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49  structures 317  species 3  interactions 1846  sequences 137  architectures

Family: Trefoil (PF00088)

Summary: Trefoil (P-type) domain

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Trefoil domain Edit Wikipedia article

Trefoil (P-type) domain
PDB 1psp EBI.jpg
Structure of pancreatic spasmolytic polypeptide.[1]
Identifiers
Symbol Trefoil
Pfam PF00088
InterPro IPR000519
SMART SM00018
PROSITE PDOC00024
SCOP 1psp
SUPERFAMILY 1psp
CDD cd00111

Trefoil (P-type) domain is a cysteine-rich domain of approximately forty five amino-acid residues has been found in some extracellular eukaryotic proteins.[2][3][4][5] It is known as either the 'P', 'trefoil' or 'TFF' domain, and contains six cysteines linked by three disulphide bonds with connectivity 1-5, 2-4, 3-6.

The domain has been found in a variety of extracellular eukaryotic proteins,[2][4][5] including protein pS2 (TFF1) a protein secreted by the stomach mucosa; spasmolytic polypeptide (SP) (TFF2), a protein of about 115 residues that inhibits gastrointestinal motility and gastric acid secretion; intestinal trefoil factor (ITF) (TFF3); Xenopus laevis stomach proteins xP1 and xP4; xenopus integumentary mucins A.1 (preprospasmolysin) and C.1, proteins which may be involved in defense against microbial infections by protecting the epithelia from the external environment; xenopus skin protein xp2 (or APEG); Zona pellucida sperm-binding protein B (ZP-B); intestinal sucrase-isomaltase (EC 3.2.1.48 / EC 3.2.1.10), a vertebrate membrane bound, multifunctional enzyme complex which hydrolyzes sucrose, maltose and isomaltose; and lysosomal alpha-glucosidase (EC 3.2.1.20).

Examples

Human gene encoding proteins containing the trefoil domain include:

References

  1. ^ Gajhede M, Petersen TN, Henriksen A, et al. (December 1993). "Pancreatic spasmolytic polypeptide: first three-dimensional structure of a member of the mammalian trefoil family of peptides". Structure. 1 (4): 253–62. doi:10.1016/0969-2126(93)90014-8. PMID 8081739. 
  2. ^ a b Otto B, Wright N (1994). "Trefoil peptides. Coming up clover". Curr. Biol. 4 (9): 835–838. doi:10.1016/S0960-9822(00)00186-X. PMID 7820556. 
  3. ^ Thim L, Wright NA, Hoffmann W, Otto WR, Rio MC (1997). "Rolling in the clover: trefoil factor family (TFF)-domain peptides, cell migration and cancer". FEBS Lett. 408 (2): 121–123. doi:10.1016/S0014-5793(97)00424-9. PMID 9187350. 
  4. ^ a b Bork P (1993). "A trefoil domain in the major rabbit zona pellucida protein". Protein Sci. 2 (4): 669–670. doi:10.1002/pro.5560020417. PMC 2142363Freely accessible. PMID 8518738. 
  5. ^ a b Hoffmann W, Hauser F (1993). "The P-domain or trefoil motif: a role in renewal and pathology of mucous epithelia?". Trends Biochem. Sci. 18 (7): 239–243. doi:10.1016/0968-0004(93)90170-R. PMID 8267796. 

This article incorporates text from the public domain Pfam and InterPro IPR000519


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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000519

A cysteine-rich domain of approximately forty five amino-acid residues has been found in some extracellular eukaryotic proteins [PUBMED:7820556, PUBMED:9187350, PUBMED:8518738, PUBMED:8267796]. It is known as either the 'P', 'trefoil' or 'TFF' domain, and contains six cysteines linked by three disulphide bonds with connectivity 1-5, 2-4, 3-6. This leads to a characteristic three leafed structure ('trefoil'). The P-type domain is clearly composed of three looplike regions. The central core of the domain consists of a short two-stranded antiparallel beta-sheet, which is capped by an irregular loop and forms a central hairpin (loop 3). The beta-sheet is preceded by a short alpha-helix, with majority of the remainder of the domain contained in two loops, which lie on either side of the central hairpin.

This domain has been found in a variety of extracellular eukaryotic proteins [PUBMED:7820556, PUBMED:8518738, PUBMED:8267796], including:

  • protein pS2 (TFF1), a protein secreted by the stomach mucosa
  • spasmolytic polypeptide (SP) (TFF2), a protein of about 115 residues that inhibits gastrointestinal motility and gastric acid secretion
  • intestinal trefoil factor (ITF) (TFF3)
  • Xenopus laevis stomach proteins xP1 and xP4
  • xenopus integumentary mucins A.1 (FIM-A.1 or preprospasmolysin) and C.1 (FIM-C.1), proteins which may be involved in defence against microbial infections by protecting the epithelia from the external environment
  • xenopus skin protein xp2 (or APEG)
  • Zona pellucida sperm-binding protein B (ZP-B)
  • intestinal sucrase-isomaltase (EC / EC), a vertebrate membrane bound, multifunctional enzyme complex which hydrolyses sucrose, maltose and isomaltose
  • lysosomal alpha-glucosidase (EC)

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 PSI (CL0630), which has the following description:

This superfamily includes a disulphide rich domain found in Plexins, semaphorins and some integrin protein. According to SCOP the common core is alpha+beta with two conserved disulfides.

The clan contains the following 3 members:

PSI PSI_integrin Trefoil

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(250)
Full
(1846)
Representative proteomes UniProt
(2927)
NCBI
(4585)
Meta
(9)
RP15
(583)
RP35
(927)
RP55
(1503)
RP75
(1760)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(250)
Full
(1846)
Representative proteomes UniProt
(2927)
NCBI
(4585)
Meta
(9)
RP15
(583)
RP35
(927)
RP55
(1503)
RP75
(1760)
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
(250)
Full
(1846)
Representative proteomes UniProt
(2927)
NCBI
(4585)
Meta
(9)
RP15
(583)
RP35
(927)
RP55
(1503)
RP75
(1760)
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.

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: Swissprot_feature_table
Previous IDs: trefoil;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 250
Number in full: 1846
Average length of the domain: 43.20 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 6.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 43
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

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

Glyco_hydro_31 Glyco_hydro_31 Trefoil

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 Trefoil domain has been found. There are 49 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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