PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLAR-CQGKTVKYFAQAVE 99
Cdd:cd20147      1 GDLVLAKVKGFPAWPAQVSEPEDWGSAPDPKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLLARtLKKKKGSDFSRAVK 80

                           90
                   ....*....|
gi 1063733455  100 QICTAFEGLQ 109
Cdd:cd20147     81 EICELYEERK 90

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLAR-CQGKTVKYFAQAVE 99
Cdd:cd20147      1 GDLVLAKVKGFPAWPAQVSEPEDWGSAPDPKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLLARtLKKKKGSDFSRAVK 80

                           90
                   ....*....|
gi 1063733455  100 QICTAFEGLQ 109
Cdd:cd20147     81 EICELYEERK 90

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWDRAPDPKK-----YFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQGKTV-KYF 94
Cdd:pfam00855    1 GDLVWAKLKGYPWWPARVVDPEELPENVLKPKkkdgeYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKKKKKkKAF 80

                           90
                   ....*....|..
gi 1063733455   95 AQAVEQICTAFE 106
Cdd:pfam00855   81 KKALEEAEEALK 92

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455    21 GDLVLAKVKGFPAWPAKI-SRPEDWD----RAPDPKKYFVQFFGTEEIAFVAPPDIQAFT 75
Cdd:smart00293    4 GDLVWAKMKGFPWWPALViSPKMTPDnimkRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63

PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLAR-CQGKTVKYFAQAVE 99
Cdd:cd20147      1 GDLVLAKVKGFPAWPAQVSEPEDWGSAPDPKKVFVHFFGTQQIGFCNPGELSEFTEEIKQSLLARtLKKKKGSDFSRAVK 80

                           90
                   ....*....|
gi 1063733455  100 QICTAFEGLQ 109
Cdd:cd20147     81 EICELYEERK 90

PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWDRAPDPKK-----YFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQGKTV-KYF 94
Cdd:pfam00855    1 GDLVWAKLKGYPWWPARVVDPEELPENVLKPKkkdgeYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKKKKKkKAF 80

                           90
                   ....*....|..
gi 1063733455   95 AQAVEQICTAFE 106
Cdd:pfam00855   81 KKALEEAEEALK 92

PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDwDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKskllarCQGKTVKY--FAQAV 98
Cdd:cd05834      4 GDLVFAKVKGYPPWPARIDEIPE-GAKIPKNKYPVFFYGTHETAFLKPKDLFPYEENKE------KYGKPRKRkgFNEGL 76

                   ...
gi 1063733455   99 EQI 101
Cdd:cd05834     77 WEI 79

PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPEDWD----RAPDPKKYFVQFFGTEEIAFVAPPDIQAFtsEAKSKLLARCQGKTVKYFAQ 96
Cdd:cd05162      1 GDLVWAKLKGYPWWPARVVDPEELPeevgKKKKKGGVLVQFFGDNDYAWVKSKNIKPF--EEGFKKEFKKKKKKSKKFKK 78

                   ....*...
gi 1063733455   97 AVEQICTA 104
Cdd:cd05162     79 AVEEAEEA 86

PWWP domain found in Hepatoma-derived growth factor (HDGF); HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISR-PEDWDRAPDpKKYFVQFFGTEEIAFVAPPDIQAFtSEAKSKLlarcqGKTVKY--FAQA 97
Cdd:cd20148      4 GDLVFAKMKGYPHWPARIDEmPEAAVKSTA-NKYQVFFFGTHETAFLGPKDLFPY-EESKEKF-----GKPNKRkgFSEG 76

                   ....
gi 1063733455   98 VEQI 101
Cdd:cd20148     77 LWEI 80

domain with conserved PWWP motif; conservation of Pro-Trp-Trp-Pro residues

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455    21 GDLVLAKVKGFPAWPAKI-SRPEDWD----RAPDPKKYFVQFFGTEEIAFVAPPDIQAFT 75
Cdd:smart00293    4 GDLVWAKMKGFPWWPALViSPKMTPDnimkRKSDENLYPVLFFGDKDTAWIPSSKLFPLT 63

PWWP domain found in Hepatoma-derived growth factor-related protein 3 (HDGFL3); HDGFL3, also called HDGF-related protein 3 (HRP-3), is the only hepatoma-derived growth factor (HDGF)-related protein (HRP) family member whose expression is almost restricted to the nervous tissue. It enhances DNA synthesis and may play a role in cell proliferation. It contains a PWWP domain, which is necessary for DNA binding.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1063733455   16 GQLVLGDLVLAKVKGFPAWPAKISRPEDWDRAPDPKKYFVQFFGTEEIAFVAPPDI 71
Cdd:cd20150      4 REYKAGDLVFAKMKGYPHWPARIDELPEGAVKPPANKYPIFFFGTHETAFLGPKDL 59

PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1063733455   17 QLVLGDLVLAKVKGFPAWPAKISR-PE-----DWDRAPDPKKYFVQFFGT 60
Cdd:cd20146      8 QLPLGSLVWAKMTGYPRWPAILTPdPIcgeyvDYDEDGEVEKYHVEFLGK 57

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins; This family includes A. thaliana ATX1 and ATX2, which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called 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 called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   20 LGDLVLAKVKGFPAWPA-KISRPEDWDRAPDPKK------YFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQgktVK 92
Cdd:cd20142      2 PGDVVWAKVKGYPMWPAlVIDEEHAERCGLEANRpgkkgtVPVQFFGTYEVARLNPKKVVGFSKGLDLKYHSKCK---AP 78

