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1  structure 215  species 0  interactions 1027  sequences 9  architectures

Family: DM (PF00751)

Summary: DM DNA binding domain

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DM domain Edit Wikipedia article

DM domain
PDB 1lpv EBI.jpg
drosophila melanogaster doublesex (dsx), nmr, 18 structures
Identifiers
Symbol DM
Pfam PF00751
InterPro IPR001275
SMART SM00718
SCOP 1rvv
SUPERFAMILY 1rvv

In molecular biology the DM domain is a protein domain first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans.[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.

References[edit]

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 

This article incorporates text from the public domain Pfam and InterPro IPR001275

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

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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

  1. 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

  2. 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

  3. 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

This tab holds annotation information from the InterPro database.

InterPro entry IPR001275

This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans [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

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Domain organisation

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Alignments

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  Seed
(26)
Full
(1027)
Representative proteomes NCBI
(930)
Meta
(0)
RP15
(112)
RP35
(146)
RP55
(271)
RP75
(380)
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  Seed
(26)
Full
(1027)
Representative proteomes NCBI
(930)
Meta
(0)
RP15
(112)
RP35
(146)
RP55
(271)
RP75
(380)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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Pfam alignments:

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Seed source: [1]
Previous IDs: DM-domain;
Type: Family
Author: Bateman A
Number in seed: 26
Number in full: 1027
Average length of the domain: 45.10 aa
Average identity of full alignment: 62 %
Average coverage of the sequence by the domain: 16.36 %

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 21.7 21.7
Trusted cut-off 22.2 21.7
Noise cut-off 21.0 21.4
Model length: 47
Family (HMM) version: 13
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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 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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