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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 209 YDLDEIDAYWLELLN-SELKEMEKPELDELTLERVLEELETLCHQNMAQAIETqegLGIEYDEDVVCDVCRSPEGEDGNE 287
Cdd:COG5141   133 YDLDEYDTMWLRYLNeSAIDENVSEEAFEIIVTRLEKEWFFFEHGLPDKHVEP---IEPSDEFDDICTKCTSTHNENSNA 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 288 MVFCDKCNVCVHQACYGILKVPTGSWLCRTCALGVQP--KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKM 365
Cdd:COG5141   210 IVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHLLSK 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 366 EPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAFHVTCAFDRGLEMRTILADN---DEVKFKSLCQEHSDGG-- 440
Cdd:COG5141   289 DPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKHYPLGyg 368

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 441 --------------PRSEPTSEP--VEPSQAVEDLEKVTLRKQrlQQLEENFYELVEPAEVAE--RLDLAEALVDfIYQY 502
Cdd:COG5141   369 rmnglryfgyeklrYKNPPTAIPrkVRAARPRATLFMKLCWKQ--PPATPSVLSRVEACDLKEkdRQDLPVNIFD-ICKY 445

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1274095890 503 WKLKRRANANQPlLTPKTDEVDNLAQQEQDVLYRRLKLFTHLRQDLERVRNLCYMVTRRERTKHTICKLQEQIFHL 578
Cdd:COG5141   446 WEMKRKSEIGGP-LVILPDIVYSLKTLEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFLNL 520

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 209 YDLDEIDAYWLELLN-SELKEMEKPELDELTLERVLEELETLCHQNMAQAIETqegLGIEYDEDVVCDVCRSPEGEDGNE 287
Cdd:COG5141   133 YDLDEYDTMWLRYLNeSAIDENVSEEAFEIIVTRLEKEWFFFEHGLPDKHVEP---IEPSDEFDDICTKCTSTHNENSNA 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 288 MVFCDKCNVCVHQACYGILKVPTGSWLCRTCALGVQP--KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKM 365
Cdd:COG5141   210 IVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHLLSK 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 366 EPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAFHVTCAFDRGLEMRTILADN---DEVKFKSLCQEHSDGG-- 440
Cdd:COG5141   289 DPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKHYPLGyg 368

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 441 --------------PRSEPTSEP--VEPSQAVEDLEKVTLRKQrlQQLEENFYELVEPAEVAE--RLDLAEALVDfIYQY 502
Cdd:COG5141   369 rmnglryfgyeklrYKNPPTAIPrkVRAARPRATLFMKLCWKQ--PPATPSVLSRVEACDLKEkdRQDLPVNIFD-ICKY 445

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1274095890 503 WKLKRRANANQPlLTPKTDEVDNLAQQEQDVLYRRLKLFTHLRQDLERVRNLCYMVTRRERTKHTICKLQEQIFHL 578
Cdd:COG5141   446 WEMKRKSEIGGP-LVILPDIVYSLKTLEDWMSKRRMREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFLNL 520

PHD finger found in protein Jade-2 and similar proteins; 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 Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15680     1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 46

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
                   ....*....|....*....|....*....|....*....|....*....
gi 1274095890  273 VCDVCRSPEgeDGNEMVFCDKCNVCVHQACYGI---LKVPTGSWLCRTC 318
Cdd:smart00249   1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPpllEEEPDGKWYCPKC 47

Patatin-like phospholipase domain containing protein 1; Members of this family share a patatin domain, initially discovered in potato tubers. Some members of PNPLA1 subfamily do not have the lipase consensus sequence Gly-X-Ser-X-Gly which is essential for hydrolase activity. This family includes PNPLA1 from Homo sapiens and Gallus gallus. Currently, there is no literature available on the physiological role, structure, or enzymatic activity of PNPLA1. It is expressed in various human tissues in low mRNA levels.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 716 LPAKKKPSpLQDGPSARTTPdKQPKKAWA--QDGKGTQGPPMRKP---PRRTSSHLPSSPAAGDCPVPATLESPPPLASE 790
Cdd:cd07219   285 CPQRSQPS-LQDGQASLEES-WQPHLARApkGDGRGLHDPPLSPPlaaPESTAEWVVESPVSSPASPLESSPSLPGSLTD 362

