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Conserved domains on  [gi|1972267200|ref|NP_001379288|]
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PHD-type domain-containing protein [Caenorhabditis elegans]

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) ...
 70-189 1.07e-15

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 cd15668:

Pssm-ID: 473978  Cd Length: 103  Bit Score: 69.26  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKR---ELFGPYYathnpikywpsflakkptakkptkiELWFHGSCVLWAPNVHLHGNQLTNLDNQIDIFWS 146
Cdd:cd15668     1 CVFCKRGPHYKglgDLFGPYY-------------------------EVWVHEDCAVWAPGVYLVGGKLYGLEEAVWVAKQ 55

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1972267200 147 QTCIVCRKTGAAISVQNK--KNTFiHYPCAKNKGYKLDE--HALLCN 189
Cdd:cd15668    56 SVCSSCQQTGATIGCLHKgcKAKY-HYPCAVESGCQLDEenFSLLCP 101
 
Name Accession Description Interval E-value
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 70-189 1.07e-15

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 69.26  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKR---ELFGPYYathnpikywpsflakkptakkptkiELWFHGSCVLWAPNVHLHGNQLTNLDNQIDIFWS 146
Cdd:cd15668     1 CVFCKRGPHYKglgDLFGPYY-------------------------EVWVHEDCAVWAPGVYLVGGKLYGLEEAVWVAKQ 55

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1972267200 147 QTCIVCRKTGAAISVQNK--KNTFiHYPCAKNKGYKLDE--HALLCN 189
Cdd:cd15668    56 SVCSSCQQTGATIGCLHKgcKAKY-HYPCAVESGCQLDEenFSLLCP 101
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 117-184 1.81e-04

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 38.85  E-value: 1.81e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1972267200 117 HGSCVLWAPNVHLHGNQ-----LTNLDNQIDIFWSQTCIVCR-KTGAAISVQNKK-NTFIHYPCAKNKGYKLDEH 184
Cdd:pfam13771   1 HVVCALWSPELVQRGNDsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNcRRAFHVTCALEAGLLMQFD 75
 
Name Accession Description Interval E-value
ePHD_RAI1_like cd15668
Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 ...
 70-189 1.07e-15

Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome.


Pssm-ID: 277138  Cd Length: 103  Bit Score: 69.26  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKR---ELFGPYYathnpikywpsflakkptakkptkiELWFHGSCVLWAPNVHLHGNQLTNLDNQIDIFWS 146
Cdd:cd15668     1 CVFCKRGPHYKglgDLFGPYY-------------------------EVWVHEDCAVWAPGVYLVGGKLYGLEEAVWVAKQ 55

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1972267200 147 QTCIVCRKTGAAISVQNK--KNTFiHYPCAKNKGYKLDE--HALLCN 189
Cdd:cd15668    56 SVCSSCQQTGATIGCLHKgcKAKY-HYPCAVESGCQLDEenFSLLCP 101
ePHD_TCF20 cd15699
Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant ...
 70-183 1.19e-09

Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain.


Pssm-ID: 277169  Cd Length: 103  Bit Score: 53.38  E-value: 1.19e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKR---ELFGPYYathnpikywpsflakkptakkptkiELWFHGSCVLWAPNVHLHGNQLTNLDNQIDIFWS 146
Cdd:cd15699     1 CCLCGKWANYRnlgDLFGPFY-------------------------EFWVHEGCILWANGIYLVCGRLYGLQEALDIARE 55

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1972267200 147 QTCIVCRKTGAAISVQNKKNTF-IHYPCAKNKGYKLDE 183
Cdd:cd15699    56 MKCSHCQEAGATLGCYNKGCSFrYHYPCAIDADCLLNE 93
ePHD1_KMT2C cd15696
Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended ...
 113-178 1.60e-06

Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains.


Pssm-ID: 277166  Cd Length: 90  Bit Score: 44.55  E-value: 1.60e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972267200 113 ELWFHGSCVLWAPNV-HLHGNQLTNLDNQIDIFWSQTCIVCRKTGAAISVQNKKNT-FIHYPCAKNKG 178
Cdd:cd15696     8 ECWAHLRCAEWSLGVcQGEEQLLVNVDKAVVSGSTERCAFCKHLGATIKCCEEKCTqMYHYPCAAGAG 75
ePHD_RAI1 cd15700
Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant ...
 70-183 9.05e-05

Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes.


Pssm-ID: 277170  Cd Length: 104  Bit Score: 40.25  E-value: 9.05e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKREL---FGPYYATHnpikywpsflakkptakkptkielWFHGSCVLWAPNVHLHGNQLTNLDNQIDIFWS 146
Cdd:cd15700     1 CCLCRNPANYKDLgdlCGPYYPEH------------------------WVHEACAVWTTGVYLVAGKLFGLQEAVQKAAD 56

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1972267200 147 QTCIVCRKTGAAISVQNKKNTF-IHYPCAKNKGYKLDE 183
Cdd:cd15700    57 AKCSSCQGAGATVGCCHKGCTQsYHYICAVEAGCLFEE 94
ePHD cd15571
Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is ...
 114-184 1.34e-04

Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His; PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has 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.


