CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325280   13 RCLAFHGPLMYEAKILKIwdpsskmytsIPNDKPggssqatkeikpqklgedesiPEeiingkcFFIHYQGWKSSWDEWV 92
Cdd:cd18983   2 RVLCFHGPLLYEAKILDV----------IPDKKE---------------------WK-------YFIHYNGWNKSWDEWV 43

                        90
                ....*....|...
gi 6325280   93 GYDRIRAYNEENI 105
Cdd:cd18983  44 PEDRVLKYTDENL 56

chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; This subgroup includes human male-specific lethal (MSL) complex subunit 3 (MSL3, also known as MSL3L1). The MSL3 chromodomain specifically recognizes the H4K20 monomethyl mark, in a DNA-dependent manner, and may be involved in chromosomal targeting of the MSL complex. Also included is MORF-related gene on chromosome 15 (MRG15, also known as MORF4L1) which specifically binds to Lys36-methylated histone H3 and plays a role in transcriptional regulation and in DNA repair. This subgroup also includes Arabidopsis thaliana Morf Related Gene 2 (MRG2) which acts as a H3K4me3/H3K36me3 reader involved in the regulation of Arabidopsis flowering. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325280   13 RCLAFHGPLMYEAKILKIwdpsskmytsIPNDKPggssqatkeikpqklgedesiPEeiingkcFFIHYQGWKSSWDEWV 92
Cdd:cd18983   2 RVLCFHGPLLYEAKILDV----------IPDKKE---------------------WK-------YFIHYNGWNKSWDEWV 43

                        90
                ....*....|...
gi 6325280   93 GYDRIRAYNEENI 105
Cdd:cd18983  44 PEDRVLKYTDENL 56

RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 6325280     63 EDESIPEEII------NGKCFFIHYQGWKSSWDEWVGYDRIR 98
Cdd:pfam11717  13 DGEWRLAEILsirpkkGKYEYYVHYVGFNKRLDEWVPEDRID 54

chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; This subgroup includes human male-specific lethal (MSL) complex subunit 3 (MSL3, also known as MSL3L1). The MSL3 chromodomain specifically recognizes the H4K20 monomethyl mark, in a DNA-dependent manner, and may be involved in chromosomal targeting of the MSL complex. Also included is MORF-related gene on chromosome 15 (MRG15, also known as MORF4L1) which specifically binds to Lys36-methylated histone H3 and plays a role in transcriptional regulation and in DNA repair. This subgroup also includes Arabidopsis thaliana Morf Related Gene 2 (MRG2) which acts as a H3K4me3/H3K36me3 reader involved in the regulation of Arabidopsis flowering. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6325280   13 RCLAFHGPLMYEAKILKIwdpsskmytsIPNDKPggssqatkeikpqklgedesiPEeiingkcFFIHYQGWKSSWDEWV 92
Cdd:cd18983   2 RVLCFHGPLLYEAKILDV----------IPDKKE---------------------WK-------YFIHYNGWNKSWDEWV 43

                        90
                ....*....|...
gi 6325280   93 GYDRIRAYNEENI 105
Cdd:cd18983  44 PEDRVLKYTDENL 56

chromo barrel domain of MOF acetyltransferase, and similar proteins; This group includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, human male-specific lethal (MSL) complex subunit 3 (MSL3), and retinoblastoma binding protein 1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The chromobarrel domains include a MOF-like subgroup which may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 6325280   55 EIKPQKLGEDESIPEEiingkcFFIHYQGWKSSWDEWVGYDRI 97
Cdd:cd18643  19 KILSVITGKDGRAPPE------YLVHYVGWNRRLDEWVAEDRV 55

malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and similar domains; PHF20L1 associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by MLL1/WDR5 complexes. It binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. PHF20L1 also reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. PHF20L1 contains one MBT (malignant brain tumor) repeat. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the MBT repeat of PHF20L1 and similar domains that contains the semi-aromatic cage that may bind methylated lysine residues.

                        10        20
                ....*....|....*....|...
gi 6325280   78 FIHYQGWKSSWDEWVGYD--RIR 98
Cdd:cd20104  32 LVHYDGWSSRYDEWIDRDseRLR 54