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Conserved domains on  [gi|1907195992|ref|XP_036010651|]
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RNA-binding motif, single-stranded-interacting protein 3 isoform X2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 73-180 7.18e-48

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.


:

Pssm-ID: 438974  Cd Length: 113  Bit Score: 159.38  E-value: 7.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  73 GYKFVYSQLPLGSLVLVKLRNWPSWPGILCPDPFKGKYVTYDQDGNVEKYYVEFLGDPHSTAWMSAAFVGHFSLTLEAAD 152
Cdd:cd20146     1 GLKYVYSQLPLGSLVWAKMTGYPRWPAILTPDPICGEYVDYDEDGEVEKYHVEFLGKPHSHAWISAKSVEPYNSNTKTPK 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907195992 153 CT-----KKKRWYRSALEEAYQLYRCSAEQRLE 180
Cdd:cd20146    81 CKtkkskKRKKSYESALEEAERLLKLTCEERLE 113
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 14-62 2.86e-14

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


:

Pssm-ID: 462181  Cd Length: 46  Bit Score: 66.56  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1907195992  14 TWVQCEneSCLKWRLLSPAAAAAVNPsEPWYCFMNTDPSYSSCSVSEED 62
Cdd:pfam07496   1 YWVQCD--SCLKWRRLPTEIDPYELP-EPWYCSMNPDPKYNSCDAPEEI 46
 
Name Accession Description Interval E-value
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 73-180 7.18e-48

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.


Pssm-ID: 438974  Cd Length: 113  Bit Score: 159.38  E-value: 7.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  73 GYKFVYSQLPLGSLVLVKLRNWPSWPGILCPDPFKGKYVTYDQDGNVEKYYVEFLGDPHSTAWMSAAFVGHFSLTLEAAD 152
Cdd:cd20146     1 GLKYVYSQLPLGSLVWAKMTGYPRWPAILTPDPICGEYVDYDEDGEVEKYHVEFLGKPHSHAWISAKSVEPYNSNTKTPK 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907195992 153 CT-----KKKRWYRSALEEAYQLYRCSAEQRLE 180
Cdd:cd20146    81 CKtkkskKRKKSYESALEEAERLLKLTCEERLE 113
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 14-62 2.86e-14

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 66.56  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1907195992  14 TWVQCEneSCLKWRLLSPAAAAAVNPsEPWYCFMNTDPSYSSCSVSEED 62
Cdd:pfam07496   1 YWVQCD--SCLKWRRLPTEIDPYELP-EPWYCSMNPDPKYNSCDAPEEI 46
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 84-169 7.68e-10

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.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 55.51  E-value: 7.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  84 GSLVLVKLRNWPSWPGILCPDPFKGKYVtYDQDGNVEKYYVEFLGDPHsTAWMSAAFVGHFSLTLEAADCTKKKRW-YRS 162
Cdd:pfam00855   1 GDLVWAKLKGYPWWPARVVDPEELPENV-LKPKKKDGEYLVRFFGDSE-FAWVKPKDLKPFDEGDEFEYLKKKKKKkKKK 78


                  ....*..
gi 1907195992 163 ALEEAYQ 169
Cdd:pfam00855  79 AFKKALE 85
 
Name Accession Description Interval E-value
PWWP_ZCWPW2 cd20146
PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins; ...
 73-180 7.18e-48

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.


Pssm-ID: 438974  Cd Length: 113  Bit Score: 159.38  E-value: 7.18e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  73 GYKFVYSQLPLGSLVLVKLRNWPSWPGILCPDPFKGKYVTYDQDGNVEKYYVEFLGDPHSTAWMSAAFVGHFSLTLEAAD 152
Cdd:cd20146     1 GLKYVYSQLPLGSLVWAKMTGYPRWPAILTPDPICGEYVDYDEDGEVEKYHVEFLGKPHSHAWISAKSVEPYNSNTKTPK 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907195992 153 CT-----KKKRWYRSALEEAYQLYRCSAEQRLE 180
Cdd:cd20146    81 CKtkkskKRKKSYESALEEAERLLKLTCEERLE 113
zf-CW pfam07496
CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four ...
 14-62 2.86e-14

CW-type Zinc Finger; This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a "highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development." Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found.


Pssm-ID: 462181  Cd Length: 46  Bit Score: 66.56  E-value: 2.86e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1907195992  14 TWVQCEneSCLKWRLLSPAAAAAVNPsEPWYCFMNTDPSYSSCSVSEED 62
Cdd:pfam07496   1 YWVQCD--SCLKWRRLPTEIDPYELP-EPWYCSMNPDPKYNSCDAPEEI 46
PWWP_ZCWPW1 cd20145
PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ...
 76-169 5.87e-12

PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins; ZCWPW1 is a histone H3K4me3 reader. It is associated with late-onset Alzheimer's disease (LOAD). In addition to the PWWP domain, ZCWPW1 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.


Pssm-ID: 438973  Cd Length: 115  Bit Score: 62.18  E-value: 5.87e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  76 FVYSQLPLGSLVLVKLRNWPSWPGILCPDPFKGKYvtYDQDGN---VEKYYVEFLGDPHSTAWMSAAFVGHFS-LTLEAA 151
Cdd:cd20145     1 LIYTKYTPGSLVWAKMPGYPWWPAMVEDDPDTEEF--FWLDEEsdiPTKYHVTFFDKPVSRAWVRASSIKPFTdNSNEPN 78

                          90
                  ....*....|....*...
gi 1907195992 152 DCTKKKRWYRSALEEAYQ 169
Cdd:cd20145    79 LTKKKGKKYKKRLNEAVE 96
PWWP pfam00855
PWWP domain; The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain ...
 84-169 7.68e-10

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.


Pssm-ID: 459964 [Multi-domain]  Cd Length: 92  Bit Score: 55.51  E-value: 7.68e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  84 GSLVLVKLRNWPSWPGILCPDPFKGKYVtYDQDGNVEKYYVEFLGDPHsTAWMSAAFVGHFSLTLEAADCTKKKRW-YRS 162
Cdd:pfam00855   1 GDLVWAKLKGYPWWPARVVDPEELPENV-LKPKKKDGEYLVRFFGDSE-FAWVKPKDLKPFDEGDEFEYLKKKKKKkKKK 78


                  ....*..
gi 1907195992 163 ALEEAYQ 169
Cdd:pfam00855  79 AFKKALE 85
PWWP cd05162
PWWP (Pro-Trp-Trp-Pro) domain; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, ...
 84-167 3.24e-09

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.


Pssm-ID: 438958 [Multi-domain]  Cd Length: 86  Bit Score: 53.66  E-value: 3.24e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  84 GSLVLVKLRNWPSWPGILCPDPFKGKYVTYDQDGNveKYYVEFLGDpHSTAWMSAAFVGHFS--LTLEAADCTKKKRWYR 161
Cdd:cd05162     1 GDLVWAKLKGYPWWPARVVDPEELPEEVGKKKKKG--GVLVQFFGD-NDYAWVKSKNIKPFEegFKKEFKKKKKKSKKFK 77


                  ....*.
gi 1907195992 162 SALEEA 167
Cdd:cd05162    78 KAVEEA 83
PWWP_NSD_rpt1 cd20144
first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins; The ...
 83-138 8.11e-06

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.


Pssm-ID: 438972  Cd Length: 114  Bit Score: 44.61  E-value: 8.11e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907195992  83 LGSLVLVKLRNWPSWPGILCPDPFKGKY--VTYDQDGNVEKYYVEFLGDPHSTAWMSA 138
Cdd:cd20144     1 VGDLVWAKVSGHPWWPCMVTYDPESGLYtkIKGSGGRTYRQYHVQFFGDNGERGWVSE 58
PWWP_ScIOC4-like cd05840
PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar ...
 84-169 1.48e-04

PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins; ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines.


Pssm-ID: 438965  Cd Length: 94  Bit Score: 40.36  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  84 GSLVLVKLRNWPSWPGILCPD---PFKGKYVTYDQDGNVEKYY-VEFLGDPhSTAWMSAAfvghfSLT-LEAADCTK--- 155
Cdd:cd05840     1 GDLVLAKVKGYPPWPAMVLPEellPKNVLKAKKRKPKSKKTVYpVQFFPDN-EYYWVSPS-----SLKpLTKEEIDKfls 74

                          90
                  ....*....|....
gi 1907195992 156 KKRWYRSALEEAYQ 169
Cdd:cd05840    75 KSKRKNKDLIEAYE 88
PWWP_HULK cd20147
PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family; The HULK family ...
 84-177 2.90e-04

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.


Pssm-ID: 438975 [Multi-domain]  Cd Length: 92  Bit Score: 39.78  E-value: 2.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907195992  84 GSLVLVKLRNWPSWPGILcpdpfkGKYVTYDQDGNVEKYYVEFLGdPHSTAWMS----AAFVGHFSLTLEAADCTKKKR- 158
Cdd:cd20147     1 GDLVLAKVKGFPAWPAQV------SEPEDWGSAPDPKKVFVHFFG-TQQIGFCNpgelSEFTEEIKQSLLARTLKKKKGs 73

                          90
                  ....*....|....*....
gi 1907195992 159 WYRSALEEAYQLYRCSAEQ 177
Cdd:cd20147    74 DFSRAVKEICELYEERKGQ 92
PWWP_HRP cd05834
PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family; The ...
 84-138 8.72e-03

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.


Pssm-ID: 438959 [Multi-domain]  Cd Length: 82  Bit Score: 35.22  E-value: 8.72e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907195992  84 GSLVLVKLRNWPSWPGILCPDPFkgkyvtyDQDGNVEKYYVEFLGDpHSTAWMSA 138
Cdd:cd05834     4 GDLVFAKVKGYPPWPARIDEIPE-------GAKIPKNKYPVFFYGT-HETAFLKP 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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