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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15671    1 CVLCPKKGGAMKSTKSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEKTGACIQCSVKSCKTAF 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 194328767 339 HVTCAFDRGLEMKTIL-AENDEVKFKSYCPKH 369
Cdd:cd15671   81 HVTCAFQHGLEMKTILeDEDDEVKFKSYCPKH 112

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15671    1 CVLCPKKGGAMKSTKSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEKTGACIQCSVKSCKTAF 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 194328767 339 HVTCAFDRGLEMKTIL-AENDEVKFKSYCPKH 369
Cdd:cd15671   81 HVTCAFQHGLEMKTILeDEDDEVKFKSYCPKH 112

PHD-zinc-finger like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767  257 PKCLLCPKKGGAMKPTrSGTKWVHVSCALWIPEVSIGSPEKMEPITkVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRT 336
Cdd:pfam13832   1 VRCCLCPLRGGALKQT-SDGRWVHVLCAIFVPEVRFGNVATMEPID-VSRIPPERWKLKCVFCKKRSGACIQCSKGRCTT 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 194328767  337 AFHVTCAFDRGLEMKtiLAENDEVKFKSYCPKH 369
Cdd:pfam13832  79 AFHVTCAQAAGVYME--PEDWPNVVVIAYCQKH 109

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 194328767  206 VCDVCQSPDgeDGNEMVFCDKCNICVHQACYGI----LKVPEGSWLCRTC 251
Cdd:pfam00628   1 YCAVCGKSD--DGGELVQCDGCDDWFHLACLGPpldpAEIPSGEWLCPEC 48

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 194328767   315 VCSLCNEKF--GASIQCSvkNCRTAFHVTCAFDRGLEmktilaenDEVKFKSYCPKH 369
Cdd:smart00249   1 YCSVCGKPDdgGELLQCD--GCDRWYHQTCLGPPLLE--------EEPDGKWYCPKC 47

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15671    1 CVLCPKKGGAMKSTKSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEKTGACIQCSVKSCKTAF 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 194328767 339 HVTCAFDRGLEMKTIL-AENDEVKFKSYCPKH 369
Cdd:cd15671   81 HVTCAFQHGLEMKTILeDEDDEVKFKSYCPKH 112

Extended PHD finger found in protein Jade-2 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 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, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15705    1 CLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 194328767 339 HVTCAFDRGLEMKTILAENDEVKFKSYCPKH 369
Cdd:cd15705   81 HVTCAFDHGLEMRTTLADNDEVKFKSFCLEH 111

PHD zinc finger-containing protein [General function prediction only];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 100 RVVSEEKSLMFIRPKKYIASSGSEPPalgyvdiRTLADSVcRYDLNDMDAAWLEVTNE-EFKEMGMPELDEYTMERVLEE 178
Cdd:COG5141   99 KFVSKHAPMSEESHDEGKKFIDIEPP-------RGLFFSV-IYDLDEYDTMWLRYLNEsAIDENVSEEAFEIIVTRLEKE 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 179 ---FEQRCYDNMNHAIETEEGLgieydeDVVCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTCALGV 255
Cdd:COG5141  171 wffFEHGLPDKHVEPIEPSDEF------DDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGE 244

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 256 QP--KCLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKN 333
Cdd:COG5141  245 YQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHLLSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFN 323

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 334 CRTAFHVTCAFDRGLEMKTILAEN---DEVKFKSYCPKHSshrkpEEGLGEGAAQE-NGAPE---SSPQSplepygSLEP 406
Cdd:COG5141  324 CTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKHY-----PLGYGRMNGLRyFGYEKlryKNPPT------AIPR 392

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 407 NREEAHRVSVRKQKLQQLEDEFYTFV------NLLDVARALRLPEEVVDfLYQYWKLKRKINFNKPLiTPKKDEEDNLAK 480
Cdd:COG5141  393 KVRAARPRATLFMKLCWKQPPATPSVlsrveaCDLKEKDRQDLPVNIFD-ICKYWEMKRKSEIGGPL-VILPDIVYSLKT 470

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*...
gi 194328767 481 REQDVLFRRLQLFTHLRQDLERVRNLTYMVTRREKIKRSVCKVQEQIF 528
Cdd:COG5141  471 LEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFL 518

Extended PHD finger found in BRPF proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including 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 lysine 4 of histone H3 (K4H3), 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15670    1 CVLCPNKGGAFKQTDDG-RWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKKRMGACIQCHKKNCYTAF 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 194328767 339 HVTCAFDRGLEMK------TILAENDEVKFKSYCPKH 369
Cdd:cd15670   80 HVTCAQQAGLYMKiepvkdPGNGTSDSVRKEAYCDKH 116

