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1  structure 198  species 0  interactions 852  sequences 48  architectures

Family: LCCL (PF03815)

Summary: LCCL domain

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LCCL domain Edit Wikipedia article

LCCL
Identifiers
Symbol LCCL
Pfam PF03815
Pfam clan CL0513
InterPro IPR004043
SCOP 1jbi
SUPERFAMILY 1jbi

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.[1][2] Secondary structure prediction suggests that the LCCL domain contains six beta strands and two alpha helices.[1]

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.[3]

References[edit]

  1. ^ a b 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. 
  2. ^ 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. 
  3. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR004043

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Literature references

  1. 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

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].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan LCCL-domain (CL0513), which has the following description:

This superfamily is characterised by an unusual fold exemplified in PDB:1jbi. Vertebrate members are the cysteine-rich secretory protein LCCL domain-containing proteins including Colchin. The fungal members are found to be necessary for histone de-acetylation.

The clan contains the following 2 members:

LCCL Rxt3

Alignments

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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.

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(68)
Full
(852)
Representative proteomes NCBI
(762)
Meta
(11)
RP15
(140)
RP35
(228)
RP55
(365)
RP75
(528)
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  Seed
(68)
Full
(852)
Representative proteomes NCBI
(762)
Meta
(11)
RP15
(140)
RP35
(228)
RP55
(365)
RP75
(528)
Alignment:
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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.

  Seed
(68)
Full
(852)
Representative proteomes NCBI
(762)
Meta
(11)
RP15
(140)
RP35
(228)
RP55
(365)
RP75
(528)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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 logo

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...

Trees

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.

Curation View help on the curation process

Seed source: TIGRFAMs
Previous IDs: none
Type: Domain
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 23.4
Noise cut-off 22.4 22.5
Model length: 96
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Structures

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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