Summary: LCCL domain
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LCCL domain Edit Wikipedia article
In molecular biology, the LCCL domain is a protein domain which has been named after several well-characterised proteins that were found to contain it, namely Limulus clotting factor C, Coch-5b2 (Cochlin) and Lgl1. It is an about 100 amino acids domain whose C-terminal part contains a highly conserved histidine in a conserved motif YxxxSxxCxAAVHxGVI. The LCCL module is thought to be an autonomously folding domain that has been used for the construction of various modular proteins through exon-shuffling. It has been found in various metazoan proteins in association with complement B-type domains, C-type lectin domains, von Willebrand type A domains, CUB domains, discoidin lectin domains or CAP domains. It has been proposed that the LCCL domain could be involved in lipopolysaccharide (LPS) binding. Secondary structure prediction suggests that the LCCL domain contains six beta strands and two alpha helices.
Some proteins known to contain a LCCL domain include Limulus factor C, an LPS endotoxin-sensitive trypsin type serine protease which serves to protect the organism from bacterial infection; vertebrate cochlear protein cochlin or coch-5b2 (Cochlin is probably a secreted protein, mutations affecting the LCCL domain of coch-5b2 cause the deafness disorder DFNA9 in humans); and mammalian late gestation lung protein Lgl1, contains two tandem copies of the LCCL domain.
- Trexler M, Banyai L, Patthy L (September 2000). "The LCCL module". Eur. J. Biochem. 267 (18): 5751–7. DOI:10.1046/j.1432-1327.2000.01641.x. PMID 10971586.
- Robertson NG, Lu L, Heller S, Merchant SN, Eavey RD, McKenna M, Nadol JB, Miyamoto RT, Linthicum FH, Lubianca Neto JF, Hudspeth AJ, Seidman CE, Morton CC, Seidman JG (November 1998). "Mutations in a novel cochlear gene cause DFNA9, a human nonsyndromic deafness with vestibular dysfunction". Nat. Genet. 20 (3): 299–303. DOI:10.1038/3118. PMID 9806553.
- Kaplan F, Ledoux P, Kassamali FQ, Gagnon S, Post M, Koehler D, Deimling J, Sweezey NB (June 1999). "A novel developmentally regulated gene in lung mesenchyme: homology to a tumor-derived trypsin inhibitor". Am. J. Physiol. 276 (6 Pt 1): L1027-36. PMID 10362728.
LCCL domain Provide feedback
No Pfam abstract.
Liepinsh E, Trexler M, Kaikkonen A, Weigelt J, Banyai L, Patthy L, Otting G; , EMBO J 2001;20:5347-5353.: NMR structure of the LCCL domain and implications for DFNA9 deafness disorder. PUBMED:11574466 EPMC:11574466
Internal database links
|Similarity to PfamA using HHSearch:||Rxt3|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004043
The LCCL domain has been named after the best characterised proteins that were found to contain it, namely Limulus factor C, Coch-5b2 and Lgl1. It is an about 100 amino acids domain whose C-terminal part contains a highly conserved histidine in a conserved motif YxxxSxxCxAAVHxGVI. The LCCL module is thought to be an autonomously folding domain that has been used for the construction of various modular proteins through exon-shuffling. It has been found in various metazoan proteins in association with complement B-type domains, C-type lectin domains, von Willebrand type A domains, CUB domains, discoidin lectin domains or CAP domains. It has been proposed that the LCCL domain could be involved in lipopolysaccharide (LPS) binding [PUBMED:10971586, PUBMED:9806553]. Secondary structure prediction suggests that the LCCL domain contains six beta strands and two alpha helices [PUBMED:10971586].
Some proteins known to contain a LCCL domain include Limulus factor C, a LPS endotoxin-sensitive trypsin type serine protease which serves to protect the organism from bacterial infection; vertebrate cochlear protein cochlin or coch-5b2 (Cochlin is probably a secreted protein, mutations affecting the LCCL domain of coch-5b2 cause the deafness disorder DFNA9 in humans); and mammalian late gestation lung protein Lgl1, contains two tandem copies of the LCCL domain [PUBMED:10362728].
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Curation and family details
|Author:||TIGRFAMs, Griffiths-Jones SR|
|Number in seed:||68|
|Number in full:||852|
|Average length of the domain:||100.40 aa|
|Average identity of full alignment:||30 %|
|Average coverage of the sequence by the domain:||19.17 %|
|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:||14|
|Download:||download the raw HMM for this family|
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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 LCCL domain has been found. There are 1 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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