Summary: Pentaxin family
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This is the Wikipedia entry entitled "Pentraxins". More...
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Pentraxins Edit Wikipedia article
CRP drawn from
Pentraxins (PTX), also known as pentaxins, are an evolutionary conserved family of proteins characterised by containing a pentraxin protein domain. Proteins of the pentraxin family are involved in acute immunological responses. They are a class of pattern recognition receptors (PRRs). They are a superfamily of multifunctional conserved proteins, some of which are components of the humoral arm of innate immunity and behave as functional ancestors of antibodies (Abs). They are known as classical acute phase proteins (APP), known for over a century.
Pentraxins are characterised by calcium dependent ligand binding and a distinctive flattened β-jellyroll structure similar to that of the legume lectins. The name "pentraxin" is derived from the Greek word for five (penta) and berries (ragos) relating to the radial symmetry of five monomers forming a ring approximately 95Å across and 35Å deep observed in the first members of this family to be identified. The "short" pentraxins include Serum Amyloid P component (SAP) and C reactive protein (CRP). The "long" pentraxins include PTX3 (a cytokine modulated molecule) and several neuronal pentraxins.
Three of the principal members of the pentraxin family are serum proteins: namely, C-reactive protein (CRP), serum amyloid P component protein (SAP), and female protein (FP). PTX3 (or TSG-14) protein is a cytokine-induced protein that is homologous to CRPs and SAPs, but its function has not yet been determined.
C-reactive protein is expressed during acute phase response to tissue injury or inflammation in mammals. The protein resembles antibody and performs several functions associated with host defence: it promotes agglutination, bacterial capsular swelling and phagocytosis, and activates the classical complement pathway through its calcium-dependent binding to phosphocholine. CRPs have also been sequenced in an invertebrate, Limulus polyphemus (Atlantic horseshoe crab), where they are a normal constituent of the hemolymph.
Serum amyloid P component
Serum amyloid P component is a vertebrate protein that is identical to tissue forms of amyloid P component. It is found in all types of amyloid deposits, in glomerular basement membrane and in elastic fibres in blood vessels. SAP binds to various lipoprotein ligands in a calcium-dependent manner, and it has been suggested that, in mammals, this may have important implications in atherosclerosis and amyloidosis.
Hamster female protein
Hamster female protein is a SAP homologue found in Mesocricetus auratus (Golden hamster). The concentration of this plasma protein is altered by sex steroids and stimuli that elicit an acute phase response.
Pentraxin proteins expressed in the nervous system are neural pentraxin I (NPTXI) and II (NPTXII). NPTXI and NPTXII are homologous and can exist within one species. It is suggested that both proteins mediate the uptake of synaptic macromolecules and play a role in synaptic plasticity. Apexin, a sperm acrosomal protein, is a homologue of NPTXII found in Cavia porcellus (Guinea pig).
Human genes encoding proteins that contain this domain include:
- Gewurz H, Zhang XH, Lint TF (1995). "Structure and function of the pentraxins". Curr. Opin. Immunol. 7 (1): 54–64. doi:10.1016/0952-7915(95)80029-8. PMID 7772283.
- Martinez de la Torre, Y; Fabbri, M (1 May 2010). "Evolution of the pentraxin family: the new entry PTX4.". Journal of immunology. 184 (9): 5055–64. doi:10.4049/jimmunol.0901672. PMID 20357257.
- Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP (January 1994). "Structure of pentameric human serum amyloid P component". Nature. 367 (6461): 338–45. doi:10.1038/367338a0. PMID 8114934.
- Romero IR, Morris C, Rodriguez M, Mold C, Du Clos TW (1998). "Inflammatory potential of C-reactive protein complexes compared to immune complexes". Clin. Immunol. Immunopathol. 87 (2): 155–162. doi:10.1006/clin.1997.4516. PMID 9614930.
- Yutani C, Shimokado K, Li XA (1998). "Serum amyloid P component associates with high density lipoprotein as well as very low density lipoprotein but not with low density lipoprotein". Biochem. Biophys. Res. Commun. 244 (1): 249–252. doi:10.1006/bbrc.1998.8248. PMID 9514915.
