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25  structures 114  species 2  interactions 238  sequences 2  architectures

Family: Crisp (PF08562)

Summary: Crisp

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This is the Wikipedia entry entitled "CAP protein family". More...

CAP protein family Edit Wikipedia article

CAP
PDB 1smb EBI.jpg
crystal structure of golgi-associated pr-1 protein
Identifiers
Symbol CAP
Pfam PF00188
InterPro IPR014044
PROSITE PDOC00835
SCOP 1s0p
SUPERFAMILY 1s0p
Crisp domain
PDB 1rc9 EBI.jpg
crystal structure of stecrisp, a member of crisp family from trimeresurus stejnegeri refined at 1.6 angstroms resolution: structural relationship of the two domains
Identifiers
Symbol Crisp
Pfam PF08562
Pfam clan CL0213
InterPro IPR013871

In molecular biology, the CAP protein family (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP)) is a large family of proteins that are found in a wide range of organisms, including prokaryotes and non-vertebrate eukaryotes.[1] [2] The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences.[3] The calcium-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate.[2][4]

Many of these proteins contain a Crisp domain. This domain is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor calcium signalling.[5] It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK.[5]

References[edit]

  1. ^ Yeats, C.; Bentley, S.; Bateman, A. (2003). "New knowledge from old: In silico discovery of novel protein domains in Streptomyces coelicolor". BMC microbiology 3: 3. PMC 151604. PMID 12625841.  edit
  2. ^ a b Milne, T. J.; Abbenante, G.; Tyndall, J. D.; Halliday, J.; Lewis, R. J. (2003). "Isolation and Characterization of a Cone Snail Protease with Homology to CRISP Proteins of the Pathogenesis-related Protein Superfamily". Journal of Biological Chemistry 278 (33): 31105–31110. doi:10.1074/jbc.M304843200. PMID 12759345.  edit
  3. ^ Gibbs, G. M.; Roelants, K.; O'Bryan, M. K. (2008). "The CAP Superfamily: Cysteine-Rich Secretory Proteins, Antigen 5, and Pathogenesis-Related 1 Proteins--Roles in Reproduction, Cancer, and Immune Defense". Endocrine Reviews 29 (7): 865–897. doi:10.1210/er.2008-0032. PMID 18824526.  edit
  4. ^ Semb, B. K.; Halvorsen, J. F.; Fossdal, J. E. (1977). "Acute gastric volvulus with necrosis of the stomach and the left lower pulmonary lobe". Acta chirurgica Scandinavica 143 (4): 256–258. PMID 906761.  edit
  5. ^ a b Gibbs GM, Scanlon MJ, Swarbrick J, Curtis S, Gallant E, Dulhunty AF, O'Bryan MK (February 2006). "The cysteine-rich secretory protein domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ signaling". J. Biol. Chem. 281 (7): 4156–63. doi:10.1074/jbc.M506849200. PMID 16339766. 

This article incorporates text from the public domain Pfam and InterPro IPR014044

This article incorporates text from the public domain Pfam and InterPro IPR013871

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.

Crisp Provide feedback

This domain is found on Crisp proteins which contain PF00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling [1]. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK [1].

Literature references

  1. Gibbs GM, Scanlon MJ, Swarbrick J, Curtis S, Gallant E, Dulhunty A, O'bryan MK; , J Biol Chem. 2005; [Epub ahead of print]: The crisp domain of Tpx-1 is related to ion channel toxins and regulates ryanodine receptor Ca2+ signalling. PUBMED:16339766 EPMC:16339766


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013871

This entry is found on Crisp proteins which contain INTERPRO and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling [PUBMED:16339766]. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK [PUBMED:16339766].

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 ShK-like (CL0213), which contains the following 2 members:

Crisp ShK

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
(26)
Full
(238)
Representative proteomes NCBI
(235)
Meta
(0)
RP15
(7)
RP35
(10)
RP55
(37)
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
(26)
Full
(238)
Representative proteomes NCBI
(235)
Meta
(0)
RP15
(7)
RP35
(10)
RP55
(37)
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
(26)
Full
(238)
Representative proteomes NCBI
(235)
Meta
(0)
RP15
(7)
RP35
(10)
RP55
(37)
RP75
(72)
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.

Pfam alignments:

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: manual
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 26
Number in full: 238
Average length of the domain: 54.30 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 22.83 %

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 20.1 20.1
Trusted cut-off 23.1 29.2
Noise cut-off 19.9 19.5
Model length: 55
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

CAP Crisp

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 Crisp domain has been found. There are 25 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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