                          90
                  ....*....|....*....
gi 1274095890 791 ILDKTAPMASDLNVQVPGP 809
Cdd:cd07219   363 LSPASLPAVHSLPSSTPGL 381

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 1274095890  383 CSLCKEC--TGTCIQCSMpsCITAFHVTCAFDRGLEmrtiladnDEVKFKSLCQEH 436
Cdd:smart00249   2 CSVCGKPddGGELLQCDG--CDRWYHQTCLGPPLLE--------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 1274095890 326 CLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 405
Cdd:cd15671     1 CVLCPKKGGAMKSTKSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEKTGACIQCSVKSCKTAF 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1274095890 406 HVTCAFDRGLEMRTIL-ADNDEVKFKSLCQEH 436
Cdd:cd15671    81 HVTCAFQHGLEMKTILeDEDDEVKFKSYCPKH 112

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 326 CLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 405
Cdd:cd15706     1 CLLCPKTGGAMKATRTGTKWAHVSCALWIPEVSIACPERMEPITKVSHIPPSRWALVCSLCKLKTGACIQCSVKSCITAF 80

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1274095890 406 HVTCAFDRGLEMRTILADNDEVKFKSLCQEH 436
Cdd:cd15706    81 HVTCAFEHSLEMKTILDEGDEVKFKSYCLKH 111

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 326 CLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 405
Cdd:cd15707     1 CILCPNKGGAMKSTRSGTKWAHVSCALWIPEVSIGCVEKMEPITKISSIPASRWALICVLCRERTGACIQCSVKTCKTAY 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1274095890 406 HVTCAFDRGLEMRTILADN--DEVKFKSLCQEH 436
Cdd:cd15707    81 HVTCGFQHGLEMKTILDEEseDGVKLRSYCQKH 113

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 1274095890 326 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 405
Cdd:cd15670     1 CVLCPNKGGAFKQTDDG-RWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKKRMGACIQCHKKNCYTAF 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1274095890 406 HVTCAFDRGLEMR------TILADNDEVKFKSLCQEH 436
Cdd:cd15670    80 HVTCAQQAGLYMKiepvkdPGNGTSDSVRKEAYCDKH 116

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 347 HVSCALWIPEVSI-GCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAFHVTCAFDRGLEMRTilaDND 425
Cdd:pfam13771   1 HVVCALWSPELVQrGNDSMGFPIEDIEKIPKRRWKLKCYLCKKKGGACIQCSKKNCRRAFHVTCALEAGLLMQF---DED 77

                          90
                  ....*....|.
gi 1274095890 426 EVKFKSLCQEH 436
Cdd:pfam13771  78 NGTFKSYCKKH 88

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 1274095890 326 CLLCPKRGGALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCITAF 405
Cdd:cd15662     1 CCLCPVVGGALKPTTDGR-WAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQRYGACIQCSNNSCRVAY 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1274095890 406 HVTCAFDRGLEMRTILADNDE-----VKFKSLCQEH 436
Cdd:cd15662    80 HPLCARAAGLCMEVADEGGEDpgdqgLRLLSYCPRH 115

PHD finger found in protein Jade-2 and similar proteins; 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 Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15680     1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 46

PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which 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. 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 Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15573     1 VCDVCRSPDSEEGNEMVFCDKCNICVHQACYGIQKIPEGSWLCRTC 46

PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15679     1 VCDVCQSPDGEDGNEMVFCDKCNICVHQACYGILKVPEGSWLCRTC 46

PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins 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. Jade proteins are 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. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that 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. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15492     1 VCDVCLDGESEDDNEIVFCDGCNVAVHQSCYGIPLIPEGDWFCRKC 46

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 1274095890 326 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITkISHIPASRW-ALSCSLCKEC----TGTCIQCSMPS 400
Cdd:cd15674     1 CELCPNRGGIFKETDTG-RWVHLVCALYTPGVAFGDVDKLSPVT-LTEMNYSKWgARECSLCEDPrfarTGVCISCDAGM 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1274095890 401 CITAFHVTCAFDRGLEMRTILADNDEVKFKSLCQEH 436
Cdd:cd15674    79 CKSYFHVTCAQREGLLSEATDEEDIADPFYAYCKQH 114

Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 326 CLLCPKRGGALKPTrSGTKWVHVSCALWIPEVSIGCPEKMEPItKISHIPASRWALSCSLC----KECTGTCIQCSMPSC 401
Cdd:cd15714     1 CCLCNLRGGALQMT-TDERWVHVICAIAVPEARFLNVIERHPV-DVSAIPEQRWKLKCVYCrkrmKKVSGACIQCSYDHC 78

                          90
                  ....*....|....*..
gi 1274095890 402 ITAFHVTCAFDRGLEMR 418
Cdd:cd15714    79 STSFHVTCAHAAGVVME 95

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 1274095890 325 KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITkISHIPASRWALSCSLCKE-------CTGTCIQCS 397
Cdd:cd15708     4 RCELCPHKDGALKRTDNG-GWAHVVCALYIPEVQFANVSTMEPIV-LQSVPHERYNKTCYICDEqgreskaATGACMTCN 81

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1274095890 398 MPSCITAFHVTCAFDRGLEMRTILADNDEVKFKSLCQEH 436
Cdd:cd15708    82 KHGCRQAFHVTCAQLAGLLCEEEGNGADNVQYCGYCKYH 120

Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1274095890 326 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSIGCPEKMEPItKISHIPASRWALSCSLCKE----CTGTCIQCSMPSC 401
Cdd:cd15713     1 CCLCSLRGGALQRAND-DKWVHVMCAVAVLEARFVNIAERSPV-DVSKIPLQRFKLKCIFCKKrrkrTAGCCVQCSHGRC 78

                          90
                  ....*....|....*..
gi 1274095890 402 ITAFHVTCAFDRGLEMR 418
Cdd:cd15713    79 PTSFHASCAQAAGVMMQ 95

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 1274095890 271 DVVCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15572     1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRC 48

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 1274095890 274 CDVCRSPEGEDGNEMVFCD--KCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15574     2 CCVCSDERGWAENPLVYCDghGCNVAVHQACYGIVQVPTGPWFCRKC 48

Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1274095890 335 ALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSmpSCITAFHVTCAFD 412
Cdd:cd15667    25 ALKCTSNGT-WCHVLCALFNEDIKFGNSKSLQPILNTESVLLKGSRQKCEICKVSGGGLVKCE--VCDDRFHVSCAQD 99

PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 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 canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1274095890 271 DVVCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15678     1 DAFCCVCLDDECHNSNVILFCDICNLAVHQECYGVPYIPEGQWLCRCC 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
                  ....*....|....*....|....*....|....
gi 1274095890 286 NEMVFCDKCNVCVHQACYGILKVPTG-SWLCRTC 318
Cdd:pfam13831   2 SPLVYCSKCSVQVHASCYGVPPIPDGdGWKCRRC 35

PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins; PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1274095890 273 VCDVCRSPEGEDgnEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 318
Cdd:cd15529     1 TCTKCGDPHDED--KMMFCDQCDRGYHTFCVGLRSIPDGRWICPLC 44

PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACY-----GILKVPTGSWLCRTC 318
Cdd:cd15578     1 VCTVCQDGSSESPNEIVLCDKCGQGYHQLCHnpkidSSVLDPDVPWLCRQC 51

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 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTG-SWLCRTC 318
Cdd:cd15494     1 KCSVCGEDEEYEDNLLLQCDKCRMMVHMRCYGVLEPPPGaLWLCNLC 47

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 1274095890 273 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVP----------TGSWLCRTC 318
Cdd:cd15561     1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGVIDESdssssassssTEPWFCEPC 56

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 1274095890 326 CLLCPKRGGALkPTRSG-------TKWVHVSCALWIPEVSigcpEKMEPITKISHIPASRW-ALSCSLCKEcTGTCIQCS 397
Cdd:cd15664     1 CALCGVYGDDE-PNDAGrllycgqDEWVHINCALWSAEVF----EEDDGSLQNVHSAVSRGrMMKCELCGK-PGATVGCC 74