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 22831735 441 LLPSLELSAVCVIPINDVWYRVQIVDTDPEDEErCVIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECILSNIEP 517
Cdd:cd20407   1 LPEPIEVGVICAAPVMNAWYRAQVVGVFEETDE-VEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

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 22831735 441 LLPSLELSAVCVIPINDVWYRVQIVDTDPEDEErCVIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECILSNIEP 517
Cdd:cd20407   1 LPEPIEVGVICAAPVMNAWYRAQVVGVFEETDE-VEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22831735 289 TYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMIRQRLP 356
Cdd:cd22395   1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKFP 68

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 22831735    443 PSLELSAVCVIPIND-VWYRVQIVDTDPEDEerCVIKFLDFGGYMNVGFNTLRQIRTDF 500
Cdd:smart00333   1 PTFKVGDKVAARWEDgEWYRARIVKVDGEQL--YEVFFIDYGNEEVVPPSDLRQLPEEL 57

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 22831735 441 LLPSLELSAVCVIPINDVWYRVQIVDTDPEDEErCVIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECILSNIEP 517
Cdd:cd20407   1 LPEPIEVGVICAAPVMNAWYRAQVVGVFEETDE-VEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22831735 289 TYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMIRQRLP 356
Cdd:cd22395   1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKFP 68

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22831735 291 EFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMIR 352
Cdd:cd00105   2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

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 22831735 418 PSHPSLPLLQKQLYDSYSTMEAP-LLPSLELSAVCVI-PINDVWYRVQ---IVDTDPEDEERCV-IKFLDFGGYMNVGFN 491
Cdd:cd20435  22 SMSSTYLKLSMKLNMYYSDPSNRiLHGKVKVGDLCAVeDENNLYHRVKvleITEKDDKTKPREVlVKFIDEGRVETVVVS 101

                        90       100
                ....*....|....*....|....*..
gi 22831735 492 TLRQIRTDFMNVPFQSTECILSNIEPI 518
Cdd:cd20435 102 QLLELPEELKSLPPQAVEVFLCNVKPV 128

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.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 22831735 459 WYRVQIVDTDPEDEERcvIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTEC 510
Cdd:cd20412  45 WYRARVLGFLENGNLD--LYFVDYGDSGYVPLEDLRALRSDFLSLPFQAIEC 94

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22831735 290 YEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMI 351
Cdd:cd22462   1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLI 62

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 22831735 450 VCV-IPINDVWYRVQIVDTDPEDEerCVIKFLDFGGYMNVGFNTLRQI 496
Cdd:cd20379   5 CAAkYEEDGKWYRARVLEVLSNDK--VEVFFVDYGNTETVPLSDLRPL 50

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 22831735 288 TTYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMIRQ 353
Cdd:cd22396   1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLIDQ 66

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 22831735    443 PSLELSAVCVIPIND-VWYRVQIVDTDPEDEerCVIKFLDFGGYMNVGFNTLRQIRTDF 500
Cdd:smart00333   1 PTFKVGDKVAARWEDgEWYRARIVKVDGEQL--YEVFFIDYGNEEVVPPSDLRQLPEEL 57

fourth 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 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        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22831735 398 DVVVSAVLSGSHIFIQhpLHPSHPSLPLLQKQLYDSYSTMEAPLLPSlelSAVCVIP-IND-VWYRVQIVDTDPEDEERC 475
Cdd:cd20439  13 DVKCSYVNSPGDFWCQ--LQTKSSELKSLMKQIQSYYLIHNDPYKHG---QIACVAKySKDgKWYRAAVLKQVSAKEVDV 87

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
gi 22831735 476 VikFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECILSNI 515
Cdd:cd20439  88 I--FVDYGNQERVLISDLRAIKPQFLLLEGQAFRCSLNNF 125

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22831735 282 EATRVKTTYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMIRQR 354
Cdd:cd22522   3 DASPPASTHELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSSERQITITGSPANISLAQYLINAR 75

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 22831735 293 LFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKV--RICTIEGTESEIDAALAMIRQRL 355
Cdd:cd22436   6 LVPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLqeRVVTVTGEPEANRKAVSLILQKI 70

fifth 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 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 22831735 459 WYRVQIVDTDPEDEERCVIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECILSNIEPI---GGT--------WSIEA 526
Cdd:cd20418  19 WYRAKLLSILEFNPVKILVRHVDYGSTAALPTSRLRQIPAELMQYPCQAIKVKLAGFKPPlndSETeripycpeWSMKA 97

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins; PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 22831735 288 TTYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSGKVRICTIEGTESEIDAALAMI 351
Cdd:cd22523   2 SSQEFLIPNDLIGCVIGRQGSKISEIRQMSGAHIKIGNQTEGTSERHVTITGSPVSITLAQYLI 65

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 22831735 289 TYEFLFPISLIGHLYGRKRAFINQIKAKTLASVSVGKNPYSgKVRICTIEGTESEIDAALAMIRQ 353
Cdd:cd22458   2 TWEIKLPQALCGRLIGAKGKNIKALSEKSGASIRLIPISNS-SQQTIHLSGTDKQIALAISSIEE 65

Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins; TDRD5 is an RNA-binding protein directly associated with piRNA precursors. It is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis. TDRD5 participates in the repression of transposable elements and prevents their mobilization, which is essential for germline integrity. TDRD5 contains three LOTUS 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22831735 401 VSAVLSGSHIFIQHPLHPSHPSLPLLQKQLYDSYST---MEAPLLPSLELS---AVCVIPINDV-WYRVQIVDTDPEDEE 473
Cdd:cd20419   2 VEYIESPSQFYVRFYSKDTSEMLEDMMIEMRRCYSNehvSERYVMPEAFIQpgqVCCVRIPEDVwWYRVIIHQVLNKQEV 81

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 22831735 474 RcvIKFLDFGGYMNVGFNTLRQIRTDFMNVPFQSTECIL 512
Cdd:cd20419  82 E--VFYPDFGDIGTVQKSRLRFLKCCYSKLPAQAIPASL 118