Lens epithelium-derived growth factor (LEDGF); LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   347 DSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFK------------------VSQ 408
Cdd:pfam11467   1 ERKLQELDLDIKSCLKLDNADVDKCLEALDELKSLQVTPLMLKKNPECVETIKKLRRYVgnleewkmdeeeeaefkeKAQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 28461167   409 VIMEKSTMLYNKFKNMFLVGEGDSVITQVLNKSLAEQRQH 448
Cdd:pfam11467  81 LIRDKATEIYNKFKSLFLVPEGEVNFWPDFNEEVKEFKEK 120

Lens epithelium-derived growth factor (LEDGF); LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   347 DSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFK------------------VSQ 408
Cdd:pfam11467   1 ERKLQELDLDIKSCLKLDNADVDKCLEALDELKSLQVTPLMLKKNPECVETIKKLRRYVgnleewkmdeeeeaefkeKAQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 28461167   409 VIMEKSTMLYNKFKNMFLVGEGDSVITQVLNKSLAEQRQH 448
Cdd:pfam11467  81 LIRDKATEIYNKFKSLFLVPEGEVNFWPDFNEEVKEFKEK 120

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28461167      5 FKPGDLIFAKMKGYPHWPARVD---EVPDGAVKPPT--NKLPIFFFGTHETAFLGPKDIFPYS 62
Cdd:smart00293   1 FKPGDLVWAKMKGFPWWPALVIspkMTPDNIMKRKSdeNLYPVLFFGDKDTAWIPSSKLFPLT 63

PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2); 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. It contains a PWWP domain, which is necessary for DNA binding.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   5 FKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNEGLWEI 84
Cdd:cd20149   1 FKPGDLVFAKMKGYPHWPARIDDIADGAVKPPPNKYPIFFFGTHETAFLGPKDLFPYDKYKDKYGKPNKRKGFNEGLWEI 80

                ....
gi 28461167  85 DNNP 88
Cdd:cd20149  81 QNNP 84

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 28461167   5 FKPGDLIFAKMKGYPHWPARVDEVPDGAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKGFNEGLWEI 84
Cdd:cd20148   1 YKCGDLVFAKMKGYPHWPARIDEMPEAAVKSTANKYQVFFFGTHETAFLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEI 80

                ....*..
gi 28461167  85 DNNPKVK 91
Cdd:cd20148  81 ENNPTVK 87

Lens epithelium-derived growth factor (LEDGF); LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   347 DSRLQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEMITTLKKIRRFK------------------VSQ 408
Cdd:pfam11467   1 ERKLQELDLDIKSCLKLDNADVDKCLEALDELKSLQVTPLMLKKNPECVETIKKLRRYVgnleewkmdeeeeaefkeKAQ 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 28461167   409 VIMEKSTMLYNKFKNMFLVGEGDSVITQVLNKSLAEQRQH 448
Cdd:pfam11467  81 LIRDKATEIYNKFKSLFLVPEGEVNFWPDFNEEVKEFKEK 120

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 28461167     8 GDLIFAKMKGYPHWPARV---DEVPDGAVKPP--TNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKR-----KGF 77
Cdd:pfam00855   1 GDLVWAKLKGYPWWPARVvdpEELPENVLKPKkkDGEYLVRFFGDSEFAWVKPKDLKPFDEGDEFEYLKKKKkkkkkKAF 80

                          90
                  ....*....|..
gi 28461167    78 NEGLWEIDNNPK 89
Cdd:pfam00855  81 KKALEEAEEALK 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 28461167   8 GDLIFAKMKGYPHWPARVDEVPDGAV----KPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNKRKG 76
Cdd:cd05162   1 GDLVWAKLKGYPWWPARVVDPEELPEevgkKKKKGGVLVQFFGDNDYAWVKSKNIKPFEEGFKKEFKKKKKKS 73

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 28461167   7 PGDLIFAKMKGYPHWPARV-DEVPDGAVKPPTNK------LPIFFFGTHETAFLGPKDIFPYSEN-KEKYGKPNKRKGFN 78
Cdd:cd20142   2 PGDVVWAKVKGYPMWPALViDEEHAERCGLEANRpgkkgtVPVQFFGTYEVARLNPKKVVGFSKGlDLKYHSKCKAPVFR 81

                ....*..
gi 28461167  79 EGLWEID 85
Cdd:cd20142  82 QALEEAE 88

PWWP domain found in protein BS69 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. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28461167   7 PGDLIFAKMKGYPHWPARVdevpdgaVKPPTNKLPIFFFG-THETAFLGPKDIFPYSENKEKYGKPNKrKGFNEGLWE 83
Cdd:cd20159   6 PHELVWAKQKGFPYWPAKV-------IQKEDNQYDVRFFGgHHQRAWIPKENIKPITTSPKQLKVKRT-AGWNKACEE 75

PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also called protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also called protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also called 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 family of ATX1 and ATX2. They are multi-domain containing protein that consists of an N-terminal PWWP domain, 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 28461167   8 GDLIFAKMKGYPHWPARV---DEVPDGAVKP--PtNKLPIFFFG---THETAFLGPKDIFPYSENKEKY-GKPNKRK--- 75
Cdd:cd20143   3 GDLVWAKVGTHPFWPARVvepAEQAEEVRRRcvP-GSLCVYFFGpggSRDYGWVRRSMIFPFTDDLARFqTQKIKNKkrp 81

                ....*....
gi 28461167  76 -GFNEGLWE 83
Cdd:cd20143  82 qEFQEALEE 90

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 28461167   6 KPGDLIFAKMKGYPHWPARVDEVPD-GAVKPPTNKLPIFFFGTHETAFLGPKDIFPYSENKEKYGKPNK-----RKGFNE 79
Cdd:cd05835   1 KIGDLVWAKLKGSPWWPGIVVSHKDcGQKPPAEGSVWVFWFGDHKVSEVPLDKILPFAEFFNKFYISKNssklyKKAVYE 80

                ..
gi 28461167  80 GL 81
Cdd:cd05835  81 AL 82

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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   5 FKPGDLIFAKMKGYPHWPAR----------VDEVPDGAVkpptNKLPIFFFGT-HETAFLGPKDIFPYSEN-KEKYGKPN 72
Cdd:cd20146   9 LPLGSLVWAKMTGYPRWPAIltpdpicgeyVDYDEDGEV----EKYHVEFLGKpHSHAWISAKSVEPYNSNtKTPKCKTK 84

                ...
gi 28461167  73 KRK 75
Cdd:cd20146  85 KSK 87

PWWP domain found in PWWP domain-containing protein 2A (PWWP2A); 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 its paralog 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28461167   8 GDLIFAKMKGYPHWPARVDEVP-----DGAVKPPTNKlpIFFFGTHETAFLGPKDIFPYSEN-KEKYGKpnKRKG 76
Cdd:cd20152  23 GDIVWAKIYGFPWWPARILAITvsrkdNGLLVRQEAR--ISWFGSPTTSFLALSQLAPFLENfQSRFNK--KRKG 93

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28461167   7 PGDLIFAKMKGYPHWPARV--DEVPDGAVKPPTNKLPIF------FFG-THETAFLGPKDIFPYsENKEKY 68
Cdd:cd20144   1 VGDLVWAKVSGHPWWPCMVtyDPESGLYTKIKGSGGRTYrqyhvqFFGdNGERGWVSEKSLMPF-EGKEKF 70

PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family; The BRPF family of 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 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The 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
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 28461167   5 FKPGDLIFAKMKGYPHWPARV-------------DEVPDGAVKPPTNKLPIF--FFGTHET 50
Cdd:cd05839   1 LEPGDLVWAKCRGYPWYPAEIvdpkdpkegngvpIPVPPDRVLKKSNEKLYLvlFFDAKRT 61

MAEBL; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167    90 VKFSSQQVSTKQSNASSDVEAEEKETSVSKEDTDQEEKASNEDvTKAADITTPKAARRGRKRKAEKQVDTEEAGVVTAAT 169
Cdd:PTZ00121 1334 AKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEA-KKKADAAKKKAEEKKKADEAKKKAEEDKKKADELKK 1412

