PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15543     2 CRKCGLSDHPEWILLCDR--CDAGYHTACLRPPLMIIPDGNWFCPPC 46

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920  2090 EEV---LRTTPSKSKQTSRVMPESPAQnSAPSTSGLQEPHRKRLPMPTMHPPLLRHQFPISAGPSHSPASL-------VP 2159
Cdd:pfam09770  197 EEVeaaMRAQAKKPAQQPAPAPAQPPA-APPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILqrpqspqPD 275

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 665408920  2160 PHAAQGMHPMLQRHLSQTVPPPQAMHLLQN--ALSAPLGQPLGCGNYGSGPNSAQHLP 2215
Cdd:pfam09770  276 PAQPSIQPQAQQFHQQPPPVPVQPTQILQNpnRLSAARVGYPQNPQPGVQPAPAHQAH 333

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15543     2 CRKCGLSDHPEWILLCDR--CDAGYHTACLRPPLMIIPDGNWFCPPC 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 665408920   1373 CQKCGKSDHPEWILLCDtpTCNKGYHCSCLSP-VLFYIPEGDWHCPPC 1419
Cdd:smart00249    2 CSVCGKPDDGGELLQCD--GCDRWYHQTCLGPpLLEEEPDGKWYCPKC 47

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920  2090 EEV---LRTTPSKSKQTSRVMPESPAQnSAPSTSGLQEPHRKRLPMPTMHPPLLRHQFPISAGPSHSPASL-------VP 2159
Cdd:pfam09770  197 EEVeaaMRAQAKKPAQQPAPAPAQPPA-APPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILqrpqspqPD 275

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 665408920  2160 PHAAQGMHPMLQRHLSQTVPPPQAMHLLQN--ALSAPLGQPLGCGNYGSGPNSAQHLP 2215
Cdd:pfam09770  276 PAQPSIQPQAQQFHQQPPPVPVQPTQILQNpnRLSAARVGYPQNPQPGVQPAPAHQAH 333

PHD finger found in Remodeling and spacing factor 1 (Rsf-1); Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15543     2 CRKCGLSDHPEWILLCDR--CDAGYHTACLRPPLMIIPDGNWFCPPC 46

PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1); PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15536     2 CEVCGRSDREDRLLLCDG--CDAGYHMECLTPPLDEVPIEEWFCPEC 46

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15545     2 CQICRSGDNEDQLLLCDG--CDRGYHTYCFKPKMTNVPEGDWFCPEC 46

PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A); BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, 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 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15629     2 CLVCRKGDNDEYLLLCDG--CDRGCHMYCHRPKMLQVPEGDWFCPNC 46

PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins; Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15605     2 CHTCGRGDGEESMLLCDG--CDDSYHTFCLLPPLSEVPKGDWRCPKC 46

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2; UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGD-WHCPPC 1419
Cdd:cd15525     2 CHVCGGKQDPEKQLLCDE--CDMAYHLYCLDPPLTSLPDDDeWYCPDC 47

PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B); BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, 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 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15630     3 CQICRKGDNEELLLLCDG--CDKGCHTYCHRPKITTIPEGDWFCPAC 47

PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A); KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPCQQE 1422
Cdd:cd15602     2 CLFCGRGNNEDKLLLCDG--CDDSYHTFCLIPPLPDVPKGDWRCPKCVAE 49

PHD finger 2 found in d4 gene family proteins; The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15530     2 CSLCGTSENDDQLLFCDD--CDRGYHMYCLSPPMSEPPEGSWSCHLC 46

PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (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 plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15510     2 CQACRQPGDDTKMLVCET--CDKGYHTSCLRPVMSSIPKYGWKCKNC 46

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2); UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEG-DWHCPPC 1419
Cdd:cd15617     2 CYVCGGKQDAHMQLLCDE--CNMAYHIYCLNPPLDKIPEDeDWYCPSC 47

PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins; Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHpewILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15532     2 CRVCKDGGE---LLCCDG--CPSSYHLHCLNPPLAEIPDGDWFCPRC 43

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 665408920 1373 CQKCGKSDHPEWILLCDtpTCNKGYHCSCLSpvLFYIPEGDWHCPPC 1419
Cdd:cd15529     2 CTKCGDPHDEDKMMFCD--QCDRGYHTFCVG--LRSIPDGRWICPLC 44

PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 665408920 1373 CQKCGKS--DHPEWILLCDTpTCNKGYHCSCLSPVLF--YIPEGD--WHCPPC 1419
Cdd:cd15504     2 CAKCQSGeaSPDNDILLCDG-GCNRAYHQKCLEPPLLteDIPPEDegWLCPLC 53

PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1); UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIP-EGDWHCPPC 1419
Cdd:cd15616     2 CHVCGGKQDPDKQLMCDE--CDMAFHIYCLNPPLSSIPdDEDWYCPEC 47

PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D); KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15595     2 CQTCRKPGEDSKMLVCEA--CDKGYHTFCLKPAMESLPTDSWKCKAC 46

PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 665408920 1373 CQKCGKsdhPEWILLCDTPTCNKGYHCSCLSpvLFYIPEGDWHCP 1417
Cdd:cd15568     2 CFRCGD---GGDLVLCDFKGCPKVYHLSCLG--LEKPPGGKWICP 41

pneumococcal surface protein PspC, choline-binding form; The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. The other form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920  882 KRIKMRPKTTNAESRRKVEAQKTQIEETTsssgEDDARirrkciAPHTKTKPTLE-EIIERKLK-KSIEMDLPektteKV 959
Cdd:NF033838  131 KKDTLEPGKKVAEATKKVEEAEKKAKDQK----EEDRR------NYPTNTYKTLElEIAESDVEvKKAELELV-----KE 195

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920  960 MEMPTQLMQKTREATPPIISlspqKKTPITKpLKKnllTQLRQEESEEETIPRKRTNSETLVPAIPASNVLCQPDERHRK 1039
Cdd:NF033838  196 EAKEPRDEEKIKQAKAKVES----KKAEATR-LEK---IKTDREKAEEEAKRRADAKLKEAVEKNVATSEQDKPKRRAKR 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 1040 RRSSEDA------NEAFSKESSPTEVPPSAVSEKlkrnNEQDIQEEVEdplamSVKDSLRSAKDQspvpegsaRRSGRRG 1113
Cdd:NF033838  268 GVLGEPAtpdkkeNDAKSSDSSVGEETLPSPSLK----PEKKVAEAEK-----KVEEAKKKAKDQ--------KEEDRRN 330

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 1114 GPAVIHSELPQPKRTRGGARDKMQPEVNAELKQESEDDEKI-STKIKSEAK------------DDPAPESPENRKKPEEK 1180
Cdd:NF033838  331 YPTNTYKTLELEIAESDVKVKEAELELVKEEAKEPRNEEKIkQAKAKVESKkaeatrlekiktDRKKAEEEAKRKAAEED 410

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 665408920 1181 PIKEEPNEEPKPKvgrgrgPRKKREVdttniiETNDSETPVRQ--SRRIAQQKIKEEAERRKQEEVALRTMKQ 1251
Cdd:NF033838  411 KVKEKPAEQPQPA------PAPQPEK------PAPKPEKPAEQpkAEKPADQQAEEDYARRSEEEYNRLTQQQ 471

PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2); NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 665408920 1373 CQKCGKSDHpewILLCDTPTCNKGYHCSCLSpvLFYIPEGDWHCP 1417
Cdd:cd15660     2 CFRCGDGGQ---LVLCDRKSCTKAYHLSCLG--LTKRPFGKWECP 41

PHD finger 3 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 third PHD finger.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 665408920 1373 CQKCGKSDHPEWILLCDTptCNKGYHCSCLSPVLFYIPEG---DWHCPPC 1419
Cdd:cd15563     2 CCVCKQTGDNSQLVRCDE--CKLCYHFGCLDPPLKKSPKQrgyGWVCEEC 49

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 665408920 1396 GYHCSCLSPVLFYIPEGDWHCPPCQQEQLIAALERQL 1432
Cdd:cd04718     1 GFHLCCLRPPLKEVPEGDWICPFCEVEKSGQSAMPQL 37

large tegument protein UL36; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2069 RMVEEEEQFSAEVAARELPGAEEVLRTTPSKSKQTSRVMPESPAQNSAPS-----TSGLQEPHRKRLPMPTmhPPLlrhq 2143
Cdd:PHA03247 2482 RPAEARFPFAAGAAPDPGGGGPPDPDAPPAPSRLAPAILPDEPVGEPVHPrmltwIRGLEELASDDAGDPP--PPL---- 2555

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2144 fpISAGPSHSPASLVPP--HAAQGMHPMLQRHLSQTVPPPQamhllQNALSAPLGQPlgcgnyGSGPNSAQhlplvmsmP 2221
Cdd:PHA03247 2556 --PPAAPPAAPDRSVPPprPAPRPSEPAVTSRARRPDAPPQ-----SARPRAPVDDR------GDPRGPAP--------P 2614

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2222 SAAAAAAHLMQSAVASATARPVETASGNPASDPKPRGRRKKVTPLRDQLQKQQTAAAVTAATSSTT----PGSAPSEKVK 2297
Cdd:PHA03247 2615 SPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPqrprRRAARPTVGS 2694

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2298 AQPLFKPHeDAAPSAPASQASVITRMPSLLPPAHGRNHGPPSGLYPSSAdlarfygQVANQQPIPAVPGSR-SPSSTSGP 2376
Cdd:PHA03247 2695 LTSLADPP-PPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPP-------AVPAGPATPGGPARPaRPPTTAGP 2766

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2377 PRhllrpqmppglppPHASLRPTYGPPPplRGSGPPTSTPSTTTNSRPAYLHGAEHHGGPSGPPmggvfSSGPPPARHAT 2456
Cdd:PHA03247 2767 PA-------------PAPPAAPAAGPPR--RLTRPAVASLSESRESLPSPWDPADPPAAVLAPA-----AALPPAASPAG 2826

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2457 PHLNPYRAPPIYGNPNYSPRLGGAPGTGSMRPGAVDYVAGPRGYSPYGYYPPPPPLSTPSAHAATSSVIVSAPhtLTPTN 2536
Cdd:PHA03247 2827 PLPPPTSAQPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESFA--LPPDQ 2904

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408920 2537 HSVPTLTHGKTPPQQTPTqssgPPPAAAPPPTITSETSSHKPPLASVITSKKLTTLEAYPIRKSPIAVVADVSGPAEPTR 2616
Cdd:PHA03247 2905 PERPPQPQAPPPPQPQPQ----PPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVP 2980

                         570       580       590       600
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 2617 SPAPIAEedsgsahdtrAPSSATGTAVVGEFSGLVSYFSSQQDDYDT 2663
Cdd:PHA03247 2981 QPAPSRE----------APASSTPPLTGHSLSRVSSWASSLALHEET 3017

PHD finger found in PHD finger protein 21B (PHF21B); PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.

                          10        20
                  ....*....|....*....|....*...
gi 665408920 1392 TCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15524    16 TCPRAYHLDCLDPPLKTAPKGVWVCPKC 43

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 665408920 1373 CQKCGKSDHPE--WILLCDTptCNKGYHCSCLSPV----LFYIPEGDWHCPPC 1419
Cdd:cd15502     2 CIVCQRGHSPKsnRIVFCDG--CNTPYHQLCHDPSiddeVVEDPDAEWFCKKC 52

PHD finger found in transcription intermediary factor 1-beta (TIF1-beta); TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 665408920 1373 CQKCGKsdhpewILLCDTptCNKGYHCSCLSPVLFYIPEGDWHCPPC 1419
Cdd:cd15623     5 CQKAGA------LVMCDQ--CEFCFHLDCHLPALQEVPGEDWKCLLC 43