The first LOTUS domain on Tudor-containing protein 5 (TDRD5); The first LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651   4 QERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIPDES 83
Cdd:cd09985    1 QEQIMERLKKDVRSLLISSKNGLTPEQLEQDYLAMVGSPLPLRSLGFRSTMELVLDMPDVVRVHPQLDGTVILKAVGDET 80

                         90
                 ....*....|....*
gi 312283651  84 TKGIASLVAKQRSSH 98
Cdd:cd09985   81 TKGIEDLVSKQRDSK 95

The third LOTUS domain on Tudor-containing protein 5 (TDRD5); The third LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 312283651 296 SSELKHKIKFVVSKFPEGLFISKLLGEYEVIFKEQLSPKKLGFLNVTELVGALSDILHVEFRKGHQDLLVFDAD 369
Cdd:cd09976    1 SRELREEIRKVVENHPNGLFIALLPTEYKVLFKEELPVKQLGFLSVTELVGSLSDILAIERREKESDWLVFDAK 74

The first LOTUS domain on Tudor-containing protein 5 (TDRD5); The first LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651   4 QERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIPDES 83
Cdd:cd09985    1 QEQIMERLKKDVRSLLISSKNGLTPEQLEQDYLAMVGSPLPLRSLGFRSTMELVLDMPDVVRVHPQLDGTVILKAVGDET 80

                         90
                 ....*....|....*
gi 312283651  84 TKGIASLVAKQRSSH 98
Cdd:cd09985   81 TKGIEDLVSKQRDSK 95

The third LOTUS domain on Tudor-containing protein 5 (TDRD5); The third LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 312283651 296 SSELKHKIKFVVSKFPEGLFISKLLGEYEVIFKEQLSPKKLGFLNVTELVGALSDILHVEFRKGHQDLLVFDAD 369
Cdd:cd09976    1 SRELREEIRKVVENHPNGLFIALLPTEYKVLFKEELPVKQLGFLSVTELVGSLSDILAIERREKESDWLVFDAK 74

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 312283651   14 EIRSLLISTKDG-LSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVIL 76
Cdd:pfam12872   1 ELISLLRSDPDGwASLSELGSEYRKLFGEDFDPRNYGFSKLSDLLKAIPDVFEIEKRGGGGLVV 64

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 312283651  302 KIKFVVSKFPEG-LFISKLLGEYEVIFKEQLSPKKLGFLNVTELVGALSDILHVEFRKGHQDLL 364
Cdd:pfam12872   1 ELISLLRSDPDGwASLSELGSEYRKLFGEDFDPRNYGFSKLSDLLKAIPDVFEIEKRGGGGLVV 64

The first LOTUS domain on Tudor-containing protein 5 (TDRD5); The first LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651   4 QERIQECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIPDES 83
Cdd:cd09985    1 QEQIMERLKKDVRSLLISSKNGLTPEQLEQDYLAMVGSPLPLRSLGFRSTMELVLDMPDVVRVHPQLDGTVILKAVGDET 80

                         90
                 ....*....|....*
gi 312283651  84 TKGIASLVAKQRSSH 98
Cdd:cd09985   81 TKGIEDLVSKQRDSK 95

The third LOTUS domain on Tudor-containing protein 5 (TDRD5); The third LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 312283651 296 SSELKHKIKFVVSKFPEGLFISKLLGEYEVIFKEQLSPKKLGFLNVTELVGALSDILHVEFRKGHQDLLVFDAD 369
Cdd:cd09976    1 SRELREEIRKVVENHPNGLFIALLPTEYKVLFKEELPVKQLGFLSVTELVGSLSDILAIERREKESDWLVFDAK 74

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 476 FVEYIISPSQFYIRI--YSRDSSELLEDMMIEMRRCYSNQLVSDRyvmPEcfiqPGHLCCVRISEDKWWYRVIIHRVLEk 553
Cdd:cd20438   10 FVEYVLNPSNFWIRTdeYNNEFQALMKNIADIYNLCGNDEELLKK---PE----PGLLCCARYSKDRHYYRAVITEVLD- 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 554 QEVEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPVEEHWTSKAILQFQK 613
Cdd:cd20438   82 LKVSVYFLDFGNTDTVPFYDVKTLLPEFSELPALAMCCSLAHVFPVEEVWTKNANDFFKK 141

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 475 VFVEYIISPSQFYIRIYSRDSSELLEDMMIEMRRCYSNQLVSDRYVmPECfiqpGHLCCVRISEDKWWYRVIIHRVLEKQ 554
Cdd:cd20408    1 GTVTEFKNPGEFYIQIYTLEVLESLVKLTSQLKKTYASVNNHKEYI-PEV----GEVCVAKYSEDQNWYRALVQTVDVQQ 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 312283651 555 E-VEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPVEEHWTSKAI 608
Cdd:cd20408   76 KkAGVFYIDYGNEETVPLNRIQPLKKDIELFPPCAIKCCLANVKPPSGSWSEECI 130

Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar proteins; dTUD is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation. It contains 11 Tudor domains. The family also includes mitochondrial A-kinase anchor protein 1 (AKAP1) and Tudor domain-containing proteins (TDRDs). AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), or dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), or protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. TDRDs have diverse biological functions and may contain one or more copies of the 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 312283651 528 PGHLCCVRISEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFL 577
Cdd:cd20379    1 VGDLCAAKYEEDGKWYRARVLEVLSNDKVEVFFVDYGNTETVPLSDLRPL 50

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 312283651   9 ECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVI 75
Cdd:cd08824    2 KQLAKQLRSLLQSYPGGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIVLSQGGERIV 68

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 473 IGVFVEYIISPSQFYIRiYSRDSSELLEDMMIEMRRcysnQLVSDRYVMPEcfIQPGHLCCVRISEDKWWYRVIIHRVLE 552
Cdd:cd20426    1 IEAYATAVDSPEYFWCQ-FATEKIQCLAVKVQEAGE----QVADRGNFIPS--IYVGDPCIVKYSEDNHWYRALVTKIND 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 312283651 553 KQeVEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPVEEHWTSKAILQF 611
Cdd:cd20426   74 NL-VSVRFVDYGNEEDVVREQVRALPSELLKIPVQAFPCCLSGFNLSEGLWSDEANDYF 131

fifth 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 fifth 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 475 VFVEYIISPSQFYIRIySRDSsELLEDMMIEMRRcYSNQLVSDRYVMPECfiqpgHLCCVRISEDKWWYRVIIHRVLEKQ 554
Cdd:cd20440   14 VYITHVYSPAKFYCQL-DRNT-EILEALMEKIAE-ISKLFNSQILDNCKT-----RLCLAKYFEDGQWYRALAHPVESSS 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 312283651 555 EVEVFYPDFGNIGIVQKSSLRFLKCCYTKL---PAQAIPCSL 593
Cdd:cd20440   86 HLSVYFVDYGNKQIVEKNEVLPIPDTAVDLlltPMQAIKCCL 127

fifth 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 fifth 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 475 VFVEYIISPSQFYIRIySRDSSelledmMIEMRRCYSNQLvSDRYVMPECFIQPGHLCCVRISeDKWWYRVIIhrVLEKQ 554
Cdd:cd20424   16 VYITYVNDPWTFYCQL-ARNAG------VLDQLASAISRL-SSEIRKLELSVNPGTLCLAKYS-DQHWYRGII--ITNKN 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 312283651 555 EVEVFYPDFGNIGIVQKSSLRFL---KCCYTKLPAQAIPCSL 593
Cdd:cd20424   85 STEVFFVDYGNTEKVEKEDMLPIpsdAYELLLLPMQAIKCSL 126

second Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five 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        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 312283651 533 CVRISEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRP 598
Cdd:cd20415   31 CVALFEDGAWYRARIIGLPGHREVEVKYVDFGNTATVTIKHVRKIKDDFLSLPEKARECRLAFIEP 96

second 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 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 481 ISPSQFYIRIYSrdSSELLEDMMIEMRRCY---SNQLVSdryvMPECFiqpGHLCCVRiSEDKWWYRVIIHRVLEKQEVE 557
Cdd:cd20437   13 VSPSKFYCQLLS--WEPELSKLTTQMTLHYesvSKELNP----SCENF---GLLCAAK-GKDGQWHRGFLQQLLPPSQVK 82

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 312283651 558 VFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLA 594
Cdd:cd20437   83 VWFIDYGNSEAVSSHSVLKLPPDFFSLPLMSFPCSLS 119

The first LOTUS domain on Tudor-containing protein 7 (TDRD7); The first LOTUS domain on Tudor-containing protein 7 (TDRD7): TDRD7 contains three N-terminal LOTUS domains and three Tudor domain repeats at the C-terminus. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD7 together with TDRD1/MTR-1, TDRD5 and TDRD6 forms a ribonucleoprotein complex in the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs) involving in RNA processing for spermatogenesis. TDRD7 is functionally essential for the differentiation of germ cells. The exact molecular function of LOTUS domain on TDRD7 remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651   9 ECLRKEIRSLLISTKDGLSPQELEKEYLLMVGNHLPLRILGYRSTMELVLDMPDVVRVCPGAGGTVILKAIPDESTKGIA 88
Cdd:cd09986    2 ELVKKMLRAVLQSSKGGVSLPRLQGEYKELTGEQIPFKQLGYHTLDALLRSMPSVVRLERSRSGEVMCFASLCNETAHIA 81

                 ....*..
gi 312283651  89 SLVAKQR 95
Cdd:cd09986   82 KLVARQR 88

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        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 482 SPSQFYIRIySRDSSELLeDMMIEMrrcysNQLVSDRYVMPECFIQPGHLCCVRISEDKWWYRVIIHRVLEKQEVEVFYP 561
Cdd:cd20441    1 SPSRFFIQL-SEDEKVIL-QLAEEL-----NETSEKSRENAAVKLKVGDLVAAEYDEDLALYRAVITAVLPGKSFKVEFI 73

