Summary: DM DNA binding domain
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DM domain Edit Wikipedia article
| DM domain | |||||||||
|---|---|---|---|---|---|---|---|---|---|
 Drosophila melanogaster doublesex (dsx), nmr, 18 structures | |||||||||
| Identifiers | |||||||||
| Symbol | DM | ||||||||
| Pfam | PF00751 | ||||||||
| InterPro | IPR001275 | ||||||||
| SMART | SM00718 | ||||||||
| SCOPe | 1rvv / SUPFAM | ||||||||
| |||||||||
In molecular biology the DM domain is a protein domain first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in C. elegans and mammalian proteins.[1] In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides.[2] These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription.[3][4]
The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences .[2][5][6] The NMR analysis of the DSX DM domain [6] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.
Proteins with this domain
Proteins with the DM domain are found in many model organisms. Many C. elegans Mab proteins contain this domain, the best-known one being mab-3.[1] Human proteins containing this domain include DMRT1, DMRT2, DMRT3, DMRTA1, DMRTA2, DMRTB1, and DMRTC2; each of these have a mouse homolog.[7]
| Dmrt1-specific | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Dmrt1 | ||||||||
| Pfam | PF12374 | ||||||||
| InterPro | IPR022114 | ||||||||
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DMRT1 homologs have an additional common domain C-terminal to the DM domain. This domain is only found in bony vertebrates, and neither its structure nor function is unknown.[8](species tree) Jpred predicts the human version of the section to be mostly coils; it also suggests a weak similarity to PDB: 6BO4 by BLAST.[9]
| DMRTA motif | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DMA | ||||||||
| Pfam | PF03474 | ||||||||
| InterPro | IPR005173 | ||||||||
| |||||||||
DMRTA proteins have an additional motif in their C-termina. This motif, ubiquitous in eukaryotes, has an unknown function. It is similar in sequence to some ubiquitin-associated motifs.[10]
References
- ^ a b Raymond CS, Shamu CE, Shen MM, Seifert KJ, Hirsch B, Hodgkin J, Zarkower D (February 1998). "Evidence for evolutionary conservation of sex-determining genes". Nature. 391 (6668): 691–5. doi:10.1038/35618. PMID 9490411.
- ^ a b Erdman SE, Chen HJ, Burtis KC (December 1996). "Functional and genetic characterization of the oligomerization and DNA binding properties of the Drosophila doublesex proteins". Genetics. 144 (4): 1639–52. PMC 1207715. PMID 8978051.
- ^ Burtis KC, Coschigano KT, Baker BS, Wensink PC (September 1991). "The doublesex proteins of Drosophila melanogaster bind directly to a sex-specific yolk protein gene enhancer". EMBO J. 10 (9): 2577–82. PMC 452955. PMID 1907913.
- ^ Shen MM, Hodgkin J (September 1988). "mab-3, a gene required for sex-specific yolk protein expression and a male-specific lineage in C. elegans". Cell. 54 (7): 1019–31. doi:10.1016/0092-8674(88)90117-1. PMID 3046751.
- ^ Yi W, Zarkower D (February 1999). "Similarity of DNA binding and transcriptional regulation by Caenorhabditis elegans MAB-3 and Drosophila melanogaster DSX suggests conservation of sex determining mechanisms". Development. 126 (5): 873–81. PMID 9927589.
- ^ a b Zhu L, Wilken J, Phillips NB, Narendra U, Chan G, Stratton SM, Kent SB, Weiss MA (July 2000). "Sexual dimorphism in diverse metazoans is regulated by a novel class of intertwined zinc fingers". Genes Dev. 14 (14): 1750–64. PMC 316782. PMID 10898790.
- ^ "Proteins matched: DM DNA-binding domain (IPR001275) filtered by species (Homo sapiens)". InterPro.
- ^ "Family: Dmrt1 (PF12374)". Pfam.
- ^ "Jpred results (MTECSGTSQPPPASVPTTAASEGRMVIQDIPAVTSRGHVENTPD)". www.compbio.dundee.ac.uk. Archived from the original on 10 April 2019. Retrieved 10 April 2019.
- ^ "Species: DMRTA motif (IPR005173)". InterPro. Retrieved 10 April 2019.
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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.
DM DNA binding domain Provide feedback
The DM domain is named after dsx and mab-3 [1]. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4 [2]. The dsx DM domain has been shown to dimerise and bind palindromic DNA [3].
Literature references
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Raymond CS, Shamu CE, Shen MM, Seifert KJ, Hirsch B, Hodgkin J, Zarkower D; , Nature 1998;391:691-695.: Evidence for evolutionary conservation of sex-determining genes. PUBMED:9490411 EPMC:9490411
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Erdman SE, Burtis KC; , EMBO J 1993;12:527-535.: The Drosophila doublesex proteins share a novel zinc finger related DNA binding domain. PUBMED:8440242 EPMC:8440242
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Erdman SE, Chen HJ, Burtis KC , Genetics 1996;144:1639-1652.: Functional and genetic characterization of the oligomerization and DNA binding properties of the Drosophila doublesex proteins. PUBMED:8978051 EPMC:8978051
External database links
| SCOP: | 1lpv |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001275
DMRT genes encode a conserved family of transcription factors that share a unique DNA binding motif, the DM domain [ PUBMED:28774758 ]. This domain was first discovered in the doublesex proteins of Drosophila melanogaster [ PUBMED:9490411 ]. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides [ PUBMED:8978051 ]. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [ PUBMED:1907913 , PUBMED:3046751 ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [ PUBMED:8978051 , PUBMED:9927589 , PUBMED:10898790 ]. The NMR analysis of the DSX DM domain [ PUBMED:10898790 ] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
| Molecular function | sequence-specific DNA binding (GO:0043565) |
| Biological process | regulation of transcription, DNA-templated (GO:0006355) |
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
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| Seed (54) |
Full (2454) |
Representative proteomes | UniProt (4863) |
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| RP15 (695) |
RP35 (1217) |
RP55 (2211) |
RP75 (2768) |
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| PP/heatmap | 1 | ||||||
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| Seed (54) |
Full (2454) |
Representative proteomes | UniProt (4863) |
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|---|---|---|---|---|---|---|---|
| RP15 (695) |
RP35 (1217) |
RP55 (2211) |
RP75 (2768) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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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.
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Curation and family details
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Curation
| Seed source: | [1] |
| Previous IDs: | DM-domain; |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Bateman A 
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| Number in seed: | 54 |
| Number in full: | 2454 |
| Average length of the domain: | 46.30 aa |
| Average identity of full alignment: | 55 % |
| Average coverage of the sequence by the domain: | 13.56 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 47 | ||||||||||||
| 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 DM domain has been found. There are 4 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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