1UW4,2L08


Conserved Protein Domain Family
RRM_like_Smg4_UPF3

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cd12455: RRM_like_Smg4_UPF3 
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RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins
This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins.
Statistics
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PSSM-Id: 409889
Aligned: 44 rows
Threshold Bit Score: 58.0378
Created: 5-Apr-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
1UW4_A         3 KVVIRRLPPtLTKEQLQEHLqpm------------pehDYFEFFsndtsl----yphmyARAYINFKNqeDIILFRDRFD 66  human
EGO26896      33 KTVIRRLPPnLPEDVFWQSVqswvt---------ddttLWKMFYpgkvgkr-inkenipSRAYIAFRNeeQLAIFSREYD 102 Serpula lacryma...
Q10267        13 KVLVFNLPPtLPEQVFLQSInsfl-----------phvEWHRFSkgkatvg--trsellSFAYLKFQSatAVQEFFRVYQ 79  fission yeast
XP_001732785  13 KVVVRDLPPhLTENVFWEAVspwvrlkadpvtneprtaSRTAFVqgkrseq-asevdtlSVAYINFSDfkYVLDFVQNFQ 91  Malassezia glob...
XP_002175177  14 KLVVRKLPAnLPASVFWDSVkpwh-----------eaiERSRFHpghlqpe--kdlevhSYAILLFKSpeQVTSFFLHYQ 80  Schizosaccharom...
XP_003195171  13 KLVIRRLPPtLPEDIFWQSVstwit---------dktcLWKSFVkgkagdsnydsrpvySRAYVLMADpeSLVNFHRAEF 83  Cryptococcus ba...
EFN59157       8 KVVVRRLPPsLQEEAFRGAVrewi-----------eraDWFSYVqgkass----kdllhSRAYLRFKDaaDVPRFQQAWD 72  Chlorella varia...
GAX79793       5 KVAVRRLPPaLTEDVFKQTVekli----------egqyDWFSFFpgkass----kkvvfGRAYINFKStqAVIAFKLAFD 70  Chlamydomonas e...
NP_001117406   9 KVVVRHLPPsLSQSDLLSQIdprf----------adryNWVSFRpgksrlg--yknqkySRAYVSFKApeDVYEFAAFFN 76  thale cress
EFJ14754       9 KVVVRRLPPtLSEDALVSRIqtrf----------arpyLWMLFRpgkst------nqihSRAYIEFERpeDVLAFHEDFH 72  Selaginella moe...
1UW4_A        67 GYVFLDnk-----------------gqEYPAIVEFAP 86  human
EGO26896     103 GHLFRDkaglsrqlslhsviemylpgnESQAVVEFAP 139 Serpula lacrymans var. lacrymans S7.9
Q10267        80 GHTFIDkk-----------------nnTYRAIVTIAP 99  fission yeast
XP_001732785  92 GHIFRDsk-----------------gqNYHAFVDNAL 111 Malassezia globosa CBS 7966
XP_002175177  81 NHAFVNkn-----------------nvRYHASVAVAP 100 Schizosaccharomyces japonicus yFS275
XP_003195171  84 QAVVEYapfq-------------ktplKTKVKVDNRQ 107 Cryptococcus bacillisporus WM276
EFN59157      73 GHAFVNer-----------------gtQFRCQVEYAA 92  Chlorella variabilis
GAX79793      71 GHVFVGak-----------------gnQYRCSVEYAP 90  Chlamydomonas eustigma
NP_001117406  77 GHVFVNek-----------------gaQFKAIVEYAP 96  thale cress
EFJ14754      73 GHVFVNek-----------------gsQYKAMVEYAP 92  Selaginella moellendorffii
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