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Conserved domains on  [gi|975136315|ref|XP_015284403|]
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PREDICTED: PHD finger protein 1-like, partial [Gekko japonicus]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 366290)

PHD (plant homeodomain) finger domain-containing protein

Gene Ontology:  GO:0008270|GO:0005515
PubMed:  16297627|21514168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1-51 1.00e-25

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 cd15582:

Pssm-ID: 473978  Cd Length: 52  Bit Score: 90.40  E-value: 1.00e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVCMG 51
Cdd:cd15582    2 CYCGGPGEWNLKMLQCCSCLQWFHEACTQCLSKPLLYGDRFYVFECSVCTG 52
 
Name Accession Description Interval E-value
PHD2_PHF1 cd15582
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ...
 1-51 1.00e-25

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: 90.40  E-value: 1.00e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVCMG 51
Cdd:cd15582    2 CYCGGPGEWNLKMLQCCSCLQWFHEACTQCLSKPLLYGDRFYVFECSVCTG 52
 
Name Accession Description Interval E-value
PHD2_PHF1 cd15582
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ...
 1-51 1.00e-25

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: 90.40  E-value: 1.00e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVCMG 51
Cdd:cd15582    2 CYCGGPGEWNLKMLQCCSCLQWFHEACTQCLSKPLLYGDRFYVFECSVCTG 52
PHD2_MTF2_PHF19_like cd15503
PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ...
 1-49 1.48e-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: 87.46  E-value: 1.48e-24
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVC 49
Cdd:cd15503    2 CYCGGPGEWNLKMLQCCKCRQWFHEACLQCLKKPLLYGDRFYNFCCSVC 50
PHD2_PHF19 cd15581
PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ...
 1-49 2.76e-20

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: 76.87  E-value: 2.76e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVC 49
Cdd:cd15581    2 CYCGGPGEWYLKMLQCYRCRQWFHEACTQCLNDPMMFGDRFYLFFCAVC 50
PHD2_MTF2 cd15580
PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ...
 1-49 5.18e-20

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: 76.09  E-value: 5.18e-20
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHEACTQCLSKPLLYGDRFYVFECCVC 49
Cdd:cd15580    2 CYCGGPGDWYLKMLQCCKCKQWFHEACVQCLEKPMLFGDRFYTFICSVC 50
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 1-49 7.66e-03

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: 31.90  E-value: 7.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 975136315   1 CYCGGPGEWNLKMLQCRRCAQWFHeacTQCLSKPLLYGDRFYVFECCVC 49
Cdd:cd15489    3 IVCGKGGDLGGELLQCDGCGKWFH---ADCLGPPLSSFVPNGKWICPVC 48
 
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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