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Cathelicidin Edit Wikipedia article
|, CAP-18, CAP18, CRAMP, FALL-39, FALL39, HSD26, LL37, cathelicidin antimicrobial peptide|
Cathelicidin-related antimicrobial peptides are a family of polypeptides primarily stored in the lysosomes of macrophages and polymorphonuclear leukocytes (PMNs). Cathelicidins serve a critical role in mammalian innate immune defense against invasive bacterial infection. The cathelicidin family of peptides are classified as antimicrobial peptides (AMPs). The AMP family also includes the defensins. Whilst the defensins share common structural features, cathelicidin-related peptides are highly heterogeneous.
Members of the cathelicidin family of antimicrobial polypeptides are characterized by a highly conserved region (cathelin domain) and a highly variable cathelicidin peptide domain.
Cathelicidin peptides have been isolated from many different species of mammals. Cathelicidins were originally found in neutrophils, but have since been found in many other cells including epithelial cells and macrophages after activation by bacteria, viruses, fungi, or the hormone 1,25-D, which is the hormonally active form of vitamin D. The protein encoded by the human cathelicidin gene, CAMP, is cleaved into the LL-37 peptide, which has several immunological functions.
Crystal Structure Analysis of the Cathelicidin Motif of Protegrins
Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures. Most cathelicidins are linear peptides with 23-37 amino acid residues, and fold into amphipathic α-helices. Additionally cathelicidins may also be small-sized molecules (12-18 residues) with beta-hairpin structures, stabilized by one or two disulphide bonds. Even larger cathelicidin peptides (39-80 amino acid residues) are also present. These larger cathelicidins display repetitive proline motifs forming extended polyproline-type structures.
The cathelicidin family shares primary sequence homology with the cystatin family of cysteine proteinase inhibitors, although amino acid residues thought to be important in such protease inhibition are usually lacking.
Mechanism of antimicrobial activity
The general rule of the mechanism triggering cathelicidin action, like that of other antimicrobial peptides, involves the disintegration (damaging and puncturing) of cell membranes of organisms toward which the peptide is active.
Cathelicidin peptides have been found in humans, monkeys, mice, rats, rabbits, guinea pigs, pandas, pigs, cattle, frogs, sheep, goats, chickens, and horses.
Currently identified cathelicidins include the following:
- Human: hCAP-18 (cleaved into LL-37 and FALL-39)
- Rhesus monkey: RL-37
- Mice:CRAMP-1/2, (Cathelicidin-related Antimicrobial Peptide
- Rats: rCRAMP
- Rabbits: CAP-18
- Guinea pig: CAP-11
- Pigs: PR-39, Prophenin, PMAP-23,36,37
- Cattle: BMAP-27,28,34 (Bovine Myeloid Antimicrobial Peptides); Bac5, Bac7
- Frogs: cathelicidin-AL (found in Amolops loloensis)
- Chickens: Four cathelicidins, fowlicidins 1,2,3 and cathelicidin Beta-1 
- Tasmanian Devil: Saha-CATH5 
- Salmonids: CATH1 and CATH2
NOTE: This article seems to be split between two pages. More about cathelicidin's clinical significance can be found on the page for its encoding gene, LL-37.
Patients with rosacea have elevated levels of cathelicidin and elevated levels of stratum corneum tryptic enzymes (SCTEs). Cathelicidin is cleaved into the antimicrobial peptide LL-37 by both kallikrein 5 and kallikrein 7 serine proteases. Excessive production of LL-37 is suspected to be a contributing cause in all subtypes of Rosacea. Antibiotics have been used in the past to treat rosacea, but antibiotics may only work because they inhibit some SCTEs.
Higher plasma levels of human cathelicidin antimicrobial protein (hCAP18), which are up-regulated by vitamin D, appear to significantly reduce the risk of death from infection in dialysis patients. Patients with a high level of this protein were 3.7 times more likely to survive kidney dialysis for a year without a fatal infection.
Vitamin D up-regulates genetic expression of cathelicidin, which exhibits broad-spectrum microbicidal activity against bacteria, fungi, and viruses. Cathelicidin rapidly destroys the lipoprotein membranes of microbes enveloped in phagosomes after fusion with lysosomes in macrophages.
- GRCh38: Ensembl release 89: ENSG00000164047 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000038357 - Ensembl, May 2017
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- "Entrez Gene: CAMP cathelicidin antimicrobial peptide".
