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Conserved domains on  [gi|2462515958|ref|XP_054195855|]
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histone-lysine N-methyltransferase SETDB1 isoform X4 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Tudor_SETDB1_rpt1 cd20382
first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 260-341 1.07e-43

first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410453  Cd Length: 82  Bit Score: 152.05  E-value: 1.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462515958 260 VGSRVVAKYKD-GNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEdISCRDFIEEYVT 338
Cdd:cd20382     1 VGSRVVAQYKDeGNQVWLYAGIVAEPPKVKNRYRYLIFFDDGYAQYVTPSDVYLVCQQSKKVWEDIH-EDSRDFIREYLE 79


                  ...
gi 2462515958 339 AYP 341
Cdd:cd20382    80 AYP 82
SET super family cl40432
SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, ...
 674-738 1.97e-33

SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily; The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site.


The actual alignment was detected with superfamily member cd10517:

Pssm-ID: 394802 [Multi-domain]  Cd Length: 288  Bit Score: 130.10  E-value: 1.97e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462515958 674 KPFYYILDITYGKEDVPLSCVNEIDTTPPPQVAYSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:cd10517     1 KPYYYICDISYGKEGVPIPCVNEIDNSSPPYVEYSKERIPGKGVNINLDPDFLVGCDCTDGCRDK 65
DUF5604 pfam18300
Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of ...
 193-250 3.56e-33

Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of proteins carrying the SET domain (pfam00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3.


:

Pssm-ID: 408109  Cd Length: 58  Bit Score: 121.33  E-value: 3.56e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462515958 193 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 250
Cdd:pfam18300   1 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 58
Tudor_SETDB1_rpt2 cd21181
second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 348-401 3.50e-30

second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


:

Pssm-ID: 410548  Cd Length: 54  Bit Score: 112.80  E-value: 3.50e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462515958 348 LKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSM 401
Cdd:cd21181     1 LKVGQLIKTEWNGKWWKARVEEVDGSLVKMLFLDDKRTEWIYRGSTRLEPLFRE 54
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 597-672 1.67e-27

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


:

Pssm-ID: 128673  Cd Length: 77  Bit Score: 105.92  E-value: 1.67e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462515958  597 KNPLLVPLLYDFRRMTARRRVNR-KMGFHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCLDPYVLVDRKFQP 672
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRsAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
 
Name Accession Description Interval E-value
Tudor_SETDB1_rpt1 cd20382
first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 260-341 1.07e-43

first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410453  Cd Length: 82  Bit Score: 152.05  E-value: 1.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462515958 260 VGSRVVAKYKD-GNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEdISCRDFIEEYVT 338
Cdd:cd20382     1 VGSRVVAQYKDeGNQVWLYAGIVAEPPKVKNRYRYLIFFDDGYAQYVTPSDVYLVCQQSKKVWEDIH-EDSRDFIREYLE 79


                  ...
gi 2462515958 339 AYP 341
Cdd:cd20382    80 AYP 82
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 674-738 1.97e-33

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 130.10  E-value: 1.97e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462515958 674 KPFYYILDITYGKEDVPLSCVNEIDTTPPPQVAYSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:cd10517     1 KPYYYICDISYGKEGVPIPCVNEIDNSSPPYVEYSKERIPGKGVNINLDPDFLVGCDCTDGCRDK 65
DUF5604 pfam18300
Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of ...
 193-250 3.56e-33

Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of proteins carrying the SET domain (pfam00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3.


Pssm-ID: 408109  Cd Length: 58  Bit Score: 121.33  E-value: 3.56e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462515958 193 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 250
Cdd:pfam18300   1 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 58
Tudor_SETDB1_rpt2 cd21181
second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 348-401 3.50e-30

second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410548  Cd Length: 54  Bit Score: 112.80  E-value: 3.50e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462515958 348 LKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSM 401
Cdd:cd21181     1 LKVGQLIKTEWNGKWWKARVEEVDGSLVKMLFLDDKRTEWIYRGSTRLEPLFRE 54
Tudor_4 pfam18358
Histone methyltransferase Tudor domain; This is a Tudor domain found in histone-lysine ...
 348-397 6.67e-29

Histone methyltransferase Tudor domain; This is a Tudor domain found in histone-lysine N-methyltransferase SETDB1 proteins (EC:2.1.1.43), also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4.


