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Cathelicidin Edit Wikipedia article
Crystal Structure Analysis of the Cathelicidin Motif of Protegrins
|Cathelicidin antimicrobial peptide|
Rendering based on PDB .
|RNA expression pattern|
Cathelicidin-related antimicrobial peptides are a family of polypeptides found in lysosomes of macrophages and polymorphonuclear leukocytes (PMNs). Cathelicidins serve a critical role in mammalian innate immune defense against invasive bacterial infection.
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 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.
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 amphiphatic 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.
Cathelicidin family components have been found in: humans, monkeys, mice, rats, rabbits, guinea pigs, pandas, pigs, cattle, frogs, sheep, goats, and horses.
Currently identified cathelicidins include the following:
- 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)
Patients with rosacea have elevated levels of cathelicidin and elevated levels of stratum corneum tryptic enzymes (SCTEs). Antibiotics have been used in the past to treat rosacea, but antibiotics may only work because they inhibit some SCTEs.
Higher 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.
- "Entrez Gene: CAMP cathelicidin antimicrobial peptide".
- Nizet V, Ohtake T, Lauth X, Trowbridge J, Rudisill J, Dorschner RA, Pestonjamasp V, Piraino J, Huttner K, Gallo RL (November 2001). "Innate antimicrobial peptide protects the skin from invasive bacterial infection". Nature 414 (6862): 454–7. doi:10.1038/35106587. PMID 11719807.
- Zanetti M (January 2004). "Cathelicidins, multifunctional peptides of the innate immunity". J. Leukoc. Biol. 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 R (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.
- Zaiou M, Nizet V, Gallo RL. (May 2003). "Antimicrobial and protease inhibitory functions of the human cathelicidin (hCAP18/LL-37) prosequence". J Invest Dermatol. 5 (120): 810–6. doi:10.1046/j.1523-1747.2003.12132.x3. PMID 12713586.
- 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.
- 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". J. Biol. Chem. 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.
- 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". Nat. Med. 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". Clin. Infect. Dis. 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". J. Mol. Med. 88 (5): 441–50. doi:10.1007/s00109-010-0590-9. PMC 2861286. PMID 20119827.
- Dürr UH, Sudheendra US, Ramamoorthy A (September 2006). "LL-37, the only human member of the cathelicidin family of antimicrobial peptides". Biochim. Biophys. 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". Nat. Med. 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 J. 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". J. Antimicrob. Chemother. 57 (5): 877–82. doi:10.1093/jac/dkl078. PMID 16556635.
- Lehrer RI, Ganz T (2002). "Cathelicidins: a family of endogenous antimicrobial peptides". Curr. Opin. Hematol. 9 (1): 18–22. doi:10.1097/00062752-200201000-00004. PMID 11753073.
- Niyonsaba F, Hirata M, Ogawa H, Nagaoka I (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 (2005). "Interactions between neutrophil-derived antimicrobial peptides and airway epithelial cells". J. Leukoc. Biol. 77 (4): 444–50. doi:10.1189/jlb.0604367. PMID 15591123.
- Agerberth B, Gunne H, Odeberg J, et al. (1995). "FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis". Proc. Natl. Acad. Sci. U.S.A. 92 (1): 195–9. doi:10.1073/pnas.92.1.195. PMC 42844. PMID 7529412.
- Cowland JB, Johnsen AH, Borregaard N (1995). "hCAP-18, a cathelin/pro-bactenecin-like protein of human neutrophil specific granules". FEBS Lett. 368 (1): 173–6. doi:10.1016/0014-5793(95)00634-L. PMID 7615076.
- Gudmundsson GH, Magnusson KP, Chowdhary BP, et al. (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". Proc. Natl. Acad. Sci. U.S.A. 92 (15): 7085–9. doi:10.1073/pnas.92.15.7085. PMC 41476. PMID 7624374.
- Larrick JW, Hirata M, Balint RF, et al. (1995). "Human CAP18: a novel antimicrobial lipopolysaccharide-binding protein". Infect. Immun. 63 (4): 1291–7. PMC 173149. PMID 7890387.
- Gudmundsson GH, Agerberth B, Odeberg J, et al. (1996). "The human gene FALL39 and processing of the cathelin precursor to the antibacterial peptide LL-37 in granulocytes". Eur. J. Biochem. 238 (2): 325–32. doi:10.1111/j.1432-1033.1996.0325z.x. PMID 8681941.
- Larrick JW, Lee J, Ma S, et al. (1997). "Structural, functional analysis and localization of the human CAP18 gene". FEBS Lett. 398 (1): 74–80. doi:10.1016/S0014-5793(96)01199-4. PMID 8946956.
- Frohm M, Agerberth B, Ahangari G, et al. (1997). "The expression of the gene coding for the antibacterial peptide LL-37 is induced in human keratinocytes during inflammatory disorders". J. Biol. Chem. 272 (24): 15258–63. doi:10.1074/jbc.272.24.15258. PMID 9182550.
- Bals R, Wang X, Zasloff M, Wilson JM (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". Proc. Natl. Acad. Sci. U.S.A. 95 (16): 9541–6. doi:10.1073/pnas.95.16.9541. PMC 21374. PMID 9689116.
- De Yang , Chen Q, Schmidt AP, et al. (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". J. Exp. Med. 192 (7): 1069–74. doi:10.1084/jem.192.7.1069. PMC 2193321. PMID 11015447.
- Agerberth B, Charo J, Werr J, et al. (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, et al. (2001). "Rhesus monkey (Macaca mulatta) mucosal antimicrobial peptides are close homologues of human molecules". Clin. Diagn. Lab. Immunol. 8 (2): 370–5. doi:10.1128/CDLI.8.2.370-375.2001. PMC 96065. PMID 11238224.
- Nagaoka I, Hirota S, Niyonsaba F, et al. (2001). "Cathelicidin family of antibacterial peptides CAP18 and CAP11 inhibit the expression of TNF-alpha by blocking the binding of LPS to CD14(+) cells". J. Immunol. 167 (6): 3329–38. PMID 11544322.
- Hase K, Eckmann L, Leopard JD, et al. (2002). "Cell differentiation is a key determinant of cathelicidin LL-37/human cationic antimicrobial protein 18 expression by human colon epithelium". Infect. Immun. 70 (2): 953–63. doi:10.1128/IAI.70.2.953-963.2002. PMC 127717. 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 (2009). "Chemistry and Biology of LL-37". Natural Product Reports, 26 (12): 1572–1584. doi:10.1039/b912533g.
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
|Similarity to PfamA using HHSearch:||Cystatin|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001894
The precursor sequences of a number of antimicrobial peptides secreted by neutrophils (polymorphonuclear leukocytes) upon activation have been found to be evolutionarily related and are collectively known as cathelicidins [PUBMED:7589491].
Structurally, these proteins consist of three domains: a signal sequence, a conserved region of about 100 residues that contains four cysteines involved in two disulphide bonds, and a highly divergent C-terminal section of variable size. It is in this C-terminal section that the antibacterial peptides are found; they are proteolytically processed from their precursor by enzymes such as elastase. This structure is shown in the following schematic representation:
+---+--------------------------------+--------------------+ |Sig| Propeptide C C C C | Antibacterial pep. | +---+----------------|--|--|--|------+--------------------+ | | | | +--+ +--+ 'C': conserved cysteine involved in a disulphide bond.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||extracellular region (GO:0005576)|
|Biological process||defense response (GO:0006952)|
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 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 4 members:Cathelicidins Cystatin PP1 Spp-24
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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...
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You can see the alignments as HTML or in three different sequence viewers:
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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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MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
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...
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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.
|Seed source:||Pfam-B_276 (release 2.1)|
|Number in seed:||8|
|Number in full:||193|
|Average length of the domain:||65.00 aa|
|Average identity of full alignment:||50 %|
|Average coverage of the sequence by the domain:||41.10 %|
|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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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:
Colouring and labels
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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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.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
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 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 Cathelicidins domain has been found. There are 5 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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