                   ....*...
gi 1063733455   93 YFAQAVEQ 100
Cdd:cd20142     79 VFRQALEE 86

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455  778 AFEGMLETLSRTRESIGRA-----TRLAIDCAK-YGLASEVVELLIRKLESEshfhRKVDLFFLVDSITQHSHSQKGIAG 851
Cdd:cd16983      2 EFNKELSSLLDSKPPVSKSkinaiTKLAIKAIKfYKHVVQSVEKFIQKCKPE----YKLPGLYVIDSIIRQSRHQYGKEK 77

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1063733455  852 ASYVPTVQaalpRLLGAAAPPGTGASDN-RRKCLKVLKLWLERKVFPESLL 901
Cdd:cd16983     78 DVYAPRFA----KNLSKTFLNLLKCPEKdKPKVKRVLNLWQKNGVFPKEII 124

PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1063733455   23 LVLAKVKGFPAWPAKISRpEDWDRApDpkkyfVQFFGTEEIAFVAPPDIQAFTSE 77
Cdd:cd20160      9 LVWAKLKGFPFWPAKALR-VNNGQV-D-----VRFFGAHDRAWVPVKDCYLYSKE 56

CTD kinase subunit gamma CTK3; The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455  777 DAFEG------MLETLSRTRESIGRATRLAIdcaKYG-LASEVVELLIRKLESeSHFHRKVDLFFLVDSITQHSHsQKGI 849
Cdd:pfam12243    1 DPFEVrsqfsqLLRKLNASVQSLQKAAHFAL---KNRdLEEDLHSCILEQLER-GDLNTRANIFYFIDTLCEESL-KNGQ 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 1063733455  850 AGASYVPTVQAALPRLLGAAAPPGTGASDNRRKCLKVLKLWLERKV 895
Cdd:pfam12243   76 SGKPYVRSLKRDIPRLVDSVAPDDGSGAANVKSVRKILQSLKLKSL 121

first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 that are critical in maintaining the chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and play nonredundant 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, through 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 (C5HCH). This model corresponds to the first PWWP domain. This family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   20 LGDLVLAKVKGFPAWPAKISRPEDWDR----APDPKK----YFVQFFGTE-EIAFVAPPDIQAFTSEAK-----SKLLAR 85
Cdd:cd20144      1 VGDLVWAKVSGHPWWPCMVTYDPESGLytkiKGSGGRtyrqYHVQFFGDNgERGWVSEKSLMPFEGKEKfeelvKELKKK 80

                   ....*...
gi 1063733455   86 CQGKTVKY 93
Cdd:cd20144     81 AKKKSKKA 88

PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar proteins; Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. BS69 is a multi-domain protein, containing bromo, plant homeodomain (PHD), proline-tryptophan-tryptophan-proline (PWWP), and MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a PHD finger, a bromodomain, and a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063733455   23 LVLAKVKGFPAWPAKISRPEDwdrapdpKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQGKTVKYFAQAVEQ 100
Cdd:cd05841      9 LVWVKLDGFPFWPAKVMGTKD-------GQVDVRFFGDYDRAWLPSKNVTLHTREIVSTLPDSSESKDKRTLKKAIKE 79

PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family; The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   21 GDLVLAKVKGFPAWPAKISRPED-WDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQGKTVKyfaQAVE 99
Cdd:cd05835      3 GDLVWAKLKGSPWWPGIVVSHKDcGQKPPAEGSVWVFWFGDHKVSEVPLDKILPFAEFFNKFYISKNSSKLYK---KAVY 79

                   ....
gi 1063733455  100 QICT 103
Cdd:cd05835     80 EALK 83

CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor arginine serine rich 15 (SFRS15) is also called CTD-binding SR-like protein RA4 or SR-related and CTD-associated factor 4 (SCAF4). It may act to physically and functionally link transcription and pre-mRNA processing. SFRS15/SCAF4 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455  777 DAFEGMLETLSRTRESIGRA-----TRLAIDCAK-YGLASEVVELLIRKLESEShfhrKVDLFFLVDSITQHSHSQ---- 846
Cdd:cd17005      1 NAFNQELFSLMDMKPPISRAkmiliTKAAIKAIKlYKHVVQIVEKFIKKCKPEY----KVPGLYVIDSIVRQSRHQfgad 76

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455  847 KGIAGASYVPTVQAALPRLLGAAappgtgaSDNRRKCLKVLKLWLERKVFPESLLRRYID 906
Cdd:cd17005     77 KDVFGPRFSKNITATFQYLYLCP-------SEDKSKIVRVLNLWQKNGVFKIEIIQPLLD 129

PWWP domain found in PWWP domain-containing protein 2B (PWWP2B); PWWP2B is a paralog of PWWP2A, a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733455   20 LGDLVLAKVKGFPAWPAK---ISRPEDWDRAPDPKKYFVQFFGTEEIAFVAPPDIQAFTSEAKSKLLARCQG---KTVKY 93
Cdd:cd20153     16 VGDIVWGKIHGFPWWPARvlsISLSQKEDGEPSWQEAKVSWFGSPTTSLLSVSKLSPFSEFFKLRFNRKKKGmyrKAITE 95

                   ....*...
gi 1063733455   94 FAQAVEQI 101
Cdd:cd20153     96 AAKAAEHL 103

PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family; The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                           10        20
                   ....*....|....*....|
gi 1063733455   20 LGDLVLAKVKGFPAWPAKIS 39
Cdd:cd20140      6 VGDIVWGKIHGFPWWPGRIL 25