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKP-----TRSGTKWVHVSCALWIPEVSIGSPEKMEPItKVSHIPSSRWALVCSLCNEKFGASIQCSVKN 333
Cdd:cd15571    1 CALCPRSGGALKGggalkTTSDGLWVHVVCALWSPEVYFDDGTLLEVE-GVSKIPKRRKKLKCSICGKRGGACIQCSYPG 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 194328767 334 CRTAFHVTCAFDRGLEMKTilaENDEVKFKSYCPKH 369
Cdd:cd15571   80 CPRSFHVSCAIRAGCLFEF---EDGPGNFVVYCPKH 112

Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTkWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSVKNCRTAF 338
Cdd:cd15662    1 CCLCPVVGGALKPTTDGR-WAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQRYGACIQCSNNSCRVAY 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 194328767 339 HVTCAFDRGLEM-----KTILAENDEVKFKSYCPKH 369
Cdd:cd15662   80 HPLCARAAGLCMevadeGGEDPGDQGLRLLSYCPRH 115

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEK-FGASIQCSVKNCRTA 337
Cdd:cd15701    1 CALCPNKGGAFKQTDDG-RWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRgSGACIQCHKANCYTA 79

                         90
                 ....*....|....
gi 194328767 338 FHVTCAFDRGLEMK 351
Cdd:cd15701   80 FHVTCAQQAGLYMK 93

Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSgTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEK-FGASIQCSVKNCRTA 337
Cdd:cd15702    1 CVLCPNKGGAFKKTDD-DRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 194328767 338 FHVTCAFDRGLEMK----TILAEND---EVKFKSYCPKH 369
Cdd:cd15702   80 FHVTCAQKAGLYMKmepvKEVTGGGttfSVRKTAYCDAH 118

PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely 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 Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194328767 206 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTCALGV 255
Cdd:cd15681    1 ICDVCRSPDSEEGNDMVFCDKCNICVHQACYGILKVPEGSWLCRTCVLGI 50

Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITkVSHIPSSRWALVCSLC------NEKFGASIQCSVK 332
Cdd:cd15675    1 CCLCCLRGGALKPTTDG-RWAHVVCAIAIPEVRFSNVPERGPID-ISKIPPARLKLKCIYCskitksMSHMGACIQCSTG 78

                         90       100
                 ....*....|....*....|
gi 194328767 333 NCRTAFHVTCAFDRGLEMKT 352
Cdd:cd15675   79 KCTTSFHVTCAHAAGVQMEP 98

Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKFGASIQCSvkNCRTAF 338
Cdd:cd15663    1 CCLCPVKGGALKPTDVEGLWVHVTCAWFRPEVCFKNEEKMEPAVGLLRIPLSTFLKACVICKQIHGSCTQCC--KCATYF 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 194328767 339 HVTCAFDRGLEMKT-ILAEN--DEVKFKSYCPKH 369
Cdd:cd15663   79 HAMCASRAGYHMELhCLEKNgvQITRMVSYCSFH 112

Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and this non-canonical ePHD finger. It can interact with histones through its PHD fingers.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITkVSHIPSSRW-ALVCSLCNEK----FGASIQCSVKN 333
Cdd:cd15674    1 CELCPNRGGIFKETDTG-RWVHLVCALYTPGVAFGDVDKLSPVT-LTEMNYSKWgARECSLCEDPrfarTGVCISCDAGM 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 194328767 334 CRTAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKH 369
Cdd:cd15674   79 CKSYFHVTCAQREGLLSEATDEEDIADPFYAYCKQH 114

Extended PHD finger found in protein AF-10 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 258 KCLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITkVSHIPSSRWALVCSLCNEK-------FGASIQCS 330
Cdd:cd15708    4 RCELCPHKDGALKRTDNG-GWAHVVCALYIPEVQFANVSTMEPIV-LQSVPHERYNKTCYICDEQgreskaaTGACMTCN 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 194328767 331 VKNCRTAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKHSSHRKPEE 377
Cdd:cd15708   82 KHGCRQAFHVTCAQLAGLLCEEEGNGADNVQYCGYCKYHYSKLKKSK 128

Extended PHD finger found in protein AF-17 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 258 KCLLCPKKGGAMKPTRSGtKWVHVSCALWIPEVSIGSPEKMEPITkVSHIPSSRWALVCSLCNEK-------FGASIQCS 330
Cdd:cd15709    4 RCELCPHKDGALKRTDNG-GWAHVVCALYIPEVQFANVLTMEPIV-LQYVPHDRFNKTCYICEEQgreskaaSGACMTCN 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 194328767 331 VKNCRTAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKHSSHRK 374
Cdd:cd15709   82 RHGCRQAFHVTCAQMAGLLCEEEVLEVDNVKYCGYCKYHFNKMK 125

PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 194328767 204 DVVCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTC 251
Cdd:cd15572    1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRC 48

PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; 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 canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 194328767 202 DEDVVCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTC 251
Cdd:cd15676    5 DEDAVCCICNDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRC 54

PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 194328767 207 CDVCQSPDGEDGNEMVFCD--KCNICVHQACYGILKVPEGSWLCRTC 251
Cdd:cd15574    2 CCVCSDERGWAENPLVYCDghGCNVAVHQACYGIVQVPTGPWFCRKC 48

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        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 194328767  206 VCDVCQSPDgeDGNEMVFCDKCNICVHQACYGI----LKVPEGSWLCRTC 251
Cdd:pfam00628   1 YCAVCGKSD--DGGELVQCDGCDDWFHLACLGPpldpAEIPSGEWLCPEC 48

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 278 WVHVSCALWIPEVSIGSPekmepitKVSHIPSSRWA---LVCSLCNEKfGASIQCSVKNCRTAFHVTCAFDRGLEMktil 354
Cdd:cd15668   24 WVHEDCAVWAPGVYLVGG-------KLYGLEEAVWVakqSVCSSCQQT-GATIGCLHKGCKAKYHYPCAVESGCQL---- 91

                         90
                 ....*....|....*
gi 194328767 355 aenDEVKFKSYCPKH 369
Cdd:cd15668   92 ---DEENFSLLCPKH 103

Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 259 CLLCPKKGGAmKPTRSG-------TKWVHVSCALWIPEVSigspEKMEPITKVSHIPSSRWALV-CSLCnEKFGASIQCS 330
Cdd:cd15664    1 CALCGVYGDD-EPNDAGrllycgqDEWVHINCALWSAEVF----EEDDGSLQNVHSAVSRGRMMkCELC-GKPGATVGCC 74

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 194328767 331 VKNCRTAFHVTCAfdrglemKTILAENDEVKfKSYCPKH 369
Cdd:cd15664   75 LKSCPANYHFMCA-------RKAECVFQDDK-KVFCPAH 105

Extended PHD finger 1 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 first ePHD finger of KMTC2C and KMTC2D. 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 plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 278 WVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRwalVCSLCNeKFGASIQCSVKNCRTAFHVTCAFDRG--LEMKTILA 355
Cdd:cd15665   10 YAHHCCAAWSEGVCQTEDGALENVDKAVAKALSQ---KCSFCL-RYGASISCRMPSCSKSFHFPCAAAAGcfQDIKTLTL 85

                         90
                 ....*....|....
gi 194328767 356 endevkfksYCPKH 369
Cdd:cd15665   86 ---------FCPEH 90

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194328767 277 KWVHVSCALWIPEVSigspekmEPIT-KVSHIPSS--RWALV-CSLCNeKFGASIQCSVKNCRTAFHVTCAFDRG---LE 349
Cdd:cd15666   25 KWVHLNCALWSYEVY-------ETQNgALMNVEEAlrRALTTtCSHCG-RTGATVPCFKPRCANVYHLPCAIKDGcmfFK 96

                         90       100
                 ....*....|....*....|
gi 194328767 350 MKTIlaendevkfksYCPKH 369
Cdd:cd15666   97 DKTM-----------LCPSH 105

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 194328767 206 VCDVCQSPdGEDGNEMVFCDKCNICVHQACYGI---LKVPEGSWLCRTC 251
Cdd:cd15489    1 SCIVCGKG-GDLGGELLQCDGCGKWFHADCLGPplsSFVPNGKWICPVC 48

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 194328767 206 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEG-SWLCRTC 251
Cdd:cd15494    1 KCSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVLEPPPGaLWLCNLC 47

Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 194328767 316 CSLCNEKfGASIQCSVKNCRTAFHVTCAFDRGlemkTILAENDEvkFKSYCPKH 369
Cdd:cd15669   66 CFYCKKK-GASIGCAVKGCRRSFHFPCGLENG----CVTQFFGE--YRSFCWEH 112

PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3); TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53).

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 194328767 206 VCDVCQSPDgeDGNEMVFCDKCNICVHQACYGILKVP--EGSWLCRTC 251
Cdd:cd15522    1 ICPICKKPD--DGSPMIGCDECDDWYHWECVGITDEPpeEDDWFCPKC 46

PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the first PHD finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 194328767 206 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPE----------GSWLCRTC 251
Cdd:cd15561    1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGVIDESDssssasssstEPWFCEPC 56