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Conserved domains on  [gi|19114306|ref|NP_593394|]
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Clr6 histone deacetylase complex, chromodomain subunit Alp13/Eaf3 [Schizosaccharomyces pombe]

Protein Classification

MRG family protein( domain architecture ID 13040224)

MRG (MORF4 related gene) family protein similar to human mortality factor 4-like protein 1, also called MORF-related gene 15 protein (MRG15), and Schizosaccharomyces pombe chromatin modification-related protein eaf3, both of which are components of the NuA4 histone acetyltransferase complex that is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MRG pfam05712
MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4 ...
 154-326 1.70e-70

MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif.


:

Pssm-ID: 461721  Cd Length: 185  Bit Score: 217.46  E-value: 1.70e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   154 ENNEKDDFEEEPPLpkhKISVPDVLKLWLVDDWENITKNQQLIAIPRNPTVRAAIAAFRESKISHLNNEI----DVDVFE 229
Cdd:pfam05712   4 DSESEDEFSKRPEI---KLDIPDELKKILVDDWENITKNNQLVPLPAKPPVDEILEDYVEHEKVKRANGSnktrDEDLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   230 QAMAGLVIYFNKCLGNMLLYRFERQQYLEIRQQY-------PDTEMCDLYGVEHLIRLFVSLPELIDRTNMDSQSIECLL 302
Cdd:pfam05712  81 EVVAGLREYFDKALGRILLYRFERPQYAELRKKWasgpnddQGKEPSDIYGAEHLLRLFVKLPELLAQTNMDEQSLNRLR 160

                         170       180
                  ....*....|....*....|....*
gi 19114306   303 NYIEEFLKYLVLHKDEYFIK-EYQN 326
Cdd:pfam05712 161 EHLEDFLEFLAKNHERYFSKqEYES 185
CBD_MSL3_like cd18983
chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; ...
 9-65 1.00e-30

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.


:

Pssm-ID: 350846  Cd Length: 57  Bit Score: 110.62  E-value: 1.00e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114306   9 ERVLCFHGPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRILQWTEENLK 65
Cdd:cd18983   1 ERVLCFHGPLLYEAKILDVIPDKKEWKYFIHYNGWNKSWDEWVPEDRVLKYTDENLR 57
 
Name Accession Description Interval E-value
MRG pfam05712
MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4 ...
 154-326 1.70e-70

MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif.


Pssm-ID: 461721  Cd Length: 185  Bit Score: 217.46  E-value: 1.70e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   154 ENNEKDDFEEEPPLpkhKISVPDVLKLWLVDDWENITKNQQLIAIPRNPTVRAAIAAFRESKISHLNNEI----DVDVFE 229
Cdd:pfam05712   4 DSESEDEFSKRPEI---KLDIPDELKKILVDDWENITKNNQLVPLPAKPPVDEILEDYVEHEKVKRANGSnktrDEDLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   230 QAMAGLVIYFNKCLGNMLLYRFERQQYLEIRQQY-------PDTEMCDLYGVEHLIRLFVSLPELIDRTNMDSQSIECLL 302
Cdd:pfam05712  81 EVVAGLREYFDKALGRILLYRFERPQYAELRKKWasgpnddQGKEPSDIYGAEHLLRLFVKLPELLAQTNMDEQSLNRLR 160

                         170       180
                  ....*....|....*....|....*
gi 19114306   303 NYIEEFLKYLVLHKDEYFIK-EYQN 326
Cdd:pfam05712 161 EHLEDFLEFLAKNHERYFSKqEYES 185
CBD_MSL3_like cd18983
chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; ...
 9-65 1.00e-30

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.


Pssm-ID: 350846  Cd Length: 57  Bit Score: 110.62  E-value: 1.00e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114306   9 ERVLCFHGPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRILQWTEENLK 65
Cdd:cd18983   1 ERVLCFHGPLLYEAKILDVIPDKKEWKYFIHYNGWNKSWDEWVPEDRVLKYTDENLR 57
Tudor-knot pfam11717
RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is ...
 6-57 3.58e-09

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.


Pssm-ID: 432022 [Multi-domain]  Cd Length: 55  Bit Score: 52.21  E-value: 3.58e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19114306     6 KVNERVLCFH-GPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRIL 57
Cdd:pfam11717   2 EIGCKVLVRKrDGEWRLAEILSIRPKKGKYEYYVHYVGFNKRLDEWVPEDRID 54
CHROMO smart00298
Chromatin organization modifier domain;
22-62 5.05e-06

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 43.36  E-value: 5.05e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 19114306     22 AKIVDTEMKGD-VTTYLIHYKGWKNSWDEWVEQDRILQWTEE 62
Cdd:smart00298   5 EKILDHRWKKKgELEYLVKWKGYSYSEDTWEPEENLLNCSKK 46
 
Name Accession Description Interval E-value
MRG pfam05712
MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4 ...
 154-326 1.70e-70

MRG; This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif.


Pssm-ID: 461721  Cd Length: 185  Bit Score: 217.46  E-value: 1.70e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   154 ENNEKDDFEEEPPLpkhKISVPDVLKLWLVDDWENITKNQQLIAIPRNPTVRAAIAAFRESKISHLNNEI----DVDVFE 229
Cdd:pfam05712   4 DSESEDEFSKRPEI---KLDIPDELKKILVDDWENITKNNQLVPLPAKPPVDEILEDYVEHEKVKRANGSnktrDEDLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114306   230 QAMAGLVIYFNKCLGNMLLYRFERQQYLEIRQQY-------PDTEMCDLYGVEHLIRLFVSLPELIDRTNMDSQSIECLL 302
Cdd:pfam05712  81 EVVAGLREYFDKALGRILLYRFERPQYAELRKKWasgpnddQGKEPSDIYGAEHLLRLFVKLPELLAQTNMDEQSLNRLR 160

                         170       180
                  ....*....|....*....|....*
gi 19114306   303 NYIEEFLKYLVLHKDEYFIK-EYQN 326
Cdd:pfam05712 161 EHLEDFLEFLAKNHERYFSKqEYES 185
CBD_MSL3_like cd18983
chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins; ...
 9-65 1.00e-30

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.


Pssm-ID: 350846  Cd Length: 57  Bit Score: 110.62  E-value: 1.00e-30
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19114306   9 ERVLCFHGPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRILQWTEENLK 65
Cdd:cd18983   1 ERVLCFHGPLLYEAKILDVIPDKKEWKYFIHYNGWNKSWDEWVPEDRVLKYTDENLR 57
CBD_RBP1_like cd18641
chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; ...
 19-57 1.90e-09

chromo barrel domain of retinoblastoma binding protein 1, and similar proteins; Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. 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 chromodomain.


Pssm-ID: 350843 [Multi-domain]  Cd Length: 59  Bit Score: 53.05  E-value: 1.90e-09
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 19114306  19 LYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRIL 57
Cdd:cd18641  15 IYEASIKSTEIDDGEVLYLVHYYGWNVRYDEWVKADRII 53
Tudor-knot pfam11717
RNA binding activity-knot of a chromodomain; This is a novel knotted tudor domain which is ...
 6-57 3.58e-09

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.


Pssm-ID: 432022 [Multi-domain]  Cd Length: 55  Bit Score: 52.21  E-value: 3.58e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19114306     6 KVNERVLCFH-GPLLYEAKIVDTEMKGDVTTYLIHYKGWKNSWDEWVEQDRIL 57
Cdd:pfam11717   2 EIGCKVLVRKrDGEWRLAEILSIRPKKGKYEYYVHYVGFNKRLDEWVPEDRID 54
CBD cd18643
chromo barrel domain of MOF acetyltransferase, and similar proteins; This group includes the ...
 9-57 4.47e-07

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.


Pssm-ID: 350845 [Multi-domain]  Cd Length: 61  Bit Score: 46.40  E-value: 4.47e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 19114306   9 ERVLCFHGPL----LYEAKIVDTEMKGDVTT---YLIHYKGWKNSWDEWVEQDRIL 57
Cdd:cd18643   1 EKVLVFEPDPkarvLYDAKILSVITGKDGRAppeYLVHYVGWNRRLDEWVAEDRVL 56
MBT_PHF20L1-like cd20104
malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and ...
 20-51 5.15e-07

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.


Pssm-ID: 439094 [Multi-domain]  Cd Length: 60  Bit Score: 46.08  E-value: 5.15e-07
                        10        20        30
                ....*....|....*....|....*....|..
gi 19114306  20 YEAKIVDTEmkGDVTTYLIHYKGWKNSWDEWV 51
Cdd:cd20104  17 YEAKIVEVD--EEENKVLVHYDGWSSRYDEWI 46
CHROMO smart00298
Chromatin organization modifier domain;
22-62 5.05e-06

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 43.36  E-value: 5.05e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 19114306     22 AKIVDTEMKGD-VTTYLIHYKGWKNSWDEWVEQDRILQWTEE 62
Cdd:smart00298   5 EKILDHRWKKKgELEYLVKWKGYSYSEDTWEPEENLLNCSKK 46
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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