Pssm-ID: 408159  Cd Length: 50  Bit Score: 108.98  E-value: 6.67e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462515958 348 LKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEP 397
Cdd:pfam18358   1 LKKGQTVKTEWNGKWWTARVLEVDASLVKVYFLSDKRTEWIYRGSTRLEP 50
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 597-672 1.67e-27

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 105.92  E-value: 1.67e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462515958  597 KNPLLVPLLYDFRRMTARRRVNR-KMGFHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCLDPYVLVDRKFQP 672
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRsAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
HMT_MBD cd01395
Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as ...
 599-660 9.23e-26

Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.


Pssm-ID: 238689  Cd Length: 60  Bit Score: 100.53  E-value: 9.23e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462515958 599 PLLVPLLYDFRRMTARRRVNrKMGFHVIYKTPCGLCLRTMQEIERYLFETgCDFLFLEMFCL 660
Cdd:cd01395     1 PLHTPLLCGFQRMKYRARVG-KVKKHVIYKAPCGRSLRNMSEVHRYLRET-CSFLTVDNFSF 60
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 594-668 7.35e-23

Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 92.81  E-value: 7.35e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462515958 594 YRGKNPLLVPLLYDFRRMTARRRVNRKMG-FHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCLDPYVLVDR 668
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGkVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSEVGR 76
Tudor_5 pfam18359
Histone methyltransferase Tudor domain 1; This is the first TUDOR domain found in SETDB1 ...
 258-309 5.37e-22

Histone methyltransferase Tudor domain 1; This is the first TUDOR domain found in SETDB1 enzymes (EC:2.1.1.43) in homosapiens, also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4. SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase (HMT) that methylates lysine 9 on histone H3 (H3K9). The enzymatic activity of SETDB1, in association with MBD1-containing chromatin-associated factor 1 (MCAF1), converts H3K9me2 to H3K9me3 and represses subsequent transcription. SETDB1 is amplified in cancers such as melanoma and lung cancer, and increased expression of SETDB1 promotes tumorigenesis in a zebrafish melanoma model. In addition, SETDB1 is required for endogenous retrovirus silencing during early embryogenesis, inhibition of adipocyte differentiation, and differentiation of mesenchymal cells into osteoblasts. The tandem Tudor domains in the N-terminal region are involved in protein-protein interactions. The second tudor domain is pfam18385.


Pssm-ID: 465723  Cd Length: 53  Bit Score: 89.58  E-value: 5.37e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462515958 258 LYVGSRVVAKYKDGN-QVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSE 309
Cdd:pfam18359   1 LPVGTRVIAKYKDSNgKSAYYAGVIAEPPKDLNRYRYLVFFDDGYAQYVVHKD 53
PreSET smart00468
N-terminal to some SET domains; A Cys-rich putative Zn2+-binding domain that occurs N-terminal ...
 679-738 1.74e-18

N-terminal to some SET domains; A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.


Pssm-ID: 128744 [Multi-domain]  Cd Length: 98  Bit Score: 80.92  E-value: 1.74e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462515958  679 ILDITYGKEDVPLSCVNEID-TTPPPQVAYSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:smart00468   1 CLDISNGKENVPVPLVNEVDeDPPPPDFEYISEYIYGQGVPIDRSPSPLVGCSCSGDCSSS 61
Pre-SET pfam05033
Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines ...
 682-738 5.22e-09

Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.


Pssm-ID: 461530 [Multi-domain]  Cd Length: 99  Bit Score: 53.96  E-value: 5.22e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462515958 682 ITYGKEDVPLSCVNEID-TTPPPQVAYSKERIPGKGVFINtgpeFLVGCDCKDgCRDK 738
Cdd:pfam05033   1 ISKGKENVPIPVVNEVDdEPPPPDFTYITSYIYPKEFLLI----IPQGCDCGD-CSSE 53
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 348-400 2.96e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 44.96  E-value: 2.96e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2462515958  348 LKSGQLIKTEWE-GTWWKSRVEEVDG-SLVRILFLDDKRCEWIYRGSTRLEPMFS 400
Cdd:smart00333   3 FKVGDKVAARWEdGEWYRARIVKVDGeQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 257-317 7.60e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 43.80  E-value: 7.60e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462515958  257 KLYVGSRVVAKYKDGNqvWLYAGIVAETPnvkNKLRFLIFFDDGYASYVTQSELYPICRPL 317
Cdd:smart00333   2 TFKVGDKVAARWEDGE--WYRARIVKVDG---EQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
 
