CpG binding protein C-terminal domain; CpG-binding protein is a transcriptional activator that exhibits a DNA binding specificity for unmethylated CpG motifs. CpG is made of a PHD1, an acidic, a basic, a coiled-coil, and a PHD2 domains. This protein contains three cysteine-rich domains identified at the N-terminal, central region and C-terminal of the protein, where the central cysteine-rich domain is located within the DNA-binding domain, found between PHD1 and the acidic domains. This domain is found in eukaryotes, and is approximately 240 amino acids in length. It is found at the C-terminal of the CpG-binding protein containing the coiled-coil and PHD2 domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  278 ATKRIFQVLPQRLQEWNLTPSRAAEETRKHLDNIRHKQSLVRFALAELEKRSEELNMVVERAKRSSIDTLGSQDTADMED 357
Cdd:pfam12269   1 ATNRIYEILPQRIQEWQLSPCVAEEENKKKLEKIRKEQQEAREALKELDARHQELDAIIERAKKLPVDTEEEENDDEDDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  358 EQSMYCITCGHEIHSRTAIKHMEKCFNKYESQASFGSIFKTRMEGNNMFCDFYNPASKTYCKRLRVLCPEHSKDPKVNDT 437
Cdd:pfam12269  81 ELSIYCVTCGHEIHSRTAIKHMEKCFNKYESQTSFGSIYKTRIEGNSMFCDFYNPQQKTYCKRLKVLCPEHTKEPKIPDT 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320541895  438 DVCGSPLVNNVFNPTGEFCRAPKKNCFKHYAWEKIRRAEIDLERVRQWLKMDDLMEQERVMRQQLTSRANLLGLM 512
Cdd:pfam12269 161 EVCGCPLVRNVFDPTGEFCRAPKKKCVKHYCWEKLRRAEIDLERVRQWLKLDELFEQERQIRTAMANRAGVLGLM 235

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 320541895  158 REPKMGKRCGTCEGCRRP-NCNQCDACRVRVGH------KPRCIFRTC 198
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPeDCGQCSFCLDMPKFggpgkkKQKCRLRRC 48

CpG binding protein C-terminal domain; CpG-binding protein is a transcriptional activator that exhibits a DNA binding specificity for unmethylated CpG motifs. CpG is made of a PHD1, an acidic, a basic, a coiled-coil, and a PHD2 domains. This protein contains three cysteine-rich domains identified at the N-terminal, central region and C-terminal of the protein, where the central cysteine-rich domain is located within the DNA-binding domain, found between PHD1 and the acidic domains. This domain is found in eukaryotes, and is approximately 240 amino acids in length. It is found at the C-terminal of the CpG-binding protein containing the coiled-coil and PHD2 domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  278 ATKRIFQVLPQRLQEWNLTPSRAAEETRKHLDNIRHKQSLVRFALAELEKRSEELNMVVERAKRSSIDTLGSQDTADMED 357
Cdd:pfam12269   1 ATNRIYEILPQRIQEWQLSPCVAEEENKKKLEKIRKEQQEAREALKELDARHQELDAIIERAKKLPVDTEEEENDDEDDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  358 EQSMYCITCGHEIHSRTAIKHMEKCFNKYESQASFGSIFKTRMEGNNMFCDFYNPASKTYCKRLRVLCPEHSKDPKVNDT 437
Cdd:pfam12269  81 ELSIYCVTCGHEIHSRTAIKHMEKCFNKYESQTSFGSIYKTRIEGNSMFCDFYNPQQKTYCKRLKVLCPEHTKEPKIPDT 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320541895  438 DVCGSPLVNNVFNPTGEFCRAPKKNCFKHYAWEKIRRAEIDLERVRQWLKMDDLMEQERVMRQQLTSRANLLGLM 512
Cdd:pfam12269 161 EVCGCPLVRNVFDPTGEFCRAPKKKCVKHYCWEKLRRAEIDLERVRQWLKLDELFEQERQIRTAMANRAGVLGLM 235

PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 320541895   43 CICRSSDCSRFMIGCDGCEEWYHGDCIGIT-EKEAKHIKQYYCRRCK 88
Cdd:pfam00628   3 AVCGKSDDGGELVQCDGCDDWFHLACLGPPlDPAEIPSGEWLCPECK 49

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 320541895  158 REPKMGKRCGTCEGCRRP-NCNQCDACRVRVGH------KPRCIFRTC 198
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPeDCGQCSFCLDMPKFggpgkkKQKCRLRRC 48

