2ADB


Conserved Protein Domain Family
RRM2_PTBP1_like

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cd12693: RRM2_PTBP1_like (this model, PSSM-Id:241137 is obsolete and has been replaced by 410093)
Click on image for an interactive view with Cn3D
RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) 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), and similar proteins found in Metazoa. 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. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian 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 may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).
Statistics
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PSSM-Id: 241137
Aligned: 14 rows
Threshold Bit Score: 184.552
Created: 14-Dec-2011
Updated: 1-Feb-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA binding
Conserved site includes 21 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Structure:2ADB; Homo sapiens polypyrimidine tract binding protein RNA recognition motif 2 binds a CUCUCU oligonucleotide, contacts at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            # #                          # # #  # # #                            #  ####
2ADB_A        31 SPVLRIIVENlfypvTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGqniynaccTLRIDFSKL 110 human
NP_001116126 188 SPVLRVIVENlfypvTLDVLHQIFSKFGTVLKVITFTKNNQFQALLQFTDGLTAQHAKLALDGqniyngccTLRISFSKL 267 zebrafish
NP_001163789 107 NTVLRVIVESlmypvSLDILHQIFQRYGKVLKIVTFTKNNSFQALIQYPDANSAQHAKSLLDGqniyngccTLRIDNSKL 186 fruit fly
XP_002115096 123 GRVLHISIDNlvypvTLDILNQIFSKFGVVEKIITFTKNNLYQALIQFTDAVDAQNAKLSLDGqsiyygccTLKIDYSKL 202 Trichoplax adha...
XP_001636058 121 GCILRIIVENmlypiTIEVLNQIFTKYGTVLKIVIFTRNNQFQALVQFSQSTEARAAKCSLDGqniyngccTLRIDYSKL 200 starlet sea ane...
XP_003386453 129 NSILRVIIENmiypiTIDVLHQIFAKYGDVLKVVTFMKNTQFHALIQYPNEIIATNAKTALDGqniyngccTLHIDYSKL 208 Amphimedon quee...
CBY24911     424 NHVLRVVVENmtyptTLEVLTHLFSQFGNVLKVITFTKNNQFQALIQMDCESNAQAAKLSLDGknvytnccTLRIDYSKL 503 Oikopleura dioica
EFX81898     165 NTVLRVIVEHmvypvTLDVLFQIFSKVGRVLKIVTFTKNNTFQALIQYPDVVTAQAAKLTLDGqniynsccTLRIEYSKL 244 common water flea
XP_002433623 171 NTVLRVVVDNqiypvSLDLLHGIFSRAGKVLKIVTFTKSNTFQALIQFSDVMGAQAAKLALDGqsiynaccTLRIEYSKL 250 black-legged tick
NP_741042     67 NSVLRTIIENmmfpvSLDVLYQLFTRYGKVLRIITFNKNNTFQALVQMSEANSAQLAKQGLENqnvyngccTLRIDYSKL 146 nematode
Feature 1          ##### ###     
2ADB_A       111 TSLNVKYNNDKSRDYT 126 human
NP_001116126 268 TSLNVKYNNDKSRDYT 283 zebrafish
NP_001163789 187 TALNVKYNNDKSRDFT 202 fruit fly
XP_002115096 203 LSINVKYNNDKSRDFT 218 Trichoplax adhaerens
XP_001636058 201 KTLSVKYNNDKTRDYT 216 starlet sea anemone
XP_003386453 209 SNLTVKFNNEKTRDFT 224 Amphimedon queenslandica
CBY24911     504 QQLNVKFNNEKSRDYT 519 Oikopleura dioica
EFX81898     245 SSLNVKYNNDKSRDYT 260 common water flea
XP_002433623 251 TNLNVKYNNDKSRDFT 266 black-legged tick
NP_741042    147 STLNVKYNNDKSRDYT 162 nematode

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