- Zanetti M (January 2004). "Cathelicidins, multifunctional peptides of the innate immunity". Journal of Leukocyte Biology. 75 (1): 39–48. doi:10.1189/jlb.0403147. PMID 12960280.
- Liu PT, Stenger S, Li H, Wenzel L, Tan BH, Krutzik SR, Ochoa MT, Schauber J, Wu K, Meinken C, Kamen DL, Wagner M, Bals R, Steinmeyer A, Zügel U, Gallo RL, Eisenberg D, Hewison M, Hollis BW, Adams JS, Bloom BR, Modlin RL (March 2006). "Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response". Science. 311 (5768): 1770–3. doi:10.1126/science.1123933. PMID 16497887.
- Gennaro R, Zanetti M (2000). "Structural features and biological activities of the cathelicidin-derived antimicrobial peptides". Biopolymers. 55 (1): 31–49. doi:10.1002/1097-0282(2000)55:1<31::AID-BIP40>3.0.CO;2-9. PMID 10931440.
- Zaiou M, Nizet V, Gallo RL (May 2003). "Antimicrobial and protease inhibitory functions of the human cathelicidin (hCAP18/LL-37) prosequence". The Journal of Investigative Dermatology. 120 (5): 810–6. doi:10.1046/j.1523-1747.2003.12132.x. PMID 12713586.
- Kościuczuk EM, Lisowski P, Jarczak J, Strzałkowska N, Jóźwik A, Horbańczuk J, Krzyżewski J, Zwierzchowski L, Bagnicka E (December 2012). "Cathelicidins: family of antimicrobial peptides. A review". Molecular Biology Reports. 39 (12): 10957–70. doi:10.1007/s11033-012-1997-x. PMC . PMID 23065264.
- Gallo RL, Kim KJ, Bernfield M, Kozak CA, Zanetti M, Merluzzi L, Gennaro R (May 1997). "Identification of CRAMP, a cathelin-related antimicrobial peptide expressed in the embryonic and adult mouse". The Journal of Biological Chemistry. 272 (20): 13088–93. doi:10.1074/jbc.272.20.13088. PMID 9148921.
- Hao X, Yang H, Wei L, Yang S, Zhu W, Ma D, Yu H, Lai R (August 2012). "Amphibian cathelicidin fills the evolutionary gap of cathelicidin in vertebrate". Amino Acids. 43 (2): 677–85. doi:10.1007/s00726-011-1116-7. PMID 22009138.
- Achanta M, Sunkara LT, Dai G, Bommineni YR, Jiang W, Zhang G (May 2012). "Tissue expression and developmental regulation of chicken cathelicidin antimicrobial peptides". Journal of Animal Science and Biotechnology. 3 (1): 15. doi:10.1186/2049-1891-3-15. PMC . PMID 22958518.
- Peel E, Cheng Y, Djordjevic JT, Fox S, Sorrell TC, Belov K (October 2016). "Cathelicidins in the Tasmanian devil (Sarcophilus harrisii)". Scientific Reports. 6: 35019. doi:10.1038/srep35019. PMC . PMID 27725697.
- Reinholz M, Ruzicka T, Schauber J (May 2012). "Cathelicidin LL-37: an antimicrobial peptide with a role in inflammatory skin disease". Annals of Dermatology. 24 (2): 126–35. doi:10.5021/ad.2012.24.2.126. PMC . PMID 22577261.
- Yamasaki K, Di Nardo A, Bardan A, Murakami M, Ohtake T, Coda A, Dorschner RA, Bonnart C, Descargues P, Hovnanian A, Morhenn VB, Gallo RL (August 2007). "Increased serine protease activity and cathelicidin promotes skin inflammation in rosacea". Nature Medicine. 13 (8): 975–80. doi:10.1038/nm1616. PMID 17676051.
- Gombart AF, Bhan I, Borregaard N, Tamez H, Camargo CA, Koeffler HP, Thadhani R (February 2009). "Low plasma level of cathelicidin antimicrobial peptide (hCAP18) predicts increased infectious disease mortality in patients undergoing hemodialysis". Clinical Infectious Diseases. 48 (4): 418–24. doi:10.1086/596314. PMID 19133797.