                         90       100       110
                 ....*....|....*....|....*....|...
gi 312283651 562 DFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLA 594
Cdd:cd20441   74 DYGNTAVVDKSNIYTLQEKFLSLPRLSIPCSLS 106

second Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the second/C-terminal 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 482 SPSQFYIRIYS---------RDSSELLEDMMIEMRRCYSNQlvSDRyvMPECFIQPGHLCCVRISEDKWwYRVIIHRVLE 552
Cdd:cd20435    1 DATHYSARILEhrssdgevtKSMSSTYLKLSMKLNMYYSDP--SNR--ILHGKVKVGDLCAVEDENNLY-HRVKVLEITE 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 312283651 553 K------QEVEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPV--EEHW 603
Cdd:cd20435   76 KddktkpREVLVKFIDEGRVETVVVSQLLELPEELKSLPPQAVEVFLCNVKPVdnDTEW 134

seventh 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 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 479 YIISPSQFYIRIYSRDSSELLEDMMI--EMRRCYsnqlvsdryVMPECFIQPGHLCCVRISEDKWWYR-VIIHRVLEKQE 555
Cdd:cd20442   10 SVSKNGTFYVRLLRNSEQLTDLESLIakEAKKCK---------FVPVEDIKEGLECLAKSKKNLKWYRaVVEHLYPETEK 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 312283651 556 VEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPVEEH 602
Cdd:cd20442   81 MLVFFVDHGITEVVSMGNIKQLSNDLLQIPRQAVLCRWNWPESSKEL 127

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 312283651   526 IQPGHLCCVRIsEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFLKC 579
Cdd:smart00333   3 FKVGDKVAARW-EDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPE 55

LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7; LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 312283651 298 ELKHKIKFVVSKFPEGLFISKLLGEYEVIFKEQLSPKKLGFLNVTELVGALSDILhVEFRKGHQDLLV 365
Cdd:cd08824    3 QLAKQLRSLLQSYPGGLPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVV-IVLSQGGERIVS 69

Tudor domain found in Tudor domain-containing protein 8 (TDRD8) and similar proteins; TDRD8, also called serine/threonine-protein kinase (EC 2.7.11.1) 31 (STK31), serine/threonine-protein kinase NYD-SPK, or Sugen kinase 396 (SgK396), is a germ cell-specific factor expressed in embryonic gonocytes of both sexes, and in postnatal spermatocytes and round spermatids in males. It acts as a cell-cycle regulated protein that contributes to the tumorigenicity of epithelial cancer cells. TDRD8 contains a Tudor domain and a serine/threonine kinase 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
                 ....*....|....*....|....*....|....*....|.
gi 312283651 537 SEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFL 577
Cdd:cd20430   30 SEDNCWYRCKVKSILSDEKCTVQYIDYGNTETVSRSSIVEL 70

third Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five 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
                 ....*....|....*....|....*....|....*....|....*..
gi 312283651 532 CCVRISEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFLK 578
Cdd:cd20416   25 CAVQIQDKKQWRRGQIIRVVSDTLVEVFLYDFGNKEVVNIDCLRKLE 71

Tudor domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. It contains 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        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 312283651 526 IQPGhLCCVRISEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRP 598
Cdd:cd20407    5 IEVG-VICAAPVMNAWYRAQVVGVFEETDEVEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

third 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 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
                 ....*....|....*....|....*....|....*....|....*....
gi 312283651 527 QPGHLCCVRISEDKWWYRVIIHRVLEKQEVEVFYPDFGNIGIVQKSSLR 575
Cdd:cd20410    4 IVGEPCCAFFSGDGNWYRAMVKEILPGGAVKVHFVDYGNVEEVTLDKLR 52

first Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the first/N-terminal 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 480 IISPSQFYIRI-----YSRDSSELLEDMMIEMRRCYSNQLVSDRYVMPECfIQPGHLCCVRISEDKWWYRVIIHRVLEKQ 554
Cdd:cd20434    6 IEDPGCFWGRIlkgsgDLVVNPEEYENLQDEMNQFYHKGYKDVEEIKPST-LEEGQVCVVFCEELKCWCRAVVESLMSSA 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 312283651 555 E---VEVFYPDFGNIGIVQKSSLRFLKCCYTKLPAQAIPCSLAWVRPVEEH---------------WTSKAILQFQKL 614
Cdd:cd20434   85 DdylAECFLVDYAKYIPVKSKDIRVALEAFMKLPYRAKKFRLYGIKPVTLHvdlcedkakivparkWDSAAIQYFQNL 162

second Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312283651 475 VFVEYIISPSQFYIRIYSRDSSELLEDMMIEMRRCYSNQLVSDRYV-MPECfiqpGHLCCVRiSEDKWwYRVIIHRVLEK 553
Cdd:cd20428    4 VRVTNVCSDGTLYCQVPSKGLSKLNEILDKIEYYFHSRQMTSEYFVsLPFC----GKICLAR-YKGKW-ARVEITNVHSS 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 312283651 554 QEVEVFYPDFGNIGIVQKSSLR-----FLKCcYTKLPAQAIPCSLAWVRPVEEHWTSKAIL 609
Cdd:cd20428   78 RALDVHFLDTGTVASVKVSELReipppFLRE-LISIPPQALKCCLADLPLNIGMWTPDAVL 137