Name Accession Description Interval E-value
Tudor_SETDB1_rpt1 cd20382
first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 260-341 1.07e-43

first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410453  Cd Length: 82  Bit Score: 152.05  E-value: 1.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462515958 260 VGSRVVAKYKD-GNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEdISCRDFIEEYVT 338
Cdd:cd20382     1 VGSRVVAQYKDeGNQVWLYAGIVAEPPKVKNRYRYLIFFDDGYAQYVTPSDVYLVCQQSKKVWEDIH-EDSRDFIREYLE 79


                  ...
gi 2462515958 339 AYP 341
Cdd:cd20382    80 AYP 82
SET_SETDB1 cd10517
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 674-738 1.97e-33

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes.


Pssm-ID: 380915 [Multi-domain]  Cd Length: 288  Bit Score: 130.10  E-value: 1.97e-33
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462515958 674 KPFYYILDITYGKEDVPLSCVNEIDTTPPPQVAYSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:cd10517     1 KPYYYICDISYGKEGVPIPCVNEIDNSSPPYVEYSKERIPGKGVNINLDPDFLVGCDCTDGCRDK 65
DUF5604 pfam18300
Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of ...
 193-250 3.56e-33

Domain of unknown function (DUF5604); This domain is often found in the N-terminal region of proteins carrying the SET domain (pfam00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3.


Pssm-ID: 408109  Cd Length: 58  Bit Score: 121.33  E-value: 3.56e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462515958 193 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 250
Cdd:pfam18300   1 SKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYD 58
Tudor_SETDB1_rpt2 cd21181
second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, ...
 348-401 3.50e-30

second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins; SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.


Pssm-ID: 410548  Cd Length: 54  Bit Score: 112.80  E-value: 3.50e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462515958 348 LKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSM 401
Cdd:cd21181     1 LKVGQLIKTEWNGKWWKARVEEVDGSLVKMLFLDDKRTEWIYRGSTRLEPLFRE 54
Tudor_4 pfam18358
Histone methyltransferase Tudor domain; This is a Tudor domain found in histone-lysine ...
 348-397 6.67e-29

Histone methyltransferase Tudor domain; This is a Tudor domain found in histone-lysine N-methyltransferase SETDB1 proteins (EC:2.1.1.43), also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4.


Pssm-ID: 408159  Cd Length: 50  Bit Score: 108.98  E-value: 6.67e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462515958 348 LKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEP 397
Cdd:pfam18358   1 LKKGQTVKTEWNGKWWTARVLEVDASLVKVYFLSDKRTEWIYRGSTRLEP 50
MBD smart00391
Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, ...
 597-672 1.67e-27

Methyl-CpG binding domain; Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain


Pssm-ID: 128673  Cd Length: 77  Bit Score: 105.92  E-value: 1.67e-27
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462515958  597 KNPLLVPLLYDFRRMTARRRVNR-KMGFHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCLDPYVLVDRKFQP 672
Cdd:smart00391   1 GDPLRLPLPCGWRRETKQRKSGRsAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNATVPVGPKFTP 77
HMT_MBD cd01395
Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as ...
 599-660 9.23e-26

Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.


Pssm-ID: 238689  Cd Length: 60  Bit Score: 100.53  E-value: 9.23e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462515958 599 PLLVPLLYDFRRMTARRRVNrKMGFHVIYKTPCGLCLRTMQEIERYLFETgCDFLFLEMFCL 660
Cdd:cd01395     1 PLHTPLLCGFQRMKYRARVG-KVKKHVIYKAPCGRSLRNMSEVHRYLRET-CSFLTVDNFSF 60
MBD pfam01429
Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one ...
 594-668 7.35e-23

Methyl-CpG binding domain; The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase.


Pssm-ID: 396147 [Multi-domain]  Cd Length: 76  Bit Score: 92.81  E-value: 7.35e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462515958 594 YRGKNPLLVPLLYDFRRMTARRRVNRKMG-FHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFCLDPYVLVDR 668
Cdd:pfam01429   1 IERKREDRLPLPPGWRREERQRKSGSKAGkVDVFYYSPTGKKLRSKSEVARYLEANGGTSPKLEDFSFTVRSEVGR 76
Tudor_5 pfam18359
Histone methyltransferase Tudor domain 1; This is the first TUDOR domain found in SETDB1 ...
 258-309 5.37e-22

Histone methyltransferase Tudor domain 1; This is the first TUDOR domain found in SETDB1 enzymes (EC:2.1.1.43) in homosapiens, also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4. SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase (HMT) that methylates lysine 9 on histone H3 (H3K9). The enzymatic activity of SETDB1, in association with MBD1-containing chromatin-associated factor 1 (MCAF1), converts H3K9me2 to H3K9me3 and represses subsequent transcription. SETDB1 is amplified in cancers such as melanoma and lung cancer, and increased expression of SETDB1 promotes tumorigenesis in a zebrafish melanoma model. In addition, SETDB1 is required for endogenous retrovirus silencing during early embryogenesis, inhibition of adipocyte differentiation, and differentiation of mesenchymal cells into osteoblasts. The tandem Tudor domains in the N-terminal region are involved in protein-protein interactions. The second tudor domain is pfam18385.


Pssm-ID: 465723  Cd Length: 53  Bit Score: 89.58  E-value: 5.37e-22
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462515958 258 LYVGSRVVAKYKDGN-QVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSE 309
Cdd:pfam18359   1 LPVGTRVIAKYKDSNgKSAYYAGVIAEPPKDLNRYRYLVFFDDGYAQYVVHKD 53
MBD cd00122
MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of ...
 599-659 4.68e-20

MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.


Pssm-ID: 238069  Cd Length: 62  Bit Score: 84.30  E-value: 4.68e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462515958 599 PLLVPLLYDFRRMTARRRVNRKMGFHVIYKTPCGLCLRTMQEIERYLFETGCDFLFLEMFC 659
Cdd:cd00122     1 PLRDPLPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFS 61
PreSET smart00468
N-terminal to some SET domains; A Cys-rich putative Zn2+-binding domain that occurs N-terminal ...
 679-738 1.74e-18

N-terminal to some SET domains; A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished.


Pssm-ID: 128744 [Multi-domain]  Cd Length: 98  Bit Score: 80.92  E-value: 1.74e-18
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462515958  679 ILDITYGKEDVPLSCVNEID-TTPPPQVAYSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:smart00468   1 CLDISNGKENVPVPLVNEVDeDPPPPDFEYISEYIYGQGVPIDRSPSPLVGCSCSGDCSSS 61
Pre-SET pfam05033
Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines ...
 682-738 5.22e-09

Pre-SET motif; This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains.


Pssm-ID: 461530 [Multi-domain]  Cd Length: 99  Bit Score: 53.96  E-value: 5.22e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462515958 682 ITYGKEDVPLSCVNEID-TTPPPQVAYSKERIPGKGVFINtgpeFLVGCDCKDgCRDK 738
Cdd:pfam05033   1 ISKGKENVPIPVVNEVDdEPPPPDFTYITSYIYPKEFLLI----IPQGCDCGD-CSSE 53
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 348-400 2.96e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 44.96  E-value: 2.96e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2462515958  348 LKSGQLIKTEWE-GTWWKSRVEEVDG-SLVRILFLDDKRCEWIYRGSTRLEPMFS 400
Cdd:smart00333   3 FKVGDKVAARWEdGEWYRARIVKVDGeQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 257-317 7.60e-06

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 43.80  E-value: 7.60e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462515958  257 KLYVGSRVVAKYKDGNqvWLYAGIVAETPnvkNKLRFLIFFDDGYASYVTQSELYPICRPL 317
Cdd:smart00333   2 TFKVGDKVAARWEDGE--WYRARIVKVDG---EQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 261-312 2.28e-04

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 39.11  E-value: 2.28e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462515958 261 GSRVVAKYKDGNQvWlYAGIVAEtpnVKNKLRFLIFFDDGYASYVTQSELYP 312
Cdd:cd04508     1 GDRVEAKWSDDGQ-W-YPATVVA---VNDDGKYTVLFDDGNEEEVSEDDIRP 47
SET_SETDB-like cd10538
SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) ...
 707-738 6.52e-04

SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins; The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site.


Pssm-ID: 380936 [Multi-domain]  Cd Length: 217  Bit Score: 41.97  E-value: 6.52e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2462515958 707 YSKERIPGKGVFINTGPEFLVGCDCKDGCRDK 738
Cdd:cd10538     5 YIKDNIVGKNVQPFSNIIDSVGCKCKDDCLDS 36
 
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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