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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 134 YDLDDLDVAWLQIVNQ-EFRQMGLPELDELTMECVLVE---LESVCEEKMQQAIETEEGLgieydeDVVCDVCRSPEGED 209
Cdd:COG5141  133 YDLDEYDTMWLRYLNEsAIDENVSEEAFEIIVTRLEKEwffFEHGLPDKHVEPIEPSDEF------DDICTKCTSTHNEN 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 210 GNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTCALGVQP--KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCP 287
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHL 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 288 EKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAFHVTCAFDHGLEMKTILAEN---DEVRFKSFCLEHsnt 364
Cdd:COG5141  286 LSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKH--- 362

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 365 stntnstfSSSGLSNGNhvtastaNGAHGGARPEWAAPGLTSELRQDQQNETNGSSDPEQRSVSHLVSVSASERAErdql 444
Cdd:COG5141  363 --------YPLGYGRMN-------GLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSVLSRVE---- 423

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 445 erekvsqrkqklQELEDEFYRLVEPREVAEnlglpvsqvdyLYQFWKLKRKANFNRPLVTLKrDEVDNLAQQEQDVLYRR 524
Cdd:COG5141  424 ------------ACDLKEKDRQDLPVNIFD-----------ICKYWEMKRKSEIGGPLVILP-DIVYSLKTLEDWMSKRR 479

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 583979517 525 LKLFTHLRQDLERVRNLCYMVTRREKMKHTLCDLQEKIFH---------LQIQLLEEDMAGE 577
Cdd:COG5141  480 MREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFLNlnyfpaqrlLQVKIIDLDVDGL 541

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 134 YDLDDLDVAWLQIVNQ-EFRQMGLPELDELTMECVLVE---LESVCEEKMQQAIETEEGLgieydeDVVCDVCRSPEGED 209
Cdd:COG5141  133 YDLDEYDTMWLRYLNEsAIDENVSEEAFEIIVTRLEKEwffFEHGLPDKHVEPIEPSDEF------DDICTKCTSTHNEN 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 210 GNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTCALGVQP--KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCP 287
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHL 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 288 EKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAFHVTCAFDHGLEMKTILAEN---DEVRFKSFCLEHsnt 364
Cdd:COG5141  286 LSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKH--- 362

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 365 stntnstfSSSGLSNGNhvtastaNGAHGGARPEWAAPGLTSELRQDQQNETNGSSDPEQRSVSHLVSVSASERAErdql 444
Cdd:COG5141  363 --------YPLGYGRMN-------GLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSVLSRVE---- 423

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 445 erekvsqrkqklQELEDEFYRLVEPREVAEnlglpvsqvdyLYQFWKLKRKANFNRPLVTLKrDEVDNLAQQEQDVLYRR 524
Cdd:COG5141  424 ------------ACDLKEKDRQDLPVNIFD-----------ICKYWEMKRKSEIGGPLVILP-DIVYSLKTLEDWMSKRR 479

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 583979517 525 LKLFTHLRQDLERVRNLCYMVTRREKMKHTLCDLQEKIFH---------LQIQLLEEDMAGE 577
Cdd:COG5141  480 MREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFLNlnyfpaqrlLQVKIIDLDVDGL 541

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTC 243
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 583979517   198 VCDVCRSPEgeDGNEMVFCDKCNVCVHQACYGI---LKVPQGNWLCRTC 243
Cdd:smart00249   1 YCSVCGKPD--DGGELLQCDGCDRWYHQTCLGPpllEEEPDGKWYCPKC 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 583979517 251 CLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAF 330
Cdd:cd15671    1 CVLCPKKGGAMKSTKSGTKWVHVSCALWIPEVSIGCPEKMEPITKISHIPMSRWALVCVLCKEKTGACIQCSVKSCKTAF 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 583979517 331 HVTCAFDHGLEMKTIL-AENDEVRFKSFCLEH 361
Cdd:cd15671   81 HVTCAFQHGLEMKTILeDEDDEVKFKSYCPKH 112

