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Conserved domains on  [gi|1063736821|ref|NP_001318757|]
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EDM2-like protein1 [Arabidopsis thaliana]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 10426798)

PHD (plant homeodomain) finger domain-containing protein

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 93-158 2.98e-12

PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger.


:

Pssm-ID: 277040  Cd Length: 51  Bit Score: 61.67  E-value: 2.98e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063736821  93 QCYACGELGSSDenfsQQVFPCSASNCGHFYHPECVARLLCADdqnkaeelqakIAARDCFACPLH 158
Cdd:cd15565     1 SCFVCKKLGSVG----GEVFKCSVASCGKFYHEECLKKWPLTT-----------ISDSKKFRCPLH 51
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 33-87 5.78e-04

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 cd15658:

Pssm-ID: 473978  Cd Length: 40  Bit Score: 37.97  E-value: 5.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063736821  33 CSICDNGGYVLCCEgSCLRSFHPtiadgietECESLGFTDktqiqalGTYLCNNC 87
Cdd:cd15658     2 CFVCARGGRLLCCE-SCPASFHP--------ECLSIEMPE-------GCWNCNEC 40
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 428-458 7.75e-03

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


The actual alignment was detected with superfamily member PLN02233:

Pssm-ID: 473071 [Multi-domain]  Cd Length: 261  Bit Score: 38.72  E-value: 7.75e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063736821 428 VENGDTVVDFCCGSNDFSCLMKEKLMETGKI 458
Cdd:PLN02233   71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKV 101
 
Name Accession Description Interval E-value
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 93-158 2.98e-12

PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger.


Pssm-ID: 277040  Cd Length: 51  Bit Score: 61.67  E-value: 2.98e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063736821  93 QCYACGELGSSDenfsQQVFPCSASNCGHFYHPECVARLLCADdqnkaeelqakIAARDCFACPLH 158
Cdd:cd15565     1 SCFVCKKLGSVG----GEVFKCSVASCGKFYHEECLKKWPLTT-----------ISDSKKFRCPLH 51
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 33-87 5.78e-04

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 37.97  E-value: 5.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063736821  33 CSICDNGGYVLCCEgSCLRSFHPtiadgietECESLGFTDktqiqalGTYLCNNC 87
Cdd:cd15658     2 CFVCARGGRLLCCE-SCPASFHP--------ECLSIEMPE-------GCWNCNEC 40
PLN02233 PLN02233
ubiquinone biosynthesis methyltransferase
 428-458 7.75e-03

ubiquinone biosynthesis methyltransferase


Pssm-ID: 177877 [Multi-domain]  Cd Length: 261  Bit Score: 38.72  E-value: 7.75e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063736821 428 VENGDTVVDFCCGSNDFSCLMKEKLMETGKI 458
Cdd:PLN02233   71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKV 101
 
Name Accession Description Interval E-value
PHD2_NSD cd15565
PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 93-158 2.98e-12

PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger.


Pssm-ID: 277040  Cd Length: 51  Bit Score: 61.67  E-value: 2.98e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063736821  93 QCYACGELGSSDenfsQQVFPCSASNCGHFYHPECVARLLCADdqnkaeelqakIAARDCFACPLH 158
Cdd:cd15565     1 SCFVCKKLGSVG----GEVFKCSVASCGKFYHEECLKKWPLTT-----------ISDSKKFRCPLH 51
PHD4_NSD3 cd15658
PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed ...
 33-87 5.78e-04

PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3); NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger.


Pssm-ID: 277128  Cd Length: 40  Bit Score: 37.97  E-value: 5.78e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063736821  33 CSICDNGGYVLCCEgSCLRSFHPtiadgietECESLGFTDktqiqalGTYLCNNC 87
Cdd:cd15658     2 CFVCARGGRLLCCE-SCPASFHP--------ECLSIEMPE-------GCWNCNEC 40
PHD4_NSD cd15567
PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 33-87 4.06e-03

PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger.


Pssm-ID: 277042 [Multi-domain]  Cd Length: 41  Bit Score: 35.30  E-value: 4.06e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1063736821  33 CSICDNGGYVLCCEgSCLRSFHPtiadgietECesLGFTDKTQiqalGTYLCNNC 87
Cdd:cd15567     2 CFICSEGGSLICCE-SCPASFHP--------EC--LGLEPPPE----GKFYCEDC 41
PHD1_Rco1 cd15535
PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and ...
 33-59 4.91e-03

PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins; Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger.


Pssm-ID: 277010 [Multi-domain]  Cd Length: 45  Bit Score: 35.47  E-value: 4.91e-03
                          10        20
                  ....*....|....*....|....*..
gi 1063736821  33 CSICDNGGYVLCCEGsCLRSFHPTIAD 59
Cdd:cd15535     2 CSACGGYGSFLCCDG-CPRSFHFSCLD 27
PLN02233 PLN02233
ubiquinone biosynthesis methyltransferase
 428-458 7.75e-03

ubiquinone biosynthesis methyltransferase


Pssm-ID: 177877 [Multi-domain]  Cd Length: 261  Bit Score: 38.72  E-value: 7.75e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1063736821 428 VENGDTVVDFCCGSNDFSCLMKEKLMETGKI 458
Cdd:PLN02233   71 AKMGDRVLDLCCGSGDLAFLLSEKVGSDGKV 101
 
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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