(332)
RP55
(623)
RP75
(901)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Prosite
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 184
Number in full: 1889
Average length of the domain: 67.90 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 17.22 %

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 22.9 22.9
Trusted cut-off 23.0 22.9
Noise cut-off 22.7 22.6
Model length: 70
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

BIR Peptidase_C14 PP2C

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 BIR domain has been found. There are 189 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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