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 2462603959  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 183 --IKPKSAPWN-SFlpppppmpGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADA 259
Cdd:pfam06003 159 nfPMGPPSPWNpSF--------PPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEA 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2462603959 260 LGSMLISWYMSGYHTGYYMfpeaSLKAEQMPA 291
Cdd:pfam06003 228 LGSMLIAWYMSGYHTGYYL----GLKQGRMEA 255

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 2462603959  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 183 --IKPKSAPWN-SFlpppppmpGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADA 259
Cdd:pfam06003 159 nfPMGPPSPWNpSF--------PPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEA 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2462603959 260 LGSMLISWYMSGYHTGYYMfpeaSLKAEQMPA 291
Cdd:pfam06003 228 LGSMLIAWYMSGYHTGYYL----GLKQGRMEA 255

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 2462603959   90 QQWKVGDKCSAIWsEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDLLSPICE 147
Cdd:smart00333   1 PTFKVGDKVAARW-EDGEWYRARIVKVD-GEQLYEVFFIDYGNEEVVPPSDLRQLPEE 56

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 2462603959  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462603959 183 --IKPKSAPWN-SFlpppppmpGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADA 259
Cdd:pfam06003 159 nfPMGPPSPWNpSF--------PPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEA 227

                         250       260       270
                  ....*....|....*....|....*....|..
gi 2462603959 260 LGSMLISWYMSGYHTGYYMfpeaSLKAEQMPA 291
Cdd:pfam06003 228 LGSMLIAWYMSGYHTGYYL----GLKQGRMEA 255

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 2462603959  95 GDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSP 144
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 2462603959  92 WKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLsPI 145
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIK-PI 53

N-terminal Gemin2-binding 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 N-terminal Gemin2-binding domain of SMN family proteins.

                          10        20        30
                  ....*....|....*....|....*....|.
gi 2462603959  29 DDSDIWDDTALIKAYDKAVASFKHALKNGDI 59
Cdd:cd22851     1 DDSDIWDDSALIKAWDEAVAEYKKYHSIRAK 31

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 2462603959  95 GDKCSAIWSEDGCIYPATIASIDFKReTCVVVYTgYGNREEQNLSDL 141
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 2462603959  93 KVGDKCSAIWSEDGCIYPATIasIDFKRETCVVV-YTGYGNREEQNLSDL 141
Cdd:cd20409    27 AVGEVCCAQFTEDNQWYRASV--LAYSSEDSVLVgYIDFGNSEEVALSRL 74

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 2462603959  93 KVGDKCSAIWsEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDLL 142
Cdd:cd20384     6 KEGSRCLAKY-DDGLWYPATVTDID-EDGKYTVKFDSYGEVAVVELDDIL 53