CpG binding protein C-terminal domain; CpG-binding protein is a transcriptional activator that exhibits a DNA binding specificity for unmethylated CpG motifs. CpG is made of a PHD1, an acidic, a basic, a coiled-coil, and a PHD2 domains. This protein contains three cysteine-rich domains identified at the N-terminal, central region and C-terminal of the protein, where the central cysteine-rich domain is located within the DNA-binding domain, found between PHD1 and the acidic domains. This domain is found in eukaryotes, and is approximately 240 amino acids in length. It is found at the C-terminal of the CpG-binding protein containing the coiled-coil and PHD2 domains.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  278 ATKRIFQVLPQRLQEWNLTPSRAAEETRKHLDNIRHKQSLVRFALAELEKRSEELNMVVERAKRSSIDTLGSQDTADMED 357
Cdd:pfam12269   1 ATNRIYEILPQRIQEWQLSPCVAEEENKKKLEKIRKEQQEAREALKELDARHQELDAIIERAKKLPVDTEEEENDDEDDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 320541895  358 EQSMYCITCGHEIHSRTAIKHMEKCFNKYESQASFGSIFKTRMEGNNMFCDFYNPASKTYCKRLRVLCPEHSKDPKVNDT 437
Cdd:pfam12269  81 ELSIYCVTCGHEIHSRTAIKHMEKCFNKYESQTSFGSIYKTRIEGNSMFCDFYNPQQKTYCKRLKVLCPEHTKEPKIPDT 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 320541895  438 DVCGSPLVNNVFNPTGEFCRAPKKNCFKHYAWEKIRRAEIDLERVRQWLKMDDLMEQERVMRQQLTSRANLLGLM 512
Cdd:pfam12269 161 EVCGCPLVRNVFDPTGEFCRAPKKKCVKHYCWEKLRRAEIDLERVRQWLKLDELFEQERQIRTAMANRAGVLGLM 235

PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF); BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 320541895  42 YCICRSS-DCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15560    1 YCICRTPyDESQFYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 320541895  42 YCICRSS-DCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15554    1 YCICRQPyDVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320541895  42 YCICRSS-DCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRCK 88
Cdd:cd15640    1 YCVCRQPyDVNRFMIECDICKDWFHGSCVQVEEHHAADIDLYHCPNCE 48

PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3; This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 320541895  39 DQAYCICRSSDCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQ----YYCRRC 87
Cdd:cd15639    2 NALYCICRQPHNNRFMICCDRCEEWFHGDCVGITEARGRLLERngedYICPNC 54

PHD finger found in histone lysine demethylase PHF8; PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 320541895  42 YCICR-SSDCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRCK 88
Cdd:cd15642    2 YCLCRlPYDVTRFMIECDVCQDWFHGSCVGVEEEKAAEIDLYHCPNCQ 49

PHD finger found in mixed lineage leukemia 5 (MLL5); MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 320541895  43 CICRSSDCSRFMIGCDGCEEWYHGDCIGITEKEAKhiKQYYCRRC 87
Cdd:cd15550    2 CICGFEHDDGFMICCDKCSVWQHGDCMGIDRENIP--DSYLCEQC 44

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).

                         10        20        30
                 ....*....|....*....|....*....|...
gi 320541895  55 IGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15517   17 VQCDGCDKWFHQFCLGLSNERYADEDKFKCPNC 49

PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins; The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger.

                         10        20        30
                 ....*....|....*....|....*....|.
gi 320541895  57 CDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15610   20 CDGCEEWFHLLCVGLSPEEVAEDEDYICPSC 50

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320541895  43 CICRSS-DCSRFMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15489    3 IVCGKGgDLGGELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48

CXXC zinc finger domain; This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 320541895  158 REPKMGKRCGTCEGCRRP-NCNQCDACRVRVGH------KPRCIFRTC 198
Cdd:pfam02008   1 RNRRKRRRCGVCEGCQRPeDCGQCSFCLDMPKFggpgkkKQKCRLRRC 48

PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins; MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 320541895  43 CIC--RSSDCSRfMIGCDGCEEWYHGDCIGI--TEKEAKHikqYYCRRC 87
Cdd:cd15556    2 CSCgtRDDDGER-MIACDVCEVWQHTRCVGIadNEEPPDH---FLCRRC 46

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 320541895  39 DQAYCICRSSDCSRfMIGCDG--CE-EWYHGDCIGIteKEAKHIKqYYCRRCKKE 90
Cdd:COG5034  220 EELYCFCQQVSYGQ-MVACDNanCKrEWFHLECVGL--KEPPKGK-WYCPECKKA 270

PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins; Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1, and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. The family corresponds to the third PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 320541895  43 CICRSSDCSR-FMIGCDGCEEWYHGDCIGITEKEAKHIKQYYCRRC 87
Cdd:cd15520    2 CGCGEGFNIAdRMIFCDRCERTVHLDCVGLSDRIVDSPSEFFCPEC 47

PHD finger found in PHD finger protein 20 (PHF20); PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 320541895  43 CICRSSDCSRFMIGCDGCEEWYHGDCIGITEKEAKhiKQYYCRRC 87
Cdd:cd15634    2 CICEVQEENDFMIQCEECLCWQHGVCMGLLEDNVP--EKYTCYIC 44

PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger.

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gi 320541895  42 YCICRSSDCSRfMIGCDGCE---EWYHGDCIGITEKEAkhiKQYYCRRCK 88
Cdd:cd15587    1 YCYCRRVSFGE-MVACDNPDckiEWFHFECVGLTETPK---GKWYCSDCK 46

PHD finger found in PHD finger protein 20-like protein 1 (P20L1); P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger.

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gi 320541895  43 CICRSSDCSRFMIGCDGCEEWYHGDCIGITEKEAKhiKQYYCRRCK 88
Cdd:cd15633    2 CICEMDEENGFMIQCEECLCWQHSVCMGLLEESIP--EQYICYICR 45