- Coe JE, Ross MJ (1997). "Electrophoretic polymorphism of a hamster pentraxin, female protein (amyloid P component)". Scand. J. Immunol. 46 (2): 180–182. doi:10.1046/j.1365-3083.1997.d01-109.x. PMID 9583999.
- Perin MS, Omeis IA, Hsu YC (1996). "Mouse and human neuronal pentraxin 1 (NPTX1): conservation, genomic structure, and chromosomal localization". Genomics. 36 (3): 543–545. doi:10.1006/geno.1996.0503. PMID 8884281.
- Reid MS, Blobel CP (1994). "Apexin, an acrosomal pentaxin". J. Biol. Chem. 269 (51): 32615–32620. PMID 7798266.
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Pentaxins are also known as pentraxins.
Srinivasan N, White HE, Emsley J, Wood SP, Pepys MB, Blundell TL; , Structure 1994;2:1017-1027.: Comparative analyses of pentraxins: implications for protomer assembly and ligand binding. PUBMED:7881902 EPMC:7881902
Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, Blundell TL, Pepys MB, Wood SP; , Nature 1994;367:338-345.: Structure of pentameric human serum amyloid P component. PUBMED:8114934 EPMC:8114934
Internal database links
|Similarity to PfamA using HHSearch:||Laminin_G_3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001759
This entry represents Pentaxins and its related proteins such as CRP (C-reactive protein) and SAP (serum amyloid P component protein) [PUBMED:9480764]. This entry also includes adhesion G-protein coupled receptor D2 from humans.
Pentaxins (or pentraxins) [PUBMED:6356809, PUBMED:7772283] are a family of proteins which show, under electron microscopy, a discoid arrangement of five noncovalently bound subunits. Proteins of the pentaxin family are involved in acute immunological responses [PUBMED:7772283]. Three of the principal members of the pentaxin family are serum proteins and Ca2+ dependent: namely, C-reactive protein (CRP) [PUBMED:9614930], serum amyloid P component protein (SAP) [PUBMED:9514915], and female protein (FP) [PUBMED:9583999]. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans.
CRP is expressed during acute phase response to tissue injury or inflammation in mammals. The protein resembles antibody and performs several functions associated with host defence: it promotes agglutination, bacterial capsular swelling and phagocytosis, and activates the classical complement pathway through its calcium-dependent binding to phosphocholine. CRPs have also been sequenced in an invertebrate, Limulus polyphemus (Atlantic horseshoe crab), where they are a normal constituent of the hemolymph [PUBMED:7881902].
SAP is a vertebrate protein that is a precursor of amyloid component P. It is found in all types of amyloid deposits, in glomerular basement menbrane and in elastic fibres in blood vessels. SAP binds to various lipoprotein ligands in a calcium-dependent manner, and it has been suggested that, in mammals, this may have important implications in atherosclerosis and amyloidosis [PUBMED:8114934].
FP is a SAP homologue found in Mesocricetus auratus (Golden hamster). The concentration of this plasma protein is altered by sex steroids and stimuli that elicit an acute phase response.
"Long" pentraxins have N-terminal extensions to the common pentraxin domain [PUBMED:8899296]; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers [PUBMED:10748068]. Pentaxin proteins expressed in the nervous system are neural pentaxin I (NPI) and II (NPII) [PUBMED:8884281]. NPI and NPII are homologous and can exist within one species. It is suggested that both proteins mediate the uptake of synaptic macromolecules and play a role in synaptic plasticity. Apexin, a sperm acrosomal protein, is a homologue of NPII found in Cavia porcellus (Guinea pig) [PUBMED:7798266].
PTX3 (or TSG-14) protein is a cytokine-induced protein that is homologous to CRPs and SAPs, but its function is not yet known.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.
The clan contains the following 43 members:Alginate_lyase2 ArabFuran-catal Bac_rhamnosid Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 Spike_NTD SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpD
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
|Number in seed:||8|
|Number in full:||1396|
|Average length of the domain:||182.70 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||24.80 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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There are 2 interactions 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 Pentaxin domain has been found. There are 197 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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