Extended PHD finger found in protein Jade-1 and similar proteins; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. 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 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 ASA 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 plant homeodomain (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 583979517 248 QPKCLLCPKRGGALKPTRSGTKWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCI 327
Cdd:cd15704    1 QPKCLLCPKKGGAMKPTRSGTKWVHVSCALWIPEVSIGSPEKMEPITKVSHIPSSRWALVCSLCNEKVGASIQCSVKNCR 80

                         90       100       110
                 ....*....|....*....|....*....|....
gi 583979517 328 VAFHVTCAFDHGLEMKTILAENDEVRFKSFCLEH 361
Cdd:cd15704   81 TAFHVTCAFDRGLEMKTILAENDEVKFKSYCPKH 114

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 134 YDLDDLDVAWLQIVNQ-EFRQMGLPELDELTMECVLVE---LESVCEEKMQQAIETEEGLgieydeDVVCDVCRSPEGED 209
Cdd:COG5141  133 YDLDEYDTMWLRYLNEsAIDENVSEEAFEIIVTRLEKEwffFEHGLPDKHVEPIEPSDEF------DDICTKCTSTHNEN 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 210 GNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTCALGVQP--KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCP 287
Cdd:COG5141  207 SNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCIYGEYQirCCSFCPSSDGAFKQTSDG-RWGHVICAMFNPELSFGHL 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 288 EKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAFHVTCAFDHGLEMKTILAEN---DEVRFKSFCLEHsnt 364
Cdd:COG5141  286 LSKDPIDNIASVSSSRWKLGCLICKEFGGTCIQCSYFNCTRAYHVTCARRAGYFDLNIYSHNgisYCIDHEPLCRKH--- 362

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 365 stntnstfSSSGLSNGNhvtastaNGAHGGARPEWAAPGLTSELRQDQQNETNGSSDPEQRSVSHLVSVSASERAErdql 444
Cdd:COG5141  363 --------YPLGYGRMN-------GLRYFGYEKLRYKNPPTAIPRKVRAARPRATLFMKLCWKQPPATPSVLSRVE---- 423

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 445 erekvsqrkqklQELEDEFYRLVEPREVAEnlglpvsqvdyLYQFWKLKRKANFNRPLVTLKrDEVDNLAQQEQDVLYRR 524
Cdd:COG5141  424 ------------ACDLKEKDRQDLPVNIFD-----------ICKYWEMKRKSEIGGPLVILP-DIVYSLKTLEDWMSKRR 479

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 583979517 525 LKLFTHLRQDLERVRNLCYMVTRREKMKHTLCDLQEKIFH---------LQIQLLEEDMAGE 577
Cdd:COG5141  480 MREVAKALQDQYQLLTLVESTAKRQLLKCQLSNLRKKFLNlnyfpaqrlLQVKIIDLDVDGL 541

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 583979517 251 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAF 330
Cdd:cd15670    1 CVLCPNKGGAFKQTDDG-RWAHVVCALWIPEVSFANTVFLEPIDGIQNIPKARWKLTCYICKKRMGACIQCHKKNCYTAF 79

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 583979517 331 HVTCAFDHGLEMK------TILAENDEVRFKSFCLEH 361
Cdd:cd15670   80 HVTCAQQAGLYMKiepvkdPGNGTSDSVRKEAYCDKH 116

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 583979517 251 CLLCPKRGGALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSMPSCIVAF 330
Cdd:cd15662    1 CCLCPVVGGALKPTTDGR-WAHLACAIWIPETCLLDVKTMEPVDGINAISKERWELSCTICKQRYGACIQCSNNSCRVAY 79

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 583979517 331 HVTCAFDHGLEM-----KTILAENDEVRFKSFCLEH 361
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 583979517 251 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREH-TGTCIQCSMPSCIVA 329
Cdd:cd15701    1 CALCPNKGGAFKQTDDG-RWAHVVCALWIPEVCFANTVFLEPIDSIEHIPPARWKLTCYICKQRgSGACIQCHKANCYTA 79