- Zasloff M (January 2002). "Antimicrobial peptides of multicellular organisms". Nature. 415 (6870): 389–95. doi:10.1038/415389a. PMID 11807545.
- Kamen DL, Tangpricha V (May 2010). "Vitamin D and molecular actions on the immune system: modulation of innate and autoimmunity". Journal of Molecular Medicine. 88 (5): 441–50. doi:10.1007/s00109-010-0590-9. PMC . PMID 20119827.
- Dürr UH, Sudheendra US, Ramamoorthy A (September 2006). "LL-37, the only human member of the cathelicidin family of antimicrobial peptides". Biochimica et Biophysica Acta. 1758 (9): 1408–25. doi:10.1016/j.bbamem.2006.03.030. PMID 16716248.
- Chromek M, Slamová Z, Bergman P, Kovács L, Podracká L, Ehrén I, Hökfelt T, Gudmundsson GH, Gallo RL, Agerberth B, Brauner A (June 2006). "The antimicrobial peptide cathelicidin protects the urinary tract against invasive bacterial infection". Nature Medicine. 12 (6): 636–41. doi:10.1038/nm1407. PMID 16751768.
- Gombart AF, Borregaard N, Koeffler HP (July 2005). "Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3". FASEB Journal. 19 (9): 1067–77. doi:10.1096/fj.04-3284com. PMID 15985530.
- López-García B, Lee PH, Gallo RL (May 2006). "Expression and potential function of cathelicidin antimicrobial peptides in dermatophytosis and tinea versicolor". The Journal of Antimicrobial Chemotherapy. 57 (5): 877–82. doi:10.1093/jac/dkl078. PMID 16556635.
- Lehrer RI, Ganz T (January 2002). "Cathelicidins: a family of endogenous antimicrobial peptides". Current Opinion in Hematology. 9 (1): 18–22. doi:10.1097/00062752-200201000-00004. PMID 11753073.
- Niyonsaba F, Hirata M, Ogawa H, Nagaoka I (September 2003). "Epithelial cell-derived antibacterial peptides human beta-defensins and cathelicidin: multifunctional activities on mast cells". Current Drug Targets. Inflammation and Allergy. 2 (3): 224–31. doi:10.2174/1568010033484115. PMID 14561157.
- van Wetering S, Tjabringa GS, Hiemstra PS (April 2005). "Interactions between neutrophil-derived antimicrobial peptides and airway epithelial cells". Journal of Leukocyte Biology. 77 (4): 444–50. doi:10.1189/jlb.0604367. PMID 15591123.
- Agerberth B, Gunne H, Odeberg J, Kogner P, Boman HG, Gudmundsson GH (January 1995). "FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis". Proceedings of the National Academy of Sciences of the United States of America. 92 (1): 195–9. doi:10.1073/pnas.92.1.195. PMC . PMID 7529412.
- Cowland JB, Johnsen AH, Borregaard N (July 1995). "hCAP-18, a cathelin/pro-bactenecin-like protein of human neutrophil specific granules". FEBS Letters. 368 (1): 173–6. doi:10.1016/0014-5793(95)00634-L. PMID 7615076.
- Gudmundsson GH, Magnusson KP, Chowdhary BP, Johansson M, Andersson L, Boman HG (July 1995). "Structure of the gene for porcine peptide antibiotic PR-39, a cathelin gene family member: comparative mapping of the locus for the human peptide antibiotic FALL-39". Proceedings of the National Academy of Sciences of the United States of America. 92 (15): 7085–9. doi:10.1073/pnas.92.15.7085. PMC . PMID 7624374.
- Larrick JW, Hirata M, Balint RF, Lee J, Zhong J, Wright SC (April 1995). "Human CAP18: a novel antimicrobial lipopolysaccharide-binding protein". Infection and Immunity. 63 (4): 1291–7. PMC . PMID 7890387.
- Gudmundsson GH, Agerberth B, Odeberg J, Bergman T, Olsson B, Salcedo R (June 1996). "The human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37 in granulocytes". European Journal of Biochemistry. 238 (2): 325–32. doi:10.1111/j.1432-1033.1996.0325z.x. PMID 8681941.
- Larrick JW, Lee J, Ma S, Li X, Francke U, Wright SC, Balint RF (November 1996). "Structural, functional analysis and localization of the human CAP18 gene". FEBS Letters. 398 (1): 74–80. doi:10.1016/S0014-5793(96)01199-4. PMID 8946956.
