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Doublecortin Edit Wikipedia article
|, DBCN, DC, LISX, SCLH, XLIS, doublecortin|
Doublecortin (DCX) is a microtubule-associated protein expressed by neuronal precursor cells and immature neurons in embryonic and adult cortical structures. Neuronal precursor cells begin to express DCX while actively dividing, and their neuronal daughter cells continue to express DCX for 2–3 weeks as the cells mature into neurons. Downregulation of DCX begins after 2 weeks, and occurs at the same time that these cells begin to express NeuN, a marker for mature neurons.
Due to the nearly exclusive expression of DCX in developing neurons, this protein has been used increasingly as a marker for neurogenesis. Indeed, levels of DCX expression increase in response to exercise, and that increase occurs in parallel with increased BrdU labelling (which is currently a "gold standard" in measuring neurogenesis).
Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins.
Knock out mouse
In mice where the Doublecortin gene has been knocked out, cortical layers are still correctly formed. However, the hippocampi of these mice show disorganisation in the CA3 region. The normally single layer of pyramidal cells in mutants is seen as a double layer. These mice also have different behavior than their wild type littermates and are epileptic.
solution structure of the N-terminal dcx domain of human doublecortin-like kinase
The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of a tandem repeat of evolutionarily conserved Doublecortin (DC) domains. These domains are found in the N terminus of proteins and consists of tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation.
Doublecortin has been shown to influence the structure of microtubules. Microtubule nucleated in vitro in the presence of Doublecortin have almost exclusively 13 protofilaments, whereas microtubule nucleated without Doublecortin are present in a range of different sizes.
Doublecortin is mutated in X-linked lissencephaly and the double cortex syndrome, and the clinical manifestations are sex-linked. In males, X-linked lissencephaly produces a smooth brain due to lack of migration of immature neurons, which normally promote folding of the brain surface. Double cortex syndrome is characterized by abnormal migration of neural tissue during development which results in two bands of misplaced neurons within the subcortical white, generating two cortices, giving the name to the syndrome; this finding generally occurs in females. The mutation was discovered by Joseph Gleeson and Christopher A. Walsh in Boston.
- GRCh38: Ensembl release 89: ENSG00000077279 - Ensembl, May 2017
- GRCm38: Ensembl release 89: ENSMUSG00000031285 - Ensembl, May 2017
- "Human PubMed Reference:".
- "Mouse PubMed Reference:".
- EntrezGene 1641
- Oomen CA, Girardi CE, Cahyadi R, Verbeek EC, Krugers H, Joëls M, Lucassen PJ (2009). "Opposite effects of early maternal deprivation on neurogenesis in male versus female rats". PLoS ONE. 4 (1): e3675. PMC . PMID 19180242. doi:10.1371/journal.pone.0003675.
- Brown JP, Couillard-Després S, Cooper-Kuhn CM, Winkler J, Aigner L, Kuhn HG (December 2003). "Transient expression of doublecortin during adult neurogenesis". J. Comp. Neurol. 467 (1): 1–10. PMID 14574675. doi:10.1002/cne.10874.
- Couillard-Despres S, Winner B, Schaubeck S, Aigner R, Vroemen M, Weidner N, Bogdahn U, Winkler J, Kuhn HG, Aigner L (January 2005). "Doublecortin expression levels in adult brain reflect neurogenesis". Eur. J. Neurosci. 21 (1): 1–14. PMID 15654838. doi:10.1111/j.1460-9568.2004.03813.x.
- Horesh D, Sapir T, Francis F, Wolf SG, Caspi M, Elbaum M, Chelly J, Reiner O (September 1999). "Doublecortin, a stabilizer of microtubules". Hum. Mol. Genet. 8 (9): 1599–610. PMID 10441322. doi:10.1093/hmg/8.9.1599.
- Nosten-Bertrand M, Kappeler C, Dinocourt C, Denis C, Germain J, Phan Dinh Tuy F, Verstraeten S, Alvarez C, Métin C, Chelly J, Giros B, Miles R, Depaulis A, Francis F (2008-06-25). "Epilepsy in Dcx knockout mice associated with discrete lamination defects and enhanced excitability in the hippocampus". PloS One. 3 (6): e2473. PMC . PMID 18575605. doi:10.1371/journal.pone.0002473.
- Sapir T, Horesh D, Caspi M, Atlas R, Burgess HA, Wolf SG, Francis F, Chelly J, Elbaum M, Pietrokovski S, Reiner O (March 2000). "Doublecortin mutations cluster in evolutionarily conserved functional domains". Hum. Mol. Genet. 9 (5): 703–12. PMID 10749977. doi:10.1093/hmg/9.5.703.