                         90
                 ....*....|....
gi 583979517 330 FHVTCAFDHGLEMK 343
Cdd:cd15701   80 FHVTCAQQAGLYMK 93

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTC 243
Cdd:cd15680    1 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTC 46

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 583979517 251 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREH-TGTCIQCSMPSCIVA 329
Cdd:cd15702    1 CVLCPNKGGAFKKTDD-DRWGHVVCALWIPEVGFANTVFIEPIDGVRNIPPARWKLTCYLCKQKgVGACIQCHKANCYTA 79

                         90
                 ....*....|....
gi 583979517 330 FHVTCAFDHGLEMK 343
Cdd:cd15702   80 FHVTCAQKAGLYMK 93

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTCALGV 247
Cdd:cd15681    1 ICDVCRSPDSEEGNDMVFCDKCNICVHQACYGILKVPEGSWLCRTCVLGI 50

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTC 243
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 583979517 251 CLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITkVSHIPASRW-ALSCSLCRE----HTGTCIQCSMPS 325
Cdd:cd15674    1 CELCPNRGGIFKETDTG-RWVHLVCALYTPGVAFGDVDKLSPVT-LTEMNYSKWgARECSLCEDprfaRTGVCISCDAGM 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 583979517 326 CIVAFHVTCAFDHGLEMKTILAENDEVRFKSFCLEH 361
Cdd:cd15674   79 CKSYFHVTCAQREGLLSEATDEEDIADPFYAYCKQH 114

Extended PHD finger found in protein AF-10 and AF-17; The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. 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 the human counterpart of 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-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 plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. 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 Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 583979517 251 CLLCPKRGGALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITkVSHIPASRWALSCSLCREH-------TGTCIQCSM 323
Cdd:cd15672    1 CELCPHKDGALKRTDNGG-WAHVVCALYIPEVRFGNVATMEPII-LQDVPQDRFNKTCYICEEQgreskasTGACMQCNK 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 583979517 324 PSCIVAFHVTCAFDHGLEMKTILAENDEVRFKSFCLEH 361
Cdd:cd15672   79 SGCKQSFHVTCAQMAGLLCEEAGNYSDNVKYCGYCSYH 116

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 583979517 250 KCLLCPKRGGALKPTRSGtKWVHVSCALWIPEVSIGCPEKMEPITkVSHIPASRWALSCSLCREH-------TGTCIQCS 322
Cdd:cd15708    4 RCELCPHKDGALKRTDNG-GWAHVVCALYIPEVQFANVSTMEPIV-LQSVPHERYNKTCYICDEQgreskaaTGACMTCN 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 583979517 323 MPSCIVAFHVTCAFDHGLEMKTILAENDEVRFKSFCLEH 361
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 583979517 251 CLLCPKRGGALKPTRSgTKWVHVSCALWIPEVSIGCPEKMEPItKVSHIPASRWALSCSLCREH----TGTCIQCSMPSC 326
Cdd:cd15713    1 CCLCSLRGGALQRAND-DKWVHVMCAVAVLEARFVNIAERSPV-DVSKIPLQRFKLKCIFCKKRrkrtAGCCVQCSHGRC 78

                         90
                 ....*....|....*..
gi 583979517 327 IVAFHVTCAFDHGLEMK 343
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 583979517 196 DVVCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQGNWLCRTC 243
Cdd:cd15572    1 DAVCCICLDGECQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRRC 48

PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana 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. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, 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 583979517 199 CDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKV-PQGNWLCRTC 243
Cdd:cd15495    2 CAVCNEGEDDDNNPLITCNRCQISVHQKCYGIREVdPDGSWVCRAC 47

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 583979517  198 VCDVCRSPEgeDGNEMVFCDKCNVCVHQACYGI----LKVPQGNWLCRTC 243
Cdd:pfam00628   1 YCAVCGKSD--DGGELVQCDGCDDWFHLACLGPpldpAEIPSGEWLCPEC 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 583979517 260 ALKPTRSGTkWVHVSCALWIPEVSIGCPEKMEPITKVSHIPASRWALSCSLCREHTGTCIQCSmpSCIVAFHVTCAFD 337
Cdd:cd15667   25 ALKCTSNGT-WCHVLCALFNEDIKFGNSKSLQPILNTESVLLKGSRQKCEICKVSGGGLVKCE--VCDDRFHVSCAQD 99

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 583979517 198 VCDVCRSPEGEDgnEMVFCDKCNVCVHQACYGILKVPQGNWLCRTC 243
Cdd:cd15529    1 TCTKCGDPHDED--KMMFCDQCDRGYHTFCVGLRSIPDGRWICPLC 44

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 583979517 198 VCDVCRSPeGEDGNEMVFCDKCNVCVHQACYGI---LKVPQGNWLCRTC 243
Cdd:cd15489    1 SCIVCGKG-GDLGGELLQCDGCGKWFHADCLGPplsSFVPNGKWICPVC 48

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACY-----GILKVPQGNWLCRTC 243
Cdd:cd15578    1 VCTVCQDGSSESPNEIVLCDKCGQGYHQLCHnpkidSSVLDPDVPWLCRQC 51

PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACY------GILKVPQGNWLCRTC 243
Cdd:cd15502    1 VCIVCQRGHSPKSNRIVFCDGCNTPYHQLCHdpsiddEVVEDPDAEWFCKKC 52

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 583979517 270 WVHVSCALWIPEVSIGCPEKMEPITKvshipASRWALS--CSLCReHTGTCIQCSMPSCIVAFHVTCAFDHG--LEMKTI 345
Cdd:cd15665   10 YAHHCCAAWSEGVCQTEDGALENVDK-----AVAKALSqkCSFCL-RYGASISCRMPSCSKSFHFPCAAAAGcfQDIKTL 83

                         90
                 ....*....|....*.
gi 583979517 346 LAendevrfksFCLEH 361
Cdd:cd15665   84 TL---------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 583979517 251 CLLCpKRGGALKPTRSG-------TKWVHVSCALWIPEV---SIGCPEKMEpitkvshiPASRWALS--CSLCREhTGTC 318
Cdd:cd15666    1 CVLC-GGEGDGDTDGPGrllnldvDKWVHLNCALWSYEVyetQNGALMNVE--------EALRRALTttCSHCGR-TGAT 70

                         90
                 ....*....|....*..
gi 583979517 319 IQCSMPSCIVAFHVTCA 335
Cdd:cd15666   71 VPCFKPRCANVYHLPCA 87

Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B); The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B 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. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this 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 583979517 251 CLLCPKRGGAlKPTRSG-------TKWVHVSCALWIPEVSigcpEKMEPITKVSHIPASRW-ALSCSLCREhTGTCIQCS 322
Cdd:cd15694    1 CALCLKYGDA-DSKDAGrllyigqNEWTHVNCAIWSAEVF----EENDGSLKNVHAAVARGrQMRCEHCQK-IGATVGCC 74

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 583979517 323 MPSCIVAFHVTCAfdhglEMKTILAENDEvrfKSFCLEH 361
Cdd:cd15694   75 LSACLSNFHFMCA-----RASRCCFQDDK---KVFCQKH 105

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 583979517 198 VCDVCRSPEGEDGNEMVFCDKCNVCVHQACYGILKVPQ----------GNWLCRTC 243
Cdd:cd15561    1 ICCVCLGDRSNDADEIIECDKCGISVHEGCYGVIDESDssssasssstEPWFCEPC 56

PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B; BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 583979517 199 CDVCRspEGEDGNEMVFCDKCNVCVHQACY--GILKVPQGNWLCRTC 243
Cdd:cd15544    2 CKVCR--KKGDPDNMILCDGCDKAFHLYCLrpALREVPSGDWFCPAC 46