2K3K,1URN,1A9N,3CUL,1M5K,1AUD,3K0J,1U6B,3L3C,1DRZ,3JB9,5LJ3


Conserved Protein Domain Family
RRM1_U1A_like

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cd12246: RRM1_U1A_like 
Click on image for an interactive view with Cn3D
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family
This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.
Statistics
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PSSM-Id: 409692
Aligned: 46 rows
Threshold Bit Score: 106.079
Created: 14-Sep-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA binding
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1          # ##  #                         # # ### ### #                       #  # ####
2K3K_A         8 TIYINNLNEK-IKKEELKKSLYAIFSqFGQILDIVALKTLKmRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85  fruit fly
3CUL_A        11 TIYINNLNEK-IKKDELKKSLHAIFSrFGQILDILVSRSLKxRGQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQYAK 88  human
XP_001307983  10 TLFVRNLTDK-IPIDDLKRNLYYLFSsVAPVVEINARKGQS-RGQAWVSFPNLESAEIIMKQFNNFPFLGKALQIEYSK 86  Trichomonas vagi...
XP_656582     22 TLYINNLDQS-IKPNRIRDSLNTVFGaYGNVLQVCVRKSLKmRGQAFVIYDTKESAQFAMESLQNHELFDRPMHINYSK 99  Entamoeba histol...
XP_001328901   9 TLYIKRINDN-VSINQLILHVFAYFSpYGQIIDISASKAIKkRGQAWVTYQNIESAINAKRDLNGIYIFSTPISIQFAK 86  Trichomonas vagi...
EER19690      19 TLYVNNLNDK-IKLDDLKPLLFELFAsFGPILAVYAGKSQSrRGQAFIAFREASNAALAMKTLNGFPFLDKPLRVAFAR 96  Perkinsus marinu...
AAX69673       7 TLYIRGLPDK-PSAEEVRRLLYLYCTqFGPVIDVLYCKSKSmYGQAFVVFTDVATATNARRELHERQFYGRIIQAFYAK 84  Trypanosoma bruc...
P40567        29 TLYVSQLNEK-INMQRLRVNLFLLFAtFGEVLKVSMNFKKQ-RGQAFITMRTIDQASLAQISLNGERFFGKPLKVEFSK 105 Saccharomyces ce...
EGP84373      10 TLYLRNLPERqVSIPLLKEGIREIVEdLGTVLDIRAGKSLKqRGQAFVVYSRVEEATEAHDILQDIELFGRKIQVQYAR 88  Mycosphaerella g...
5LJ3_Y        29 TLYVSQLNEK-INMQRLRVNLFLLFAtFGEVLKVSMNFKKQ-RGQAFITMRTIDQASLAQISLNGERFFGKPLKVEFSK 105 Saccharomyces ce...

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