- Caspi M, Atlas R, Kantor A, Sapir T, Reiner O (September 2000). "Interaction between LIS1 and doublecortin, two lissencephaly gene products". Hum. Mol. Genet. 9 (15): 2205–13. PMID 11001923. doi:10.1093/oxfordjournals.hmg.a018911.
- Online Mendelian Inheritance in Man (OMIM) Doublecortin -300121
- Gleeson JG, Allen KM, Fox JW, Lamperti ED, Berkovic S, Scheffer I, Cooper EC, Dobyns WB, Minnerath SR, Ross ME, Walsh CA (January 1998). "Doublecortin, a brain-specific gene mutated in human X-linked lissencephaly and double cortex syndrome, encodes a putative signaling protein". Cell. 92 (1): 63–72. PMID 9489700. doi:10.1016/S0092-8674(00)80899-5.
- Lowenstein DH (2011). "Seizures and Epilepsy". In Loscalzo J, Longo DL, Fauci AS, Kasper DL, Hauser SL. Harrison's Principles of Internal Medicine (18th ed.). McGraw-Hill Professional. pp. 3251–3269. ISBN 0-07-174889-X.
- des Portes V, Pinard JM, Smadja D, et al. (1997). "Dominant X linked subcortical laminar heterotopia and lissencephaly syndrome (XSCLH/LIS): evidence for the occurrence of mutation in males and mapping of a potential locus in Xq22.". J. Med. Genet. 34 (3): 177–83. PMC . PMID 9132485. doi:10.1136/jmg.34.3.177.
- des Portes V, Pinard JM, Billuart P, et al. (1998). "A novel CNS gene required for neuronal migration and involved in X-linked subcortical laminar heterotopia and lissencephaly syndrome.". Cell. 92 (1): 51–61. PMID 9489699. doi:10.1016/S0092-8674(00)80898-3.
- Gleeson JG, Allen KM, Fox JW, et al. (1998). "Doublecortin, a brain-specific gene mutated in human X-linked lissencephaly and double cortex syndrome, encodes a putative signaling protein.". Cell. 92 (1): 63–72. PMID 9489700. doi:10.1016/S0092-8674(00)80899-5.
- des Portes V, Francis F, Pinard JM, et al. (1999). "doublecortin is the major gene causing X-linked subcortical laminar heterotopia (SCLH).". Hum. Mol. Genet. 7 (7): 1063–70. PMID 9618162. doi:10.1093/hmg/7.7.1063.
- Sossey-Alaoui K, Hartung AJ, Guerrini R, et al. (1998). "Human doublecortin (DCX) and the homologous gene in mouse encode a putative Ca2+-dependent signaling protein which is mutated in human X-linked neuronal migration defects.". Hum. Mol. Genet. 7 (8): 1327–32. PMID 9668176. doi:10.1093/hmg/7.8.1327.
- Pilz DT, Matsumoto N, Minnerath S, et al. (1999). "LIS1 and XLIS (DCX) mutations cause most classical lissencephaly, but different patterns of malformation.". Hum. Mol. Genet. 7 (13): 2029–37. PMID 9817918. doi:10.1093/hmg/7.13.2029.
- Gleeson JG, Minnerath SR, Fox JW, et al. (1999). "Characterization of mutations in the gene doublecortin in patients with double cortex syndrome.". Ann. Neurol. 45 (2): 146–53. PMID 9989615. doi:10.1002/1531-8249(199902)45:2<146::AID-ANA3>3.0.CO;2-N.
- Kato M, Kimura T, Lin C, et al. (1999). "A novel mutation of the doublecortin gene in Japanese patients with X-linked lissencephaly and subcortical band heterotopia.". Hum. Genet. 104 (4): 341–4. PMID 10369164. doi:10.1007/s004390050963.
- Gleeson JG, Lin PT, Flanagan LA, Walsh CA (1999). "Doublecortin is a microtubule-associated protein and is expressed widely by migrating neurons.". Neuron. 23 (2): 257–71. PMID 10399933. doi:10.1016/S0896-6273(00)80778-3.
- Pilz DT, Kuc J, Matsumoto N, et al. (2000). "Subcortical band heterotopia in rare affected males can be caused by missense mutations in DCX (XLIS) or LIS1.". Hum. Mol. Genet. 8 (9): 1757–60. PMID 10441340. doi:10.1093/hmg/8.9.1757.
