UBR-box found in RING-type E3 ubiquitin-protein ligase UBR7 and similar proteins; UBR7 (EC 2.3.2.27; also called N-recognin-7) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR7 may play an important role in spermiogenesis and fertilization.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149025393  45 KCSYSQGSvKRQALYACSTCTPEG-EEPAGICLACSYECHGSHKLFELYTKRNFRCDCGNSKFKNLECKLFP 115
Cdd:cd19677    1 ECTYSKGY-IRQAVYACLTCTPAGaDQPAGICLACSLSCHEGHELEELYTKRNFRCDCGNSKFPSNPCKLFP 71

UBR-box found in RING-type E3 ubiquitin-protein ligase UBR7 and similar proteins; UBR7 (EC 2.3.2.27; also called N-recognin-7) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR7 may play an important role in spermiogenesis and fertilization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149025393  45 KCSYSQGSvKRQALYACSTCTPEG-EEPAGICLACSYECHGSHKLFELYTKRNFRCDCGNSKFKNLECKLFP 115
Cdd:cd19677    1 ECTYSKGY-IRQAVYACLTCTPAGaDQPAGICLACSLSCHEGHELEELYTKRNFRCDCGNSKFPSNPCKLFP 71

Putative zinc finger in N-recognin (UBR box); This region is found in E3 ubiquitin ligases that recognize N-recognins.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149025393   56 QALYACSTCTPEgeEPAGICLACSYEC-HGSHKlFELYTKRN-FRCDCGNSKFKNLE--CKL 113
Cdd:pfam02207   9 QPVYRCLTCSLD--PTCVICYSCFINCdHEGHD-YELFTSRGgGCCDCGDPEAWKEEgfCKL 67

UBR-box found in RING-type E3 ubiquitin-protein ligase UBR7 and similar proteins; UBR7 (EC 2.3.2.27; also called N-recognin-7) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR7 may play an important role in spermiogenesis and fertilization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149025393  45 KCSYSQGSvKRQALYACSTCTPEG-EEPAGICLACSYECHGSHKLFELYTKRNFRCDCGNSKFKNLECKLFP 115
Cdd:cd19677    1 ECTYSKGY-IRQAVYACLTCTPAGaDQPAGICLACSLSCHEGHELEELYTKRNFRCDCGNSKFPSNPCKLFP 71

UBR-box found in UBR4, UBR5, UBR6/FBOX11, UBR7 and similar proteins; This family includes UBR4 (EC 2.3.2.27), UBR5 (EC 2.3.2.26), UBR6/FBOX11 and UBR7 (EC 2.3.2.27). Both UBR4 (also called 600 kDa retinoblastoma protein-associated factor, or N-recognin-4, or retinoblastoma-associated factor of 600 kDa, or RBAF600, or p600, or zinc finger UBR1-type protein 1) and UBR7 (also called N-recognin-7) are RING-type E3 ubiquitin ligases of the Arg/N-end rule degradation pathway. They recognize and bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR5 (also called E3 ubiquitin-protein ligase, HECT domain-containing 1, E3 ligase identified by differential display (EDD), hyperplastic discs protein homolog (HYD), progestin-induced protein, or N-recognin-5) is a HECT (homologous to E6-AP C-terminus)-type E3 ubiquitin-protein ligase that acts as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. It is required for Wnt signal responses in Drosophila and human cell lines downstream of activated Armadillo/beta-catenin. It also plays a key role in ciliogenesis by regulating centriolar satellite stability and primary cilia. UBR6 (also called FBOX11, protein arginine N-methyltransferase 9 (PRMT9), or vitiligo-associated protein 1 (VIT-1)), is an E3 ubiquitin ligase and a type II methyltransferase, which functions as a key regulator of tumor initiation and progression. UBR6 is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. UBR6 does not bind N-terminal signals.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 149025393  46 CSYS--QGSVKRQALYACSTCTPEGeePAGICLACSYECHGSHKLFELYTkRNFRCDCGNSkfKNLECKLFP 115
Cdd:cd19671    1 CTFEktGRKYIKQPWYHCYTCGLID--GLGVCEACARKCHKGHDLVYIGY-SNFYCDCGSS--GPGKCKCES 67

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

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 149025393 134 YCICKRPYpdpedEVPDEMIQCVVCEDWFHGRHLGAIPPESGDFQEMVCQSC 185
Cdd:cd15554    1 YCICRQPY-----DVTRFMIECDVCKDWFHGSCVGVEEHQANDIERYHCPNC 47

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

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 149025393 134 YCICKRPYPDPEdevpdEMIQCVVCEDWFHGRHLGAIPPESGDFQEMVCQSC 185
Cdd:cd15560    1 YCICRTPYDESQ-----FYIGCDRCQDWFHGRCVGILQSEAEKIDEYVCPQC 47

PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3; PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 149025393 134 YCICKRPYPDpedevpDEMIQCVVCEDWFHGRHLGAIPPESGDF----QEMVCQSC 185
Cdd:cd15552    1 YCICRKPHNN------RFMICCDRCEEWFHGDCVGITEAQGKEMeeniEEYVCPKC 50

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 149025393 135 CICKRPYPDPedevpDEMIQCVVCEDWFHGRHLGAIPPESGDFQEMVCQSC 185
Cdd:cd15489    3 IVCGKGGDLG-----GELLQCDGCGKWFHADCLGPPLSSFVPNGKWICPVC 48

UBR-box found in RING-type E3 ubiquitin-protein ligase UBR4 and similar proteins; UBR4 (EC 2.3.2.27; also called 600 kDa retinoblastoma protein-associated factor, N-recognin-4, retinoblastoma-associated factor of 600 kDa, RBAF600, p600, or zinc finger UBR1-type protein 1) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR4 acts as a multifunctional protein with roles in anoikis, viral transformation, and protein degradation, as well as in neurogenesis, neuronal migration, neuronal signaling, and survival. The family also includes Arabidopsis thaliana auxin transport protein BIG (also called protein attenuated shade avoidance 1, protein corymbosa1, protein dark over-expression of cab 1, protein low phosphate-resistant root 1, protein transport inhibitor response 3, or protein umbrella 1). It is a calossin-like protein required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses in Arabidopsis.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 149025393  44 EKCSYSQG--SVKRQALYACSTCTPEGEEpaGICLACSYECHGSHKLFELYTKRnFRCDCGNSKFKNLeCK 112
Cdd:cd19674    1 NVCTFASTgkNYARQHWYECYTCFLNGNE--GVCEVCARVCHKGHDLVYSKTSS-FFCDCGAGGGPSK-CK 67

PHD finger found in CXXC-type zinc finger protein 1 (Cfp1); Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide.

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                 ....*....|....*....|....*....|....*....|....*....|..
gi 149025393 134 YCICKRPypdpedEVPDEMIQCVVCEDWFHGRHLGAIPPESGDFQEMVCQSC 185
Cdd:cd15553    1 YCICRSS------DISRFMIGCDNCEEWYHGDCINITEKEAKAIKEWYCQQC 46

PHD finger 2 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 second PHD finger.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 149025393 134 YCICKRPypdpedeVPDEMIQCVVCEDWFHGR 165
Cdd:cd15606    1 YCICRKP-------FSGFMLQCELCKDWFHSS 25