Summary: Extracellular link domain
This is the Wikipedia entry entitled "Xlinkdomain". More...
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Extracellular link domain Provide feedback
No Pfam abstract.
Brissett NC, Perkins SJ; , FEBS Lett 1996;388:211-216.: The protein fold of the hyaluronate-binding proteoglycan tandem repeat domain of link protein, aggrecan and CD44 is similar to that of the C-type lectin superfamily. PUBMED:8690089 EPMC:8690089
Internal database links
|SCOOP:||Herpes_UL45 Chordopox_A33R Intimin_C|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000538The link domain [PUBMED:8318021] is a hyaluronan(HA)-binding region found in proteins of vertebrates that are involved in the assembly of extracellular matrix, cell adhesion, and migration. The structure has been shown [PUBMED:8797823] to consist of two alpha helices and two antiparallel beta sheets arranged around a large hydrophobic core similar to that of C-type lectin. This domain contains four conserved cysteines involved in two disulphide bonds. The link domain has also been termed HABM [PUBMED:8318021] (HA binding module) and PTR [PUBMED:8690089] (proteoglycan tandem repeat). Proteins with such a domain include the proteoglycans aggrecan, brevican, neurocan and versican, which are expressed in the CNS; the cartilage link protein (LP), a proteoglycan that together with HA and aggrecan forms multimolecular aggregates; Tumour necrosis factor-inducible protein TSG-6, which may be involved in cell-cell and cell-matrix interactions during inflammation and tumourgenesis; and CD44 antigen, the main cell surface receptor for HA.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||hyaluronic acid binding (GO:0005540)|
|Biological process||cell adhesion (GO:0007155)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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This clan contains domains that have a C-type lectin fold. Many of these are known or expected to mediate interactions with sugars.
The clan contains the following 7 members:APT C4 Chordopox_A33R Herpes_UL45 Intimin_C Lectin_C Xlink
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Author:||Sonnhammer ELL, Bateman A|
|Number in seed:||12|
|Number in full:||1651|
|Average length of the domain:||93.40 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||15.67 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Xlink domain has been found. There are 14 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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