Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580     23 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETPDKPKGTAR--RKPAKKNKSQKKNATTPLKQWKVGDKCSAVWS 100
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPGkkRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    101 EDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLLSPTCEVANSTEQNTQENESQVSTDDSEHSSRSLRSKAHS-- 178
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETESSTDESDRSSGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    179 -KSKAAPWT-SFlpppppmpGSGLGPGKPGLkfnGPPPPPPLPPPPFLPCWMPPFPSGPPIIPPPPPISPDCLDDTDALG 256
Cdd:pfam06003 161 pMGPPSPWNpSF--------PPGPPPPPPGF---GRHGEKPRTLGPFLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALG 229

                         250       260       270
                  ....*....|....*....|....*....|...
gi 6755580    257 SMLISWYMSGYHTGYYMGFRQNKKE---GKCSH 286
Cdd:pfam06003 230 SMLIAWYMSGYHTGYYLGLKQGRMEaaaSKKSH 262

Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580     23 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETPDKPKGTAR--RKPAKKNKSQKKNATTPLKQWKVGDKCSAVWS 100
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPGkkRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    101 EDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLLSPTCEVANSTEQNTQENESQVSTDDSEHSSRSLRSKAHS-- 178
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETESSTDESDRSSGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    179 -KSKAAPWT-SFlpppppmpGSGLGPGKPGLkfnGPPPPPPLPPPPFLPCWMPPFPSGPPIIPPPPPISPDCLDDTDALG 256
Cdd:pfam06003 161 pMGPPSPWNpSF--------PPGPPPPPPGF---GRHGEKPRTLGPFLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALG 229

                         250       260       270
                  ....*....|....*....|....*....|...
gi 6755580    257 SMLISWYMSGYHTGYYMGFRQNKKE---GKCSH 286
Cdd:pfam06003 230 SMLIAWYMSGYHTGYYLGLKQGRMEaaaSKKSH 262

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 6755580      87 KQWKVGDKCSAVWsEDGCIYPATITSIDfKRETCVVVYTGYGNREEQNLSDL 138
Cdd:smart00333   1 PTFKVGDKVAARW-EDGEWYRARIVKVD-GEQLYEVFFIDYGNEEVVPPSDL 50

Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580     23 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETPDKPKGTAR--RKPAKKNKSQKKNATTPLKQWKVGDKCSAVWS 100
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPGkkRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    101 EDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLLSPTCEVANSTEQNTQENESQVSTDDSEHSSRSLRSKAHS-- 178
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETESSTDESDRSSGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6755580    179 -KSKAAPWT-SFlpppppmpGSGLGPGKPGLkfnGPPPPPPLPPPPFLPCWMPPFPSGPPIIPPPPPISPDCLDDTDALG 256
Cdd:pfam06003 161 pMGPPSPWNpSF--------PPGPPPPPPGF---GRHGEKPRTLGPFLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALG 229

                         250       260       270
                  ....*....|....*....|....*....|...
gi 6755580    257 SMLISWYMSGYHTGYYMGFRQNKKE---GKCSH 286
Cdd:pfam06003 230 SMLIAWYMSGYHTGYYLGLKQGRMEaaaSKKSH 262

Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing factor 30 (SPF30), and similar proteins; This group contains SMN, SPF30, Tudor domain-containing protein 3 (TDRD3), DNA excision repair protein ERCC-6-like 2 (ERCC6L2), and similar proteins. SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. 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. TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing 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. Members of this group contain a single 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 6755580   92 GDKCSAVWSEDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLLSP 141
Cdd:cd21182   1 GDKCLAPYSDDGKYYEATIEEITEESDTATVVFDGYGNSEEVPLSDLKPL 50

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 6755580   89 WKVGDKCSAVWSEDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLL 139
Cdd:cd20413   1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIK 51

C-terminal oligomerization domain of the Survival Motor Neuron family; The survival motor neuron (SMN) protein family includes metazoan SMN and fungal SMN-like protein 1 (SMN1). SMN forms the oligomeric core of a multiprotein complex, called the SMN complex, that functions in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is expressed in all tissues of metazoan organisms, but is particularly expressed at high levels in motor neurons. Schizosaccharomyces pombe SMN1 is essential for viability and has been shown to interact with human SMN and Sm proteins. Loss of function mutations in the SMN gene of humans cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. While most eukaryotes have a single copy of the SMN gene, humans have two; the telomeric SMN1 gene is deleted or mutated in SMA patients, whereas the centromeric SMN2 gene is unaffected and can be present in multiple copies. SMN has three highly conserved domains: a short N-terminal region that is responsible for binding with high affinity to Gemin2; a central Tudor domain that recognizes symmetric dimethylarginine (sDMA) modifications in arginine/glycine rich regions of a number of proteins involved in RNA processing, including the Sm proteins; and a C-terminal domain called the YG-box that is primarily responsible for oligomerization. This model represents the C-terminal oligomerization domain of SMN family proteins.

                        10        20
                ....*....|....*....|....*....
gi 6755580  251 DTDALGSMLISWYMSGYHTGYYMGFRQNK 279
Cdd:cd22852   1 DDEALKNLLMSWYMAGYYTGYYQGLQQAQ 29

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 6755580   92 GDKCSAVWSEDGCIYPATITSIDFKReTCVVVYTgYGNREEQNLSDL 138
Cdd:cd04508   1 GDRVEAKWSDDGQWYPATVVAVNDDG-KYTVLFD-DGNEEEVSEDDI 45

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 6755580   90 KVGDKCSAVWSEDGCIYPATItsIDFKRETCVVV-YTGYGNREEQNLSDL 138
Cdd:cd20409  27 AVGEVCCAQFTEDNQWYRASV--LAYSSEDSVLVgYIDFGNSEEVALSRL 74

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
                ....*....|....*....|....*....|....*....|....*....
gi 6755580   91 VGDKCSAVWSEDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLL 139
Cdd:cd20408  49 VGEVCVAKYSEDQNWYRALVQTVDVQQKKAGVFYIDYGNEETVPLNRIQ 97

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
                ....*....|....*....|....*....|....*....|....*.
gi 6755580   95 CSAVWSEDGCIYPATITSIDFKRETCVVVYTGYGNREEQNLSDLLS 140
Cdd:cd20423   9 CLAKYSEDGKWCRALIDNVYEPVEMVEVTYVDYGNKELVSLKNLRS 54

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
                ....*....|....*....|....*....|....*....|....*...
gi 6755580   91 VGDKCSAVWSEDGCIYPATITSIDfKRETCVVVYTGYGNREEQNLSDL 138
Cdd:cd20379   1 VGDLCAAKYEEDGKWYRARVLEVL-SNDKVEVFFVDYGNTETVPLSDL 47