Conserved Protein Domain Family

cd12232: RRM3_U2AF65 
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RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins
This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.
PSSM-Id: 409679
Aligned: 63 rows
Threshold Bit Score: 66.8426
Created: 15-Sep-2011
Updated: 25-Oct-2021
Aligned Rows:
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:polypeptide substrate binding site [polypeptide binding site]

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1             #  #         ## ### ### ##                                                 
1O0P_A         4 TEVLCLMNMVlpeellddEEYEEIVEDVRDECskYGLVKSIEIPrpvd------------gvevPGCGKIFVEFTSvfDC 71  human
CBK21427     341 SPVLRMSNIIsledleedEDYEALLEDLREGCekLGTVLNMHVPrihsg-----------ekeiPGLGFAFVQYSSviEA 409 Blastocystis ho...
EAY17566     309 ETVLCLYNIAkdyilmdpELTNEFLSDITEECqkYGTILDYKIDpme---------------hqNDYGVVKIRYKTpeEA 373 Trichomonas vag...
XP_001321846 319 SRFLKIYNVLkrd--tpsEEVNTVIGDMKEECekYGKVLNAYAEttfp------------kfssIIPTPIVIEYEKteDA 384 Trichomonas vag...
CAI73511     311 GRYLHLVQIVlpetveaeVEYLDVLDDVKEEFgkHGKIKSALIIaprhk----------emakdFQAGDMMIEFEDedSL 380 Theileria annul...
EEQ99513      11 SRIVRFAQVVrvgpnttkEEYNDVIEDMKSGCggFGKLDAVYVAsadihdp-------steglvLAAGDVCLEYSDlgGA 83  Perkinsus marin...
EAA21097     433 TKYLRVLEIVspes-indEDYESILDDIKDGFhnQGIIINAVLInqkys-----------nntpFNIGDVIIEFENpnSV 500 Plasmodium yoel...
CBZ55301     279 SRVVHIACPSkie---kdEEYDEILNDILTECnkCGHALAALIIrpele----------qylpsVTVGDIYLEYASciQA 345 Neospora caninu...
XP_002142262 281 SSIMRLIQVVtpsniediYEYDEIFEDVKEGCekFGKILSGRILkpgeteelnevqkirnnnitLNTADVFLEFESsnIL 360 Cryptosporidium...
XP_002506172 490 QRVLAFSNVLvrg--gsrEDRAAATEDTLAECdgFGNVLSTHVVdggaega------egaeeldAVRDCLFVEFARveTA 561 Micromonas sp. ...
Feature 1              # #####   #   
1O0P_A        72 QKAMQGLtGRKFANRVVVTK 91  human
CBK21427     410 AQAAKQLrLLTFNGKQVQVD 429 Blastocystis hominis
EAY17566     374 KRAQLNLaGRRYEGRLVITS 393 Trichomonas vaginalis G3
XP_001321846 385 VKAQKIIaGLQYCGRALITC 404 Trichomonas vaginalis G3
CAI73511     381 LSCVQNMsNRKYENRLIQMK 400 Theileria annulata strain Ankara
EEQ99513      84 EACMRGMhGRKYDGQVVHMS 103 Perkinsus marinus ATCC 50983
EAA21097     501 ENSIITMsNRKYEGKPIRMT 520 Plasmodium yoelii yoelii str. 17XNL
CBZ55301     346 DHIILTFsGRMYDGKPLQLQ 365 Neospora caninum Liverpool
XP_002142262 361 QYCLTSMlNRSYEGKPLKME 380 Cryptosporidium muris RN66
XP_002506172 562 TIAAHAFhRREYDGRVVECR 581 Micromonas sp. RCC299

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