- Sakamoto M, Ono J, Okada S, et al. (2000). "Genetic alteration of the DCX gene in Japanese patients with subcortical laminar heterotopia or isolated lissencephaly sequence.". J. Hum. Genet. 45 (3): 167–70. PMID 10807542. doi:10.1007/s100380050204.
- Caspi M, Atlas R, Kantor A, et al. (2001). "Interaction between LIS1 and doublecortin, two lissencephaly gene products.". Hum. Mol. Genet. 9 (15): 2205–13. PMID 11001923. doi:10.1093/oxfordjournals.hmg.a018911.
- Matsumoto N, Leventer RJ, Kuc JA, et al. (2001). "Mutation analysis of the DCX gene and genotype/phenotype correlation in subcortical band heterotopia.". Eur. J. Hum. Genet. 9 (1): 5–12. PMID 11175293. doi:10.1038/sj.ejhg.5200548.
- Demelas L, Serra G, Conti M, et al. (2001). "Incomplete penetrance with normal MRI in a woman with germline mutation of the DCX gene.". Neurology. 57 (2): 327–30. PMID 11468322. doi:10.1212/wnl.57.2.327.
- Friocourt G, Chafey P, Billuart P, et al. (2001). "Doublecortin interacts with mu subunits of clathrin adaptor complexes in the developing nervous system.". Mol. Cell. Neurosci. 18 (3): 307–19. PMID 11591131. doi:10.1006/mcne.2001.1022.
- Kato M, Kanai M, Soma O, et al. (2001). "Mutation of the doublecortin gene in male patients with double cortex syndrome: somatic mosaicism detected by hair root analysis.". Ann. Neurol. 50 (4): 547–51. PMID 11601509. doi:10.1002/ana.1231.
- des Portes V, Abaoub L, Joannard A, et al. (2002). "So-called 'cryptogenic' partial seizures resulting from a subtle cortical dysgenesis due to a doublecortin gene mutation.". Seizure : the journal of the British Epilepsy Association. 11 (4): 273–7. PMID 12027577. doi:10.1053/seiz.2001.0607.
- Kizhatil K, Wu YX, Sen A, Bennett V (2002). "A new activity of doublecortin in recognition of the phospho-FIGQY tyrosine in the cytoplasmic domain of neurofascin.". J. Neurosci. 22 (18): 7948–58. PMID 12223548.
- D'Agostino MD, Bernasconi A, Das S, et al. (2002). "Subcortical band heterotopia (SBH) in males: clinical, imaging and genetic findings in comparison with females.". Brain. 125 (Pt 11): 2507–22. PMID 12390976. doi:10.1093/brain/awf248.
- Meyer G, Perez-Garcia CG, Gleeson JG (2003). "Selective expression of doublecortin and LIS1 in developing human cortex suggests unique modes of neuronal movement.". Cereb. Cortex. 12 (12): 1225–36. PMID 12427674. doi:10.1093/cercor/12.12.1225.
- Media related to doublecortin at Wikimedia Commons
- GeneReviews/NCBI/NIH/UW entry on DCX-Related Disorders
- OMIM entries on DCX-Related Disorders
- doublecortin protein at the US National Library of Medicine Medical Subject Headings (MeSH)
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.
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003533
X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder [PUBMED:9489699]. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling [PUBMED:10441322]. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s).
The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain, which is ubiquitin-like. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation [PUBMED:10749977].
Some proteins known to contain a DC domain are listed below:
- Doublecortin. It is required for neuronal migration [PUBMED:9489699]. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains [PUBMED:10749977].
- Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain [PUBMED:10533048].
- Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 [PUBMED:10401003].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||intracellular signal transduction (GO:0035556)|
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 example describes an architecture with one
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This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 59 members:APG12 APG5 Atg8 AUX_IAA Blt1 Caps_synth_GfcC CHIPS CIDE-N Cobl CRIM DCX DIX DUF2407 DUF3534 DUF4430 DWNN FERM_f0 FERM_N Flg_new GABP-alpha IgG_binding_B Lambda_tail_I Multi_ubiq NLE NQRA_SLBB Oxidored_molyb PB1 Phenol_monoox PI3K_p85B PI3K_rbd Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RAWUL RBD SAP18 SLBB Staphylokinase Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 USP7_C2 USP7_ICP0_bdg YchF-GTPase_C YukD
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...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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.
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.
|Number in seed:||264|
|Number in full:||2143|
|Average length of the domain:||58.20 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||14.88 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|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.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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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.
Too many species/sequences
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.
You can use the tree controls to manipulate how the interactive tree is displayed:
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 2 interactions 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 DCX domain has been found. There are 22 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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