1CVJ,4F02


Conserved Protein Domain Family
RRM1_I_PABPs

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cd12378: RRM1_I_PABPs 
Click on image for an interactive view with Cn3D
RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins
This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.
Statistics
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PSSM-Id: 409812
Aligned: 46 rows
Threshold Bit Score: 151.631
Created: 13-Sep-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA bindingoligomer
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:RNA binding site [nucleic acid binding site]
Evidence:
  • Structure:1CVJ; human poly(A)-binding protein RNA recognition motifs RRM1/2 binds polyadenylate RNA, contacts at 4A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        # #         #                  ## ###  #  # # # #                        # #####
1CVJ_A        12 SLYVGDLHPdVTEAMLYEKFsp--aGPILSIRVCRDMITRRSLGYAYVNFQqpaDAERALDTmNFDVIKGKPVRIMWSQR 89  human
Q7S6N6        61 SLYVGELDPsVTEAMLFELFsq--iGSVASIRVCRDAVTRRSLGYAYVNYNttaDGEKALEElNYTLIKGRPCRIMWSQR 138 Neurospora cras...
Q4P8R9        48 SLYVGELDPsVTEAMLFEIFsm--iGTVASIRVCRDAVTRRSLGYAYVNFLnaaDGERAMEQlNYSLIRNRPCRIMWSQR 125 Ustilago maydis...
3123239       81 SLYVGELDPsVTEAMLFELFns--iGPVASIRVCRDAVTRRSLGYAYVNFHnmeDGEKALDElNYTLIKGRPCRIMWSQR 158 fission yeast
Q1ZXC2       185 SLYVGDLAAdVNEIILNELFskvgrNAIASIHVCRDSNTLRSLGYAYVNFFnnhDAERALDTlNYTLVHGKPCRIMWSYR 264 Dictyostelium d...
XP_002782349  49 SLYAGDLAPdVNEAVLYEVFng--iGPVASIRVCRDSVTRKSLGYAYINFHnvaDAERALDTlNYSPINGRPCRLMWSHR 126 Perkinsus marin...
XP_002294914  10 SLYIGDLLPeVNEGFLFEIFna--vGPVASIRVCRDAVTRRSLGYAYVNYHqvaDAERALDSmNFTEIKGKPCRIMWSQR 87  Thalassiosira p...
EEY61004      46 SLYVGDIHPdVTEALLFEIFna--vGPVASIRVCRDAVTRRSLGYAYVNFHnvaDAERALDTmNFTSIKGVPCRIMWSQR 123 Phytophthora in...
GAB69072      17 SLYVGDLNEdVTEAVLYEIFnt--vGHVSSIRVCRDSVTRKSLGYAYVNYHnlaDAERALDTlNYTNIKGQPARLMWSHR 94  Plasmodium cyno...
P04147        39 SLYVGDLEPsVSEAHLYDIFsp--iGSVSSIRVCRDAITKTSLGYAYVNFNdheAGRKAIEQlNYTPIKGRLCRIMWSQR 116 Saccharomyces c...
Feature 1          
1CVJ_A        90 DP 91  human
Q7S6N6       139 DP 140 Neurospora crassa OR74A
Q4P8R9       126 DP 127 Ustilago maydis 521
3123239      159 DP 160 fission yeