Chromo-like domain superfamily (IPR016197)
Short name: Chromo-like_dom_sf
- Chromo/chromo shadow domain (IPR000953)
- DNA-binding 7kDa protein (IPR003212)
- MRG (IPR008676)
- Histone H3-K9 methyltransferase (IPR011381)
- Chromo domain subgroup (IPR017984)
- Chromo domain (IPR023780)
- RNA binding activity-knot of a chromodomain (IPR025995)
- Signal recognition particle 43kDa protein (IPR030300)
- Chromodomain-helicase-DNA-binding protein 8 (IPR034724)
- Chromo domain-containing protein 1 (IPR037780)
- Histone acetyltransferase Esa1/KAT5/Tip60 (IPR037995)
- Chromobox protein homologue 3 (IPR038033)
This entry represents a chromo (CHRromatin Organization MOdifier) structural domain, which consists of an SH3-like beta-barrel capped by a C-terminal helix. Chromo domains are conserved modules of around 60 amino acids that are implicated in the recognition of lysine-methylated histone tails and nucleic acids. Chromo domains were originally identified in Drosophila modifiers of variegation, proteins that alter the structure of chromatin to the condensed morphology of heterochromatin. Domains with a chromo domain structural fold include:
- Chromo domain, which lacks the first strand of the SH3-like beta-barrel.
- Shadow chromo domain, in which the first strand of the SH3-like beta-barrel is altered by insertions.
- Chromo barrel domain, which is a typical SH3-like beta-barrel fold (similar sequence motif to the canonical chromo domain).
- Histone-like DNA-binding proteins from Archaea [PMID: 9731772].
Chromo domains can be found in various nuclear proteins, including heterochromatin protein 1 (HP1) (N-terminal chromo domain and C-terminal chromo shadow domain), where the chromo domain recognises histone tails with specifically methylated lysines [PMID: 11859155]; polycomb protein Pc, which is essential for maintaining the silencing state of homeotic genes during development (chromo domain important for chromatin targeting) [PMID: 12897052]; histone methyltransferase clr4, which regulates silencing and switching at the mating-type loci and to affect chromatin structure at centromeres [PMID: 11273706]; and the ATP-dependent helicase CHD1, which regulates ATP-dependent nucleosome assembly and mobilisation through conserved double chromo domains and a SWI2/SNF2 helicase/ATPase domain [PMID: 16372014].
Chromo barrel domains are found in various histone acetyltransferases, such as MYST1 from Mus musculus (Mouse) and MOF from Drosophila melanogaster (Fruit fly) [PMID: 15964847]. This domain can also be found in the human mortality factor 4-like protein, MRG15.
- SSF54160 (SSF54160)