Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 443692967  202 ETWVTIFGFPPAASSFILQQFSQYGNITKHIISP-DGNWMHLHFQSKLQAKKALSKNGKVFGNSIMVGVTAC--IDKSVM 278
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHVPGPtNGNWMHLTYSSRSSAQKALSENGTIINGSVIVGVSYCpaTDKQVI 80

RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains.

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 443692967 202 ETWVTIFGFPPAASSFILQQFSQYGNITKHIISPDGNWMHLHFQSKLQAKKALSKNGKVFGNSIMVGVTACID 274
Cdd:cd12441    1 DTWVTVFGFPPSNASLVLREFSKCGDIVEHEYPPGGNWIHIRYENRLQAERALSKNGRVLNGNVMIGVKPCTD 73

RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains.

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gi 443692967 205 VTIFGFPPAASSFILQQFSQYGNI-------------TKHIISPDGNWMHLHFQSKLQAKKALSKNGKVFGNSIMVGV 269
Cdd:cd12721    4 VIVFGFPETITSQVIEHFSGFGEIledfsvprsgkalQKYPIPTGSNWLKLTYAEPSSALRALRENGEILNGQCMIGC 81

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

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                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 443692967 205 VTIFGFPPAAS-SFILQQFSQYGNITKHIISPDG-----NWMHLHFQSKLQAKKALSK-NGKVFGNSIM 266
Cdd:cd00590    1 LFVGNLPPDTTeEDLRELFSKFGEVVSVRIVRDRdgkskGFAFVEFESPEDAEKALEAlNGTELGGRPL 69