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32  structures 559  species 0  interactions 7958  sequences 107  architectures

Family: DCX (PF03607)

Summary: Doublecortin

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

Doublecortin Edit Wikipedia article

Doublecortin (DCX) is a microtubule-associated protein expressed almost exclusively in immature neurons. Neuronal precursors begin to express DCX shortly after exiting the cell cycle, and 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, a marker for mature neurons.

Due to the nearly exclusive expression of DCX in developping neurons, this protein has been used increasingly as a marker for [[1]]. Indeed, the levels of DCX expression increase in response to exercise, in parallel with increased [[2]] labelling, currently a "gold standard" in measuring neurogenesis.

References

Couillard-Despres S, Winner B, Schaubeck S, Aigner R, Vroemen M, Weidner N, Bogdahn U, Winkler J, Kuhn HG, Aigner L. (2005) Doublecortin expression levels in adult brain reflect neurogenesis. Eur J Neurosci. Jan;21(1):1-14.

Brown JP, Couillard-Despres S, Cooper-Kuhn CM, Winkler J, Aigner L, Kuhn HG. (2003) Transient expression of doublecortin during adult neurogenesis. J Comp Neurol. Dec 1;467(1):1-10.

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.

Doublecortin Provide feedback

No Pfam abstract.

Internal database links

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 controlling neuronal migration in the developing brain [ PUBMED:10533048 , PUBMED:16684769 ].
  • Retinitis pigmentosa 1 protein. It is required for the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 [ PUBMED:10401003 , PUBMED:19657028 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(205)
Full
(7958)
Representative proteomes UniProt
(13038)
RP15
(1016)
RP35
(2308)
RP55
(5845)
RP75
(8105)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(205)
Full
(7958)
Representative proteomes UniProt
(13038)
RP15
(1016)
RP35
(2308)
RP55
(5845)
RP75
(8105)
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
(205)
Full
(7958)
Representative proteomes UniProt
(13038)
RP15
(1016)
RP35
(2308)
RP55
(5845)
RP75
(8105)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: PROSITE
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Griffiths-Jones SR
Number in seed: 205
Number in full: 7958
Average length of the domain: 59.4 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 14.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 60
Family (HMM) version: 20
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 DCX domain has been found. There are 32 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044QYV4 View 3D Structure Click here
A0A044R479 View 3D Structure Click here
A0A044U415 View 3D Structure Click here
A0A077ZAN1 View 3D Structure Click here
A0A077ZES5 View 3D Structure Click here
A0A0G2L2L4 View 3D Structure Click here
A0A0K0E2I2 View 3D Structure Click here
A0A0K0E753 View 3D Structure Click here
A0A0K0ERR7 View 3D Structure Click here
A0A0N4U808 View 3D Structure Click here
A0A0N4UCV6 View 3D Structure Click here
A0A158N8S7 View 3D Structure Click here
A0A2R8Q0Q7 View 3D Structure Click here
A0A3P7DTL5 View 3D Structure Click here
A0A3P7DYR0 View 3D Structure Click here
A0A3P7EVX5 View 3D Structure Click here
A0A5K1IAB7 View 3D Structure Click here
A0A5K4F1L4 View 3D Structure Click here
A0A5K4F1Y6 View 3D Structure Click here
A0A5K4F4Z8 View 3D Structure Click here
A0A5K4FEV7 View 3D Structure Click here
A0A5S6PU18 View 3D Structure Click here
A0A7I4NLF2 View 3D Structure Click here
A2A121 View 3D Structure Click here
A2VCK2 View 3D Structure Click here
A8MYV0 View 3D Structure Click here
B4GXC2 View 3D Structure Click here
B4IMC3 View 3D Structure Click here
B4NSS9 View 3D Structure Click here
B5DK35 View 3D Structure Click here
B8A4M4 View 3D Structure Click here
C0H4E4 View 3D Structure Click here
D2I3C6 View 3D Structure Click here
D3ZR10 View 3D Structure Click here
D4ABP8 View 3D Structure Click here
E7F630 View 3D Structure Click here
E9QBD0 View 3D Structure Click here
F1LWF2 View 3D Structure Click here
F1QA54 View 3D Structure Click here
F1QB18 View 3D Structure Click here