- Frohm M, Agerberth B, Ahangari G, Stâhle-Bäckdahl M, Lidén S, Wigzell H, Gudmundsson GH (June 1997). "The expression of the gene coding for the antibacterial peptide LL-37 is induced in human keratinocytes during inflammatory disorders". The Journal of Biological Chemistry. 272 (24): 15258–63. doi:10.1074/jbc.272.24.15258. PMID 9182550.
- Bals R, Wang X, Zasloff M, Wilson JM (August 1998). "The peptide antibiotic LL-37/hCAP-18 is expressed in epithelia of the human lung where it has broad antimicrobial activity at the airway surface". Proceedings of the National Academy of Sciences of the United States of America. 95 (16): 9541–6. doi:10.1073/pnas.95.16.9541. PMC . PMID 9689116.
- Chen Q, Schmidt AP, Anderson GM, Wang JM, Wooters J, Oppenheim JJ, Chertov O (October 2000). "LL-37, the neutrophil granule- and epithelial cell-derived cathelicidin, utilizes formyl peptide receptor-like 1 (FPRL1) as a receptor to chemoattract human peripheral blood neutrophils, monocytes, and T cells". The Journal of Experimental Medicine. 192 (7): 1069–74. doi:10.1084/jem.192.7.1069. PMC . PMID 11015447.
- Agerberth B, Charo J, Werr J, Olsson B, Idali F, Lindbom L, Kiessling R, Jörnvall H, Wigzell H, Gudmundsson GH (November 2000). "The human antimicrobial and chemotactic peptides LL-37 and alpha-defensins are expressed by specific lymphocyte and monocyte populations". Blood. 96 (9): 3086–93. PMID 11049988.
- Bals R, Lang C, Weiner DJ, Vogelmeier C, Welsch U, Wilson JM (March 2001). "Rhesus monkey (Macaca mulatta) mucosal antimicrobial peptides are close homologues of human molecules". Clinical and Diagnostic Laboratory Immunology. 8 (2): 370–5. doi:10.1128/CDLI.8.2.370-375.2001. PMC . PMID 11238224.
- Nagaoka I, Hirota S, Niyonsaba F, Hirata M, Adachi Y, Tamura H, Heumann D (September 2001). "Cathelicidin family of antibacterial peptides CAP18 and CAP11 inhibit the expression of TNF-alpha by blocking the binding of LPS to CD14(+) cells". Journal of Immunology. 167 (6): 3329–38. doi:10.4049/jimmunol.167.6.3329. PMID 11544322.
- Hase K, Eckmann L, Leopard JD, Varki N, Kagnoff MF (February 2002). "Cell differentiation is a key determinant of cathelicidin LL-37/human cationic antimicrobial protein 18 expression by human colon epithelium". Infection and Immunity. 70 (2): 953–63. doi:10.1128/IAI.70.2.953-963.2002. PMC . PMID 11796631.
- Giuliani A, Pirri G, Nicoletto S (2007). "Antimicrobial peptides: an overview of a promising class of therapeutics". Cent. Eur. J. Biol. 2 (1): 1–33. doi:10.2478/s11535-007-0010-5.
- Burton MF, Steel PG (December 2009). "The chemistry and biology of LL-37". Natural Product Reports. 26 (12): 1572–84. doi:10.1039/b912533g. PMID 19936387.
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.
Cathelicidin Provide feedback
A novel protein family, showing a conserved proregion and a variable carboxyl-terminal antimicrobial domain. This region shows similarity to cystatins.
Internal database links
|SCOOP:||Cystatin Spp-24 SQAPI|
|Similarity to PfamA using HHSearch:||Cystatin|
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
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 cystatins and cathelicidins . The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. Stefins - included in Pfam:PF00031 - remain encoded by a single or a small number of genes throughout the eukaryotes, whereas the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications .
The clan contains the following 12 members:Cathelicidins Cystatin DUF3889 FTP Latexin Monellin PP1 Spp-24 SQAPI Staphopain_pro YebF YPEB
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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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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|Seed source:||Pfam-B_276 (release 2.1)|
|Number in seed:||8|
|Number in full:||263|
|Average length of the domain:||95.80 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||58.25 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|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....
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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.
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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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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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 Cathelicidins domain has been found. There are 12 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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