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Conserved domains on  [gi|558472760|ref|NP_001273771|]
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PHD finger protein 19 isoform d [Homo sapiens]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 10427326)

PHD (plant homeodomain) finger domain-containing protein contains a C4HC3 zinc-finger-like motif

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Mtf2_C pfam14061
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ...
 322-369 1.04e-27

Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics.


:

Pssm-ID: 464077  Cd Length: 48  Bit Score: 102.90  E-value: 1.04e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 558472760  322 SLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTT 369
Cdd:pfam14061   1 SMSDLKSSINSYFGAAGRIACGERYAVLAKRVTPNGKVQYLVEWEGTT 48
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1-39 4.71e-26

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15581:

Pssm-ID: 473978  Cd Length: 52  Bit Score: 98.82  E-value: 4.71e-26
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVCNQ 39
Cdd:cd15581   14 MLQCYRCRQWFHEACTQCLNDPMMFGDRFYLFFCAVCNQ 52
 
Name Accession Description Interval E-value
Mtf2_C pfam14061
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ...
 322-369 1.04e-27

Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics.


Pssm-ID: 464077  Cd Length: 48  Bit Score: 102.90  E-value: 1.04e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 558472760  322 SLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTT 369
Cdd:pfam14061   1 SMSDLKSSINSYFGAAGRIACGERYAVLAKRVTPNGKVQYLVEWEGTT 48
PHD2_PHF19 cd15581
PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
 1-39 4.71e-26

PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. It binds H3K36me3 through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the second PHD finger.


Pssm-ID: 277056  Cd Length: 52  Bit Score: 98.82  E-value: 4.71e-26
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVCNQ 39
Cdd:cd15581   14 MLQCYRCRQWFHEACTQCLNDPMMFGDRFYLFFCAVCNQ 52
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1-37 2.18e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.18e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 558472760     1 MLQCYRCRQWFHEActqCLNEPMMFGDRFYLFFCSVC 37
Cdd:smart00249  14 LLQCDGCDRWYHQT---CLGPPLLEEEPDGKWYCPKC 47
 
Name Accession Description Interval E-value
Mtf2_C pfam14061
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ...
 322-369 1.04e-27

Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics.


Pssm-ID: 464077  Cd Length: 48  Bit Score: 102.90  E-value: 1.04e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 558472760  322 SLSHLKSSITNYFGAAGRLACGEKYQVLARRVTPEGKVQYLVEWEGTT 369
Cdd:pfam14061   1 SMSDLKSSINSYFGAAGRIACGERYAVLAKRVTPNGKVQYLVEWEGTT 48
PHD2_PHF19 cd15581
PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
 1-39 4.71e-26

PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. It binds H3K36me3 through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the second PHD finger.


Pssm-ID: 277056  Cd Length: 52  Bit Score: 98.82  E-value: 4.71e-26
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVCNQ 39
Cdd:cd15581   14 MLQCYRCRQWFHEACTQCLNDPMMFGDRFYLFFCAVCNQ 52
PHD2_MTF2_PHF19_like cd15503
PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1-39 5.61e-24

PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The PCL family includes PHD finger protein1 (PHF1) and its homologs metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD finger of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the second PHD finger.


Pssm-ID: 276978  Cd Length: 52  Bit Score: 93.24  E-value: 5.61e-24
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVCNQ 39
Cdd:cd15503   14 MLQCCKCRQWFHEACLQCLKKPLLYGDRFYNFCCSVCNN 52
PHD2_MTF2 cd15580
PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1-39 6.90e-21

PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or Polycomb-like protein 2 (PCL2), complexes with the Polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. This model corresponds to the second PHD finger.


Pssm-ID: 277055  Cd Length: 52  Bit Score: 84.95  E-value: 6.90e-21
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVCNQ 39
Cdd:cd15580   14 MLQCCKCKQWFHEACVQCLEKPMLFGDRFYTFICSVCNS 52
PHD2_PHF1 cd15582
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ...
 1-37 9.78e-18

PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the second PHD finger.


Pssm-ID: 277057  Cd Length: 52  Bit Score: 76.14  E-value: 9.78e-18
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 558472760   1 MLQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVC 37
Cdd:cd15582   14 MLQCCSCLQWFHEACTQCLSKPLLYGDRFYVFECSVC 50
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1-37 1.14e-05

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 42.30  E-value: 1.14e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 558472760   1 MLQCYRCRQWFHeacTQCLNEPMMFGDRFYLFFCSVC 37
Cdd:cd15489   15 LLQCDGCGKWFH---ADCLGPPLSSFVPNGKWICPVC 48
PHD smart00249
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ...
 1-37 2.18e-04

PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers.


Pssm-ID: 214584 [Multi-domain]  Cd Length: 47  Bit Score: 38.73  E-value: 2.18e-04
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 558472760     1 MLQCYRCRQWFHEActqCLNEPMMFGDRFYLFFCSVC 37
Cdd:smart00249  14 LLQCDGCDRWYHQT---CLGPPLLEEEPDGKWYCPKC 47
PHD_ash2p_like cd15583
PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and ...
 2-37 2.37e-04

PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins; spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity.


Pssm-ID: 277058  Cd Length: 50  Bit Score: 38.48  E-value: 2.37e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 558472760   2 LQCYRCRQWFHEACTQCLNEPMMFGDRFYLFFCSVC 37
Cdd:cd15583   15 LQCSICLKWFHAKCVSIDNGSCLPFMTNYQFVCKRC 50
PHD_UBR7 cd15542
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ...
 1-37 4.71e-03

PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear.


Pssm-ID: 277017  Cd Length: 54  Bit Score: 35.04  E-value: 4.71e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 558472760   1 MLQCYRCRQWFHEACTQCLNePMMFGDRFYLFFCSVC 37
Cdd:cd15542   19 MIQCVLCEDWFHGRHLGLTP-PEPDPDEFDEMICSGC 54
PHD_SPP1 cd16039
PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS ...
 1-37 5.81e-03

PHD finger found in Set1 complex component SPP1; Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif.


Pssm-ID: 277186  Cd Length: 46  Bit Score: 34.37  E-value: 5.81e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 558472760   1 MLQCYRCRQWFHeacTQCLNEPMMFGDRFYLFFCSVC 37
Cdd:cd16039   13 MIACDGCDEWYH---FTCVNIPEADVELVDSFFCPPC 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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