Conserved Protein Domain Family

cd12422: RRM2_PTBP1_hnRNPL_like 
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RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins
This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.
PSSM-Id: 409856
Aligned: 30 rows
Threshold Bit Score: 79.5391
Created: 13-Sep-2011
Updated: 25-Oct-2021
Aligned Rows:
RNA binding
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
  • Structure:2ADB; Homo sapiens polypyrimidine tract binding protein RNA recognition motif 2 binds a CUCUCU oligonucleotide, contacts at 4A.
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Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1          # #                           # # #     # #                                   
2E5I_A        25 VLLLSIQNply-piTVDVLYTVCNPVGkvqRIVIFKRn--gIQAMVEFEsvLCAQKAKAALNGadiy-------agccTL 94  house mouse
Q9MAC5       244 VLLGLIENmqy-avTVDVLHTVFSAYGtvqKIAIFEKng-sTQALIQYSdiPTAAMAKEALEGhciyd------ggycKL 315 thale cress
XP_001459217  16 VILVVITNkanktlSHDKYFKVFSPFGtiqRMLIFERsl-tWKTFVEFDnpESALKARSQMNDkffcd------dntlLM 88  Paramecium tetr...
Q9FGL9       112 VLLVTIEGddarmvSIDVLHLVFSAFGfvhKITTFEKta-gYQALVQFTdaETATAAKLALDGrsipryllaetvgqcSL 190 thale cress
EER16818     128 ILLFTITNvvy-pvNVSMIAQVMSRYNaleKVVIFTRgn-aTHCLIQTSslEAAVAAKTQLDGqnif-------thcnTI 198 Perkinsus marin...
A0E9X1        10 VLLVIVQNpqsiilPHSLFYRYFSNFGevnKILIFEKgk-qWKCFIEMAtlQQARFSQQQLNGcqly--------dqtIM 80  Paramecium tetr...
A0CTN0         6 VVLLCIQNkkqitiTHDQIYKHFSQYGqieKILIFEKtq-iWKVFLETKnkETAQNLIKQCTNniln--------qdaSL 76  Paramecium tetr...
XP_001448291   6 VVLICIQNpdfiniTVTHVYQNFIQFGtieKILIFERnkpiWKALVQFDsvRSALNALQLNNTimh----------glSI 75  Paramecium tetr...
CDW74237     186 IILVTITNiry-pvNADVLFTTFHKFGepqRIVIFPRql-gEQALVEFAsvEQAKKAKQEMDGksiys------nssnLM 257 Stylonychia lemnae
Feature 1        #  ##      #####
2ADB_A       104 RIDFSk--lTSLNVKY 117 human
2E5I_A        95 KIEYAr--pTRLNVIR 108 house mouse
Q9MAC5       316 RLSYSr--hTDLNVKA 329 thale cress
XP_001459217  89 NVYASk--lTYITFQE 102 Paramecium tetraurelia strain d4-2
Q9FGL9       191 KITYSa--hTDLTVKF 204 thale cress
EER16818     199 RVQFSe--lSKLEVKY 212 Perkinsus marinus ATCC 50983
A0E9X1        81 NVYYSt--lQNVTFLN 94  Paramecium tetraurelia
A0CTN0        77 RMQLYpsnlENPTFSD 92  Paramecium tetraurelia
XP_001448291  76 LVYESn--rKGLDFQA 89  Paramecium tetraurelia strain d4-2
CDW74237     258 KIQFSe--mKKLEINS 271 Stylonychia lemnae

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