Summary: Pentaxin family
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Pentraxins Edit Wikipedia article
CRP drawn from
|SCOPe||1sac / SUPFAM|
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 Î²-jellyroll structure similar to that of the legume lectins. The name "pentraxin" is derived from the Greek word for five (penta) and axle (axis) relating to the radial symmetry of five monomers forming a ring approximately 95Ã… across and 35Ã… 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.
Pentraxin 3 (PTX3) is an acute phase protein whose levels rise during severe infections in humans. In case of central nervous system infections PTX3 helps distinguishes between bacterial and aseptic meningoencephalitis: in fact, it is significantly much higher in bacterial meningoencephalitis.
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 (February 1995). "Structure and function of the pentraxins". Current Opinion in Immunology. 7 (1): 54â€“64. doi:10.1016/0952-7915(95)80029-8. PMID 7772283.
- Martinez de la Torre Y, Fabbri M, Jaillon S, Bastone A, Nebuloni M, Vecchi A, et al. (May 2010). "Evolution of the pentraxin family: the new entry PTX4". Journal of Immunology. 184 (9): 5055â€“64. doi:10.4049/jimmunol.0901672. PMID 20357257.
- Emsley J, White HE, O'Hara BP, Oliva G, Srinivasan N, Tickle IJ, et al. (January 1994). "Structure of pentameric human serum amyloid P component". Nature. 367 (6461): 338â€“45. Bibcode:1994Natur.367..338E. doi:10.1038/367338a0. PMID 8114934.
- Romero IR, Morris C, Rodriguez M, Du Clos TW, Mold C (May 1998). "Inflammatory potential of C-reactive protein complexes compared to immune complexes". Clinical Immunology and Immunopathology. 87 (2): 155â€“62. doi:10.1006/clin.1997.4516. PMID 9614930.
- Li XA, Yutani C, Shimokado K (March 1998). "Serum amyloid P component associates with high density lipoprotein as well as very low density lipoprotein but not with low density lipoprotein". Biochemical and Biophysical Research Communications. 244 (1): 249â€“52. doi:10.1006/bbrc.1998.8248. PMID 9514915.
- Coe JE, Ross MJ (August 1997). "Electrophoretic polymorphism of a hamster pentraxin, female protein (amyloid P component)". Scandinavian Journal of Immunology. 46 (2): 180â€“6. doi:10.1046/j.1365-3083.1997.d01-109.x. PMID 9583999.
- Zatta M, Di Bella S, Bottazzi B, Rossi F, D'Agaro P, Segat L, et al. (December 2019). "Determination of pentraxin 3 levels in cerebrospinal fluid during central nervous system infections". European Journal of Clinical Microbiology & Infectious Diseases. doi:10.1007/s10096-019-03767-w. PMID 31813079.
- Omeis IA, Hsu YC, Perin MS (September 1996). "Mouse and human neuronal pentraxin 1 (NPTX1): conservation, genomic structure, and chromosomal localization". Genomics. 36 (3): 543â€“5. doi:10.1006/geno.1996.0503. PMID 8884281.
- Reid MS, Blobel CP (December 1994). "Apexin, an acrosomal pentaxin". The Journal of Biological Chemistry. 269 (51): 32615â€“20. PMID 7798266.
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Pentaxin family Provide feedback
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 receptors D2 and G6 from humans.
Pentraxins (or pentaxins) [ 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 pentraxin family are involved in acute immunological responses [ PUBMED:7772283 ]. Three of the principal members of the pentraxin family are serum proteins and Ca 2 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 ]. Pentraxin proteins expressed in the nervous system are neural pentraxin 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 is a long pentraxin that provides defence against infectious agents and plays several functions in tissue repair and regulation of cancer-related inflammation [ PUBMED:31019517 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 50 members:Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin bCoV_S1_N Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 DUF6250 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 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_KRE6_Sbg1 SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpD
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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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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:||4224|
|Average length of the domain:||182.40 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||22.50 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|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.
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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.
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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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The tree shows the occurrence of this domain across different species. More...
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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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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 200 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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