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   170 ASNVKASPKRGRPAATEVKipkprgrpKVVKQPCPSESDMVIDEDKSK---KKGPEEKPPKKQLKKEEEGQKEEEKPRKE 246
Cdd:PTZ00121 1413 AAAAKKKADEAKKKAEEKK--------KADEAKKKAEEAKKADEAKKKaeeAKKAEEAKKKAEEAKKADEAKKKAEEAKK 1484

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   247 PDKKEGKKEVESKRKNLAKPGVTSTSDSEEDDDQEGEKKRKGGRHFQAAHRRNMLKGQHEKEAADRKRKQEEQMETEQQT 326
Cdd:PTZ00121 1485 ADEAKKKAEEAKKKADEAKKAAEAKKKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKK 1564

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   327 KDEGKKPEVKKVEKKRETSMDSRlQRIHAEIKNSLKIDNLDVNRCIEALDELASLQVTMQQAQKHTEM---ITTLKKIRR 403
Cdd:PTZ00121 1565 KAEEAKKAEEDKNMALRKAEEAK-KAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEkkkVEQLKKKEA 1643

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   404 FKVSQVIMEKSTMLYNKFKNMFLV--GEGDSVITQVLNKSLAEQRQHEEANKTKDQGKKGPNKKLEKEQTGTKSLNGGSD 481
Cdd:PTZ00121 1644 EEKKKAEELKKAEEENKIKAAEEAkkAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|..
gi 28461167   482 AQESNHPQHNGDSAEESKDSREAGSKTKTPGEEREAEVSLKE 523
Cdd:PTZ00121 1724 AEEENKIKAEEAKKEAEEDKKKAEEAKKDEEEKKKIAHLKKE 1765

PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins; MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   5 FKPGDLIFAKMKGYPHWPARVDEVP-DGAVKPPTNKLPI---FFFGTHETAFLGPKDIFPYSENKEK---------YGKP 71
Cdd:cd05837   1 FSPGDLVWAKLEGYPWWPSLVCNHPtTGFHKKFGKKGEVhvqFFDDPPSRAWVKAKNVKPFTGSDDKefqkggmffSKDP 80

                ....*...
gi 28461167  72 NKRKGFNE 79
Cdd:cd05837  81 KWKKAVKE 88

second PWWP domain found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins; NSD2, also called histone-lysine N-methyltransferase NSD2, 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, through 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, an high mobility group (HMG) box, five PHD (plant-homeodomain) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD domains mediate chromatin interaction and recognition of histone marks. This model corresponds to the second PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   9 DLIFAKMKGYPHWPARV---DEVPDG--AVKPPTNKLPIFFFGTHETAFLGPKDIFPYSE 63
Cdd:cd20165   4 DIIWVKLGNYRWWPAEVchpKNVPPNiqKMKHEIGEFPVFFFGSKDYYWTHQARVFPYME 63

DNA topoisomerase 2-like protein; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167    85 DNNPKVKFSSQQVSTKQSNASSDVEAEEKETSVSKEDTDQEEKASNEDVTKAADITTPKAARRGRKRK-AEKQVDTEEAG 163
Cdd:PTZ00108 1182 KKSSADKSKKASVVGNSKRVDSDEKRKLDDKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNsSKSSEDNDEFS 1261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28461167   164 VVTAATASNVKASPKRGRPAATEVkiPKPRGRPKVVKQPCPSESDMVIDEDKSKKKGPEEKPPKKQLKKEEEGQKEEEKP 243
Cdd:PTZ00108 1262 SDDLSKEGKPKNAPKRVSAVQYSP--PPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKT 1339

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 28461167   244 RKEPDKKEGKKEVESKRKNLakpgvTSTSDSEEDDDQEGEK 284
Cdd:PTZ00108 1340 RVKQASASQSSRLLRRPRKK-----KSDSSSEDDDDSEVDD 1375