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0  structures 16  species 0  interactions 1257  sequences 170  architectures

Family: GVQW (PF13900)

Summary: Putative binding domain

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This is the Wikipedia entry entitled "Caspase". More...

Caspase Edit Wikipedia article

Caspase domain
PDB 1ice EBI.jpg
Structure of interleukin-1 beta-converting enzyme.[1]
Identifiers
Symbol Peptidase_C14
Pfam PF00656
Pfam clan CL0093
InterPro IPR002398
PROSITE PS50208
MEROPS C14
SCOP 1ice
SUPERFAMILY 1ice

Caspases, or cysteine-aspartic proteases or cysteine-dependent aspartate-directed proteases are a family of cysteine proteases that play essential roles in apoptosis (programmed cell death), necrosis, and inflammation.[2]

Caspases are essential in cells for apoptosis, or programmed cell death, in development and most other stages of adult life, and have been termed "executioner" proteins for their roles in the cell. Some caspases are also required in the immune system for the maturation of lymphocytes. Failure of apoptosis is one of the main contributions to tumour development and autoimmune diseases; this, coupled with the unwanted apoptosis that occurs with ischemia or Alzheimer's disease, has stimulated interest in caspases as potential therapeutic targets since they were discovered in the mid-1990s.

Types of caspase proteins[edit]

As of November 2009, twelve caspases have been identified in humans.[3] There are two types of apoptotic caspases: initiator (apical) caspases and effector (executioner) caspases. Initiator caspases (e.g., CASP2, CASP8, CASP9, and CASP10) cleave inactive pro-forms of effector caspases, thereby activating them. Effector caspases (e.g., CASP3, CASP6, CASP7) in turn cleave other protein substrates within the cell, to trigger the apoptotic process. The initiation of this cascade reaction is regulated by caspase inhibitors.

CASP4 and CASP5, which are overexpressed in some cases of vitiligo and associated autoimmune diseases caused by NALP1 variants,[4] are not currently classified as initiator or effector in MeSH,[5] because they are inflammatory enzymes that, in concert with CASP1, are involved in T-cell maturation.

Caspase cascade[edit]

Caspases are regulated at a post-translational level, ensuring that they can be rapidly activated. They are first synthesized as inactive pro-caspases, that consist of a prodomain, a small subunit and a large subunit. Initiator caspases possess a longer prodomain than the effector caspases, whose prodomain is very small. The prodomain of the initiator caspases contain domains such as a CARD domain (e.g., caspases-2 and -9) or a death effector domain (DED) (caspases-8 and -10) that enables the caspases to interact with other molecules that regulate their activation. These molecules respond to stimuli that cause the clustering of the initiator caspases. Such clustering allows them to activate automatically, so that they can proceed to activate the effector caspases.

The caspase cascade can be activated by:

Overview of signal transduction pathways involved in apoptosis.

Some of the final targets of caspases include:

  • nuclear lamins
  • ICAD/DFF45 (inhibitor of caspase activated DNase or DNA fragmentation factor 45)
  • PARP (poly-ADP ribose polymerase)
  • PAK2 (P 21-activated kinase 2).

The role of caspase substrate cleavage in the morphology of apoptosis is not clear. However, ICAD/DFF45 acts to restrain CAD (caspase-activated DNase). The cleavage and inactivation of ICAD/DFF45 by a caspase allows CAD to enter the nucleus and fragment the DNA, causing the characteristic 'DNA ladder' in apoptotic cells.

In 2009, Queensland researchers announced caspase 1 and 3 in macrophages are regulated by p202 (a double-stranded DNA binding protein) reducing caspase response, and AIM2 (another double-stranded DNA binding protein) increasing caspase activation.[1]

Discovery of caspases, functions[edit]

H. Robert Horvitz initially established the importance of caspases in apoptosis and found that the ced-3 gene is required for the cell death that took place during the development of the nematode C. elegans. Horvitz and his colleague Junying Yuan found in 1993 that the protein encoded by the ced-3 gene is cysteine protease with similar properties to the mammalian interleukin-1-beta converting enzyme (ICE) (now known as caspase 1), which at the time was the only known caspase.[6] Other mammalian caspases were subsequently identified, in addition to caspases in organisms such as fruit fly Drosophila melanogaster.

Researchers decided upon the nomenclature of the caspase in 1996. In many instances, a particular caspase had been identified simultaneously by more than one laboratory, who would each give the protein a different name. For example, caspase 3 was variously known as CPP32, apopain and Yama. Caspases, therefore, were numbered in the order in which they were identified.[2] ICE was, therefore, renamed as caspase 1. ICE was the first mammalian caspase to be characterised because of its similarity to the nematode death gene ced-3, but it appears that the principal role of this enzyme is to mediate inflammation rather than cell death.

For the discovery of caspases and other aspects of apoptosis, see articles by Danial and Korsmeyer,[7] Yuan and Horvitz,[8] and by Li et al.[9] in the January 23, 2004 edition of the journal Cell.

Recent studies have demonstrated that caspase proteases are also regulators of non-death functions, the most notable ones being those involving the maturation of a wide variety of cells such as red blood cells and skeletal muscle myoblasts.[10]

See also[edit]

References[edit]

  1. ^ Wilson KP, Black JA, Thomson JA, et al. (July 1994). "Structure and mechanism of interleukin-1 beta converting enzyme". Nature 370 (6487): 270–5. doi:10.1038/370270a0. PMID 8035875. 
  2. ^ a b Alnemri ES, Emad S; et al. (1996). "Human ICE/CED-3 Protease Nomenclature". Cell 87 (2): 171. doi:10.1016/S0092-8674(00)81334-3. PMID 8861900. Retrieved 6 March 2011. 
  3. ^ HUGO Gene Nomenclature Committee
  4. ^ Gregersen, P.K. (22 March 2007). "Modern genetics, ancient defenses, and potential therapies". N Engl J Med. 356 (12): 1263–6. doi:10.1056/NEJMe078017. PMID 17377166. [PMID 17377166]
  5. ^ NIH Medical Subject Headings
  6. ^ Yuan, J et al. (1993). "The C. elegans cell death gene ced-3 encodes a protein similar to mammalian interleukin-1 beta-converting enzyme". Cell 75 (4): 641–652. doi:10.1016/0092-8674(93)90485-9. PMID 8242740. 
  7. ^ . Danial, N. N.; Korsmeyer, S. J. (January 2004). "Cell Death: Critical Control Points". Cell 116 (2): 205–219. doi:10.1016/S0092-8674(04)00046-7. PMID 14744432. Retrieved 2006-11-06. 
  8. ^ Yuan, J.; Horvitz, H. R. (January 2004). "A First Insight into the Molecular Mechanisms of Apoptosis". Cell 116 (2 Suppl): 53–56. doi:10.1016/S0092-8674(04)00028-5. PMID 15055582. Retrieved 2006-11-06. 
  9. ^ Li, P.; et al. (January 2004). "Mitochondrial Activation of Apoptosis". Cell 116 (2 Suppl): 57–59. doi:10.1016/S0092-8674(04)00031-5. PMID 15055583. Retrieved 2006-11-06. 
  10. ^ Lamkanfi, M.; et al. (January 2007). "Caspases in cell survival, proliferation and differentiation". Cell Death and Differentiation 14 (1): 44–55. doi:10.1038/sj.cdd.4402047. PMID 17053807. Retrieved 2011-02-28. 

External links[edit]

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.

Putative binding domain Provide feedback

This short domain is often found nested inside other longer domains. The function is not known, but the domain carries a highly conserved GVQW motif. The members are rich in proline and cysteine. This may be a binding domain.

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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 Peptidase_CD (CL0093), which has the following description:

The members of this clan are all endopeptidase that have the catalytic dyad histidine followed by cysteine. The catalytic histidine is preceded by a block of hydrophobic residues and a glycine, where as the cysteine is preceded by a block of hydrophobic residues and a glutamine and an alanine. The members with a know structure adopt an alpha/beta fold [1].

The clan contains the following 9 members:

CHAT GVQW Peptidase_C11 Peptidase_C13 Peptidase_C14 Peptidase_C25 Peptidase_C50 Peptidase_C80 Raptor_N

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
(35)
Full
(1257)
Representative proteomes NCBI
(778)
Meta
(423)
RP15
(55)
RP35
(60)
RP55
(61)
RP75
(72)
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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
(35)
Full
(1257)
Representative proteomes NCBI
(778)
Meta
(423)
RP15
(55)
RP35
(60)
RP55
(61)
RP75
(72)
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
(35)
Full
(1257)
Representative proteomes NCBI
(778)
Meta
(423)
RP15
(55)
RP35
(60)
RP55
(61)
RP75
(72)
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.

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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.

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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: Jackhmmer:Q6ZWE1
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 35
Number in full: 1257
Average length of the domain: 41.40 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 18.50 %

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 28.1 28.1
Trusted cut-off 28.1 28.1
Noise cut-off 27.9 28.0
Model length: 48
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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