Pssm-ID: 277046 [Multi-domain]  Cd Length: 112  Bit Score: 39.88  E-value: 1.34e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1972267200 114 LWFHGSCVLWAPNVhLHGNQLTNLDNQIDIF----WSQTCIVCRKT-GAAISVQNKK--NTFiHYPCAKNKGYKLDEH 184
Cdd:cd15571    24 LWVHVVCALWSPEV-YFDDGTLLEVEGVSKIpkrrKKLKCSICGKRgGACIQCSYPGcpRSF-HVSCAIRAGCLFEFE 99
zf-HC5HC2H pfam13771
PHD-like zinc-binding domain; The members of this family are annotated as containing PHD ...
 117-184 1.81e-04

PHD-like zinc-binding domain; The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH.


Pssm-ID: 463977 [Multi-domain]  Cd Length: 88  Bit Score: 38.85  E-value: 1.81e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1972267200 117 HGSCVLWAPNVHLHGNQ-----LTNLDNQIDIFWSQTCIVCR-KTGAAISVQNKK-NTFIHYPCAKNKGYKLDEH 184
Cdd:pfam13771   1 HVVCALWSPELVQRGNDsmgfpIEDIEKIPKRRWKLKCYLCKkKGGACIQCSKKNcRRAFHVTCALEAGLLMQFD 75
ePHD_JADE cd15671
Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended ...
 115-181 2.07e-04

Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.


Pssm-ID: 277141  Cd Length: 112  Bit Score: 39.35  E-value: 2.07e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1972267200 115 WFHGSCVLWAPNVHLhGN-----QLTNLDNQIDIFWSQTCIVCR-KTGAAI--SVQNKKNTFiHYPCAKNKGYKL 181
Cdd:cd15671    20 WVHVSCALWIPEVSI-GCpekmePITKISHIPMSRWALVCVLCKeKTGACIqcSVKSCKTAF-HVTCAFQHGLEM 92
ePHD2_KMT2C_like cd15666
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); ...
 112-174 2.38e-03

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.


Pssm-ID: 277136  Cd Length: 105  Bit Score: 36.13  E-value: 2.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1972267200 112 IELWFHGSCVLWAPNVH-LHGNQLTNLDNQIDIFWSQTCIVCRKTGAAISV--QNKKNTFiHYPCA 174
Cdd:cd15666    23 VDKWVHLNCALWSYEVYeTQNGALMNVEEALRRALTTTCSHCGRTGATVPCfkPRCANVY-HLPCA 87
ePHD2_KMT2D cd15698
Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended ...
 70-188 2.91e-03

Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions.


Pssm-ID: 277168  Cd Length: 107  Bit Score: 35.80  E-value: 2.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1972267200  70 CALCHENGEKrelfgpyyATHNPIKYwpsflakkptakKPTKIELWFHGSCVLWAPNVH-LHGNQLTNLDNQIDIFWSQT 148
Cdd:cd15698     1 CCFCHEEGDG--------ATDGPARL------------LNLDLDLWVHLNCALWSTEVYeTQGGALMNVEVALHRGLLTK 60

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1972267200 149 CIVCRKTGAAISVQNKK--NTFiHYPCA-KNKGYKLDEHALLC 188
Cdd:cd15698    61 CSLCQKTGATNSCNRLRcpNVY-HFACAiRAKCMFFKDKTMLC 102
ePHD_BRPF1 cd15701
Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and ...
 115-178 3.93e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling.


Pssm-ID: 277171 [Multi-domain]  Cd Length: 121  Bit Score: 35.82  E-value: 3.93e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972267200 115 WFHGSCVLWAPNVHLHGNQLTNLDNQIDIF----WSQTCIVCRKTGAAISVQNKKN---TFIHYPCAKNKG 178
Cdd:cd15701    19 WAHVVCALWIPEVCFANTVFLEPIDSIEHIpparWKLTCYICKQRGSGACIQCHKAncyTAFHVTCAQQAG 89
ePHD_BRPF3 cd15703
Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and ...
 115-178 5.55e-03

Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.


Pssm-ID: 277173 [Multi-domain]  Cd Length: 118  Bit Score: 35.42  E-value: 5.55e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1972267200 115 WFHGSCVLWAPNVHLHGN----QLTNLDNQIDIFWSQTCIVCRKTGAAISVQ-NKKNTF--IHYPCAKNKG 178
Cdd:cd15703    19 WAHVVCAIWIPEVCFANTvflePVEGVNNIPPARWKLTCYLCKQKGRGAAIQcHKVNCYtaFHVTCAQRAG 89
ePHD_RNO cd15707
Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and ...
 115-181 9.84e-03

Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277177 [Multi-domain]  Cd Length: 113  Bit Score: 34.49  E-value: 9.84e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972267200 115 WFHGSCVLWAPNVHL----HGNQLTNLDNQIDIFWSQTCIVCR-KTGAAI--SVQNKKNTFiHYPCAKNKGYKL 181
Cdd:cd15707    20 WAHVSCALWIPEVSIgcveKMEPITKISSIPASRWALICVLCReRTGACIqcSVKTCKTAY-HVTCGFQHGLEM 92
ePHD_JADE3 cd15706
Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant ...
 115-181 9.88e-03

Extended PHD finger found in protein Jade-3 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs.


Pssm-ID: 277176  Cd Length: 111  Bit Score: 34.70  E-value: 9.88e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1972267200 115 WFHGSCVLWAPNVHLHGNQ----LTNLDNQIDIFWSQTCIVCR-KTGAAI--SVQNKKNTFiHYPCAKNKGYKL 181
Cdd:cd15706    20 WAHVSCALWIPEVSIACPErmepITKVSHIPPSRWALVCSLCKlKTGACIqcSVKSCITAF-HVTCAFEHSLEM 92
 
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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