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Cysteine-rich DNA binding domain, (DM domain) superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   Cysteine-rich DNA binding domain, (DM domain) [ 82926]
Superfamily:   Cysteine-rich DNA binding domain, (DM domain) [ 82927]
Families:   Cysteine-rich DNA binding domain, (DM domain) [ 82928]

 Superfamily statistics
Genomes (120) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 739 1,142 1
Proteins 698 1,113 1

 Functional annotation
General category Regulation
Detailed category DNA-binding

Document: Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 1.463e-10 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.2779 Least Informative Inherited
Biological Process (BP) reproduction 2.076e-15 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0009633 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 6.574e-07 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.03921 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1017 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.001598 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.01957 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.06033 Moderately Informative Inherited
Biological Process (BP) organ development 0.3876 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1829 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.007687 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 0.03936 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 0.02817 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.06524 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 1.693e-09 Informative Direct
Biological Process (BP) regulation of organelle organization 4.29e-05 Informative Direct
Biological Process (BP) single organism reproductive process 0.0001807 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0007706 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0008707 Informative Direct
Biological Process (BP) reproductive system development 3.416e-08 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.006016 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.001897 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.001418 Informative Inherited
Biological Process (BP) gonad development 8.344e-13 Highly Informative Direct
Biological Process (BP) positive regulation of organelle organization 2.194e-07 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 0.001493 Highly Informative Inherited
Biological Process (BP) negative regulation of RNA metabolic process 0.001304 Highly Informative Inherited
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.0037 Highly Informative Inherited
Molecular Function (MF) binding 4.144e-05 Least Informative Direct
Molecular Function (MF) organic cyclic compound binding 3.82e-15 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 3.07e-15 Moderately Informative Direct
Molecular Function (MF) protein binding 1 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 1.559e-10 Informative Direct

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal reproductive system morphology0.001042Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism segment morphology variant0.02969Moderately InformativeInherited
Worm Phenotype (WP)male morphology variant1.966e-05InformativeDirect
Worm Phenotype (WP)male tail morphology variant7.122e-07Highly InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)portion of tissue0Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processTranscription regulation0Moderately InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationActivator5.215e-12Moderately InformativeDirect
Post-translational modificationRepressor1.262e-11Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001275 SSF82927 Protein matches
Abstract This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans [PubMed9490411]. In D. melanogaste the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides [PubMed8978051]. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [PubMed1907913, PubMed3046751]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [PubMed8978051, PubMed9927589, PubMed10898790]. The NMR analysis of the DSX DM domain [PubMed10898790] 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.

InterPro database

PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.

Alignments of sequences to 1 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Cysteine-rich DNA binding domain, (DM domain) domain.

Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 1 hidden Markov models representing the Cysteine-rich DNA binding domain, (DM domain) superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.