Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865697228 777 WKPGDQCLALYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLLT 330
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865697228 777 WKPGDQCLALYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLLT 330
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHPSGtTAVVVFSDYGNCEEVLLHNIKP 828
Cdd:pfam00567  49 AVGDGCVAAFSEDGKWYRAKITESLDDG-LVEVLFIDYGNTETVPLSDLRP 98

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMDNNNNLEVALNFL 328
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865697228 777 WKPGDQCLALYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLLT 330
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins; SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. Overexpression of SPF30 causes apoptosis. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1865697228 777 WKPGDQCLALYWEDNKFYRARIDAVHPSGTTAvVVFSDYGNCEEVLLHNIKPVHMD 832
Cdd:cd20399     1 WKVGDKCMAVWSEDGQYYEATIEEISEDGTCT-VTFDGYGNTEVTPLSQLKPREEG 55

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1865697228  777 WKPGDQCLAlYWEDNKFYRARIDAVHPSGTtAVVVFSDYGNCEEVLLHNIKPVHMDS 833
Cdd:smart00333   3 FKVGDKVAA-RWEDGEWYRARIVKVDGEQL-YEVFFIDYGNEEVVPPSDLRQLPEEL 57

second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHpSGTTAVVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20409    27 AVGEVCCAQFTEDNQWYRASVLAYS-SEDSVLVGYIDFGNSEEVALSRLRPI 77

Tudor domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHPSGtTAVVVFSDYGNCEEVLLHNIKP 828
Cdd:pfam00567  49 AVGDGCVAAFSEDGKWYRAKITESLDDG-LVEVLFIDYGNTETVPLSDLRP 98

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMDNNNNLEVALNFL 328
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865697228 780 GDQCLALYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNCEEVLLHNIKPVHMD 832
Cdd:cd20408    50 GEVCVAKYSEDQNWYRALVQTVDVQQKKAGVFYIDYGNEETVPLNRIQPLKKD 102

Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene. It contains multiple Staphylococcal nuclease (SN) domains and a C-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHPSGtTAVVVFSDYGNCEEVLLHNIKPVH 830
Cdd:cd20433    29 RKGDLCAAKFVEDGEWYRAKVEKVEGDK-KVHVLYIDYGNREVLPSTRLAALP 80

Tudor domain found in Schizosaccharomyces pombe splicing factor spf30 (SpSPF30) and similar proteins; SpSPF30, also called survival of motor neuron-related-splicing factor 30, is necessary for spliceosome assembly. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1865697228 777 WKPGDQCLAlYW--EDNKFYRARIDAVHPSGTTAV--VVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20446     1 FKPGEVVMA-RWksGDGKFYPARITSITGSSINPIytVKFLDYGEIDTVYLKDIRPL 56

UBA domain found in a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE) and similar proteins; P. Yoelii ubiquitin-conjugating enzyme and other uncharacterized family members show high sequence similarity to the human Huntingtin interacting protein-2 (HIP2) which belongs to a class II E2 ubiquitin-conjugating enzyme family. These proteins may play roles in the ubiquitin-mediated protein degradation pathway. They all contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1865697228 294 ERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLL 329
Cdd:cd14314     2 EEKIKKLLEMGFPRDQARKALEKNGWDETLALNTLL 37

Tudor domain found in DNA excision repair protein ERCC-6-like 2 (ERCC6L2) and similar proteins; ERCC6L2, also called DNA repair and recombination protein RAD26-like (RAD26L), may be involved in early DNA damage response. It regulates RNA Pol II-mediated transcription via its interaction with DNA-dependent protein kinase (DNA-PK) to resolve R loops and minimize transcription-associated genome instability. ERCC6L2 gene mutations have been associated with bone marrow failure that includes developmental delay and microcephaly. It contains an N-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1865697228 777 WKPGDQCLALYWEDNKFYRARIDAVH--PSGTT-AVVVFSDYG--NCEEVLLHNIK 827
Cdd:cd20400     1 WHVGDRCLAPYSGDGKLYEAVIKSIStdENGKSfAVVKFLGYEsdEDEKVPVSKLQ 56

Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins; TDRD9 is an ATP-dependent DEAD-like RNA helicase required during spermatogenesis. It is involved in the biosynthesis of PIWI-interacting RNAs (piRNAs). A recessive deleterious mutation mutation in TDRD9 causes non-obstructive azoospermia in infertile men. TDRD9 contains an N-terminal HrpA-like RNA helicase module and a Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1865697228 779 PGDQCLALY--WEDNKFYRARIdaVHPSGTTAVVVFSDYGNCEEV---LLHNIKPVHMD 832
Cdd:cd20431    43 PNLLCLAPFtdADMKKYYRAKI--LYVSGSSAEVFFVDYGNTSQVpssLLREIPETLLT 99

UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins; HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1865697228 292 VDERALRDIMEMGFNKEAARQALMdNNNNLEVALNFLLTND 332
Cdd:cd14288     1 VNEAHLQQLMDMGFTREHALEALL-HTSTLEQATEYLLTHP 40

UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins; TNRC6C is one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1865697228 295 RALRDIMEMGFNKEAARQALMDNNNNLEVALNFLLT 330
Cdd:cd14283     2 RLLKQLTDMGFKREPAEEALKSNNMNLEQAVSALLS 37

third Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1865697228 774 LNNWKPGDQCLALYWEDNKFYRARIDAVHpsGTTAVVVFSDYGNCEEVLLHNIK 827
Cdd:cd20438    52 LKKPEPGLLCCARYSKDRHYYRAVITEVL--DLKVSVYFLDFGNTDTVPFYDVK 103

sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHPSGTTAvVVFSDYGNCEEVLLHNI 826
Cdd:cd20441    39 KVGDLVAAEYDEDLALYRAVITAVLPGKSFK-VEFIDYGNTAVVDKSNI 86

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1865697228 294 ERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLLTN 331
Cdd:cd14307     1 EEAVASLLEMGIPREVAIEALRETNGDVEAAANYIFSN 38

fourth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1865697228 778 KPGDQCLALYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20423     4 LPNPVCLAKYSEDGKWCRALIDNVYEPVEMVEVTYVDYGNKELVSLKNLRSI 55

Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins; ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1865697228 774 LNNWKPGDQCLALYwEDNKFYRARIDAVHPSGTTAvVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20384     2 FSSLKEGSRCLAKY-DDGLWYPATVTDIDEDGKYT-VKFDSYGEVAVVELDDILPL 55

UBA domain found in Schizosaccharomyces pombe UBA domain-containing protein mud1 and similar proteins; Schizosaccharomyces pombe mud1 is an ortholog of the Saccharomyces cerevisiae DNA-damage response protein Ddi1. S. cerevisiae Ddi1, also called v-SNARE-master 1 (Vsm1), belongs to a family of proteins known as the ubiquitin receptors which can bind ubiquitinated substrates and the proteasome. It is involved in the degradation of the F-box protein Ufo1, involved in the G1/S transition. It also participates in Mec1-mediated degradation of Ho endonuclease. Both S. pombe mud1 and S. cerevisiae Ddi1 contain an N-terminal ubiquitin-like (UBL) domain, an aspartyl protease-like domain, and a C-terminal ubiquitin-associated (UBA) domain. S. pombe mud1 binds to K48-linked polyubiquitin (polyUb) through UBA domain.

                          10        20        30
                  ....*....|....*....|....*....|...
gi 1865697228 297 LRDIMEMGFNKEAARQALMDNNNNLEVALNFLL 329
Cdd:cd14308     4 VRQLVDMGFTPTDAGRALKAANGDVTVAAEWLL 36

seventh Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the seventh one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1865697228 780 GDQCLALYWEDNKFYRARIDAVHPSGTTavVVFSDYGNCEEVLLHNIKPV 829
Cdd:cd20426    50 GDPCIVKYSEDNHWYRALVTKINDNLVS--VRFVDYGNEEDVVREQVRAL 97

Tudor domain found in PHD finger protein 20 (PHF20), PHF20-like protein 1 (PHF20L1), and similar proteins; PHF20, also called Glioma-expressed antigen 2, hepatocellular carcinoma-associated antigen 58, novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds to Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53-mediated signaling. PHF20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Both PHF20 and PHF20L1 contain an N-terminal malignant brain tumor (MBT) domain, a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1865697228 777 WKPGDQCLAlYWEDNKFYRARIDAVHPSGTTAVVVFSDYGNceevllhNIKPVHMDSW 834
Cdd:cd20386     1 FKVGEEVLA-RWSDCKFYPAKILKVLDNGTYEVLFYDGFKK-------TVKASNLKKM 50

UBA2 domain of Rad23 proteins found in eukaryotes; The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1865697228 293 DERALRDIMEMGFNKEAARQALMDNNNNLEVALNFLL 329
Cdd:cd14281     2 EREAIERLVALGFSRDQAIEAYLACDKNEELAANYLF 38

UBA domain found in Saccharomyces cerevisiae EH domain-containing and endocytosis protein 1 (Ede1) and similar proteins; Ede1, also bud site selection protein 15, is the mammalian protein Eps15 homolog found in yeast and functions at the internalization step of endocytosis. Both Ede1 and Eps15 are endocytic scaffold proteins that may involve in stabilization of the adaptor-cargo complex. They both contain contains three N-terminal Eps15 homology (EH) domains and C-terminal ubiquitin-binding motifs. Whereas Eps15 has two ubiquitin interacting motifs (UIM), Ede1 harbors a single ubiquitin-associated (UBA) domain. This model corresponds to Ede1 UBA domain that is responsible for the binding of monoubiquitinated proteins and negatively regulates EH domain-mediated protein-protein interactions.

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gi 1865697228 296 ALRDIMEMGFNKEAARQALMDNNNNLEVALNFLL 329
Cdd:cd14285     1 AIEELSGMGFTEEEARKALEKCNWDLEAATNFLL 34

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

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gi 1865697228 767 SESSAHGLNNWKPGDQCLALYWEDNKFYRARIDAVHPSGtTAVVVFSDYGNCEEVLLHNIKPVHMD 832
Cdd:cd20412    19 SEENRHTLLTVQVGDIVAAPFRHDGSWYRARVLGFLENG-NLDLYFVDYGDSGYVPLEDLRALRSD 83