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0  structures 1053  species 0  interactions 2479  sequences 25  architectures

Family: LicD (PF04991)

Summary: LicD family

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Fukutin". More...

Fukutin Edit Wikipedia article

Fukutin
Identifiers
Symbols FKTN; CMD1X; FCMD; LGMD2M; MDDGA4; MDDGB4; MDDGC4
External IDs OMIM607440 MGI2179507 HomoloGene31402 GeneCards: FKTN Gene
Orthologs
Species Human Mouse
Entrez 2218 246179
Ensembl ENSG00000106692 ENSMUSG00000028414
UniProt O75072 Q8R507
RefSeq (mRNA) NM_001079802 NM_139309
RefSeq (protein) NP_001073270 NP_647470
Location (UCSC) Chr 9:
108.32 – 108.4 Mb
Chr 4:
53.71 – 53.77 Mb
PubMed search [1] [2]
Fukutin-related
Identifiers
Symbol Fukutin-related
Pfam PF04991
InterPro IPR009644

Fukutin is a eukaryotic protein necessary for the maintenance of muscle integrity, cortical histogenesis, and normal ocular development. Mutations in the fukutin gene have been shown to result in Fukuyama congenital muscular dystrophy characterised by brain malformation - one of the most common autosomal-recessive disorders in Japan.[1] In humans this protein is encoded by the FCMD gene (also named FKTN), located on chromosome 9q31.[2][3][4] Human fukutin exhibits a length of 461 amino acids and a predicted molecular mass of 53.7 kDa.

Function[edit]

Although its function is mostly unknown, fukutin is a putative transmembrane protein that is ubiquitously expressed, although at higher levels in skeletal muscle, heart and brain.[5] It is localized to the cis-Golgi compartment, where it may be involved in the glycosylation of α-dystroglycan in skeletal muscle. The encoded protein is thought to be a glycosyltransferase and could play a role in brain development.[3]

Clinical significance[edit]

Defects in this gene are a cause of Fukuyama congenital muscular dystrophy (FCMD), Walker-Warburg syndrome (WWS), limb-girdle muscular dystrophy type 2M (LGMD2M), and dilated cardiomyopathy type 1X (CMD1X).[3][6]

See also[edit]

References[edit]

  1. ^ Kobayashi K, Shimizu T, Arai K, Nakamura Y, Fukui T, Toda T, Matsumura K, Imamura M, Takeda S, Kondo M, Sasaki J, Kurahashi H, Kano H, Misaki K, Tachikawa M, Murakami T, Sunada Y, Fujikado T, Terashima T (2003). "Fukutin is required for maintenance of muscle integrity, cortical histiogenesis and normal eye development". Hum. Mol. Genet. 12 (12): 1449–1459. doi:10.1093/hmg/ddg153. PMID 12783852. 
  2. ^ Toda T, Segawa M, Nomura Y, Nonaka I, Masuda K, Ishihara T, Sakai M, Tomita I, Origuchi Y, Suzuki M [corrected to Sakai M (November 1993). "Localization of a gene for Fukuyama type congenital muscular dystrophy to chromosome 9q31-33". Nat. Genet. 5 (3): 283–6. doi:10.1038/ng1193-283. PMID 8275093. 
  3. ^ a b c "Entrez Gene: fukutin". 
  4. ^ Online 'Mendelian Inheritance in Man' (OMIM) 607440
  5. ^ Hayashi YK, Ogawa M, Tagawa K, Noguchi S, Ishihara T, Nonaka I, Arahata K (July 2001). "Selective deficiency of alpha-dystroglycan in Fukuyama-type congenital muscular dystrophy". Neurology 57 (1): 115–21. PMID 11445638. 
  6. ^ Murakami T, Hayashi YK, Noguchi S, et al. (November 2006). "Fukutin gene mutations cause dilated cardiomyopathy with minimal muscle weakness". Ann. Neurol. 60 (5): 597–602. doi:10.1002/ana.20973. PMID 17036286. 

Further reading[edit]

External links[edit]

This article incorporates text from the United States National Library of Medicine, which is in the public domain.


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

LicD family Provide feedback

The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent [1]. These proteins are part of the nucleotidyltransferase superfamily [2].

Literature references

  1. Zhang JR, Idanpaan-Heikkila I, Fischer W, Tuomanen EI; , Mol Microbiol 1999;31:1477-1488.: Pneumococcal licD2 gene is involved in phosphorylcholine metabolism. PUBMED:10200966 EPMC:10200966

  2. Kuchta K, Knizewski L, Wyrwicz LS, Rychlewski L, Ginalski K;, Nucleic Acids Res. 2009; [Epub ahead of print]: Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human. PUBMED:19833706 EPMC:19833706


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007074

The LicD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent [PUBMED:10200966].

Fukutin, which is a member of the LicD family, is a human protein which may be involved in the modification of glycan moieties of alpha-dystroglycan; defects in Fukutin are associated with congential muscular dystrophy [PUBMED:11445638].

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 NTP_transf (CL0260), which has the following description:

This clan contains a diverse set of nucleotidyltransferase enzymes.

The clan contains the following 22 members:

Adenyl_cycl_N Adenyl_transf Aminoglyc_resit DNA_pol_B_palm DUF1693 DUF1814 DUF2204 DUF294 DUF925 DZF GlnE GrpB LicD Mab-21 MdcG Mmp37 NTP_transf_2 NTP_transf_5 Nuc-transf PolyA_pol Pox_polyA_pol RelA_SpoT

Alignments

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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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.

  Seed
(142)
Full
(2479)
Representative proteomes NCBI
(1816)
Meta
(209)
RP15
(221)
RP35
(392)
RP55
(560)
RP75
(634)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(142)
Full
(2479)
Representative proteomes NCBI
(1816)
Meta
(209)
RP15
(221)
RP35
(392)
RP55
(560)
RP75
(634)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(142)
Full
(2479)
Representative proteomes NCBI
(1816)
Meta
(209)
RP15
(221)
RP35
(392)
RP55
(560)
RP75
(634)
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.

Note: You can also download the data file for the tree.

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: Pfam-B_5278 (release 7.6)
Previous IDs: none
Type: Domain
Author: Moxon SJ, Bateman A
Number in seed: 142
Number in full: 2479
Average length of the domain: 187.40 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 55.89 %

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 22.9 22.6
Noise cut-off 22.4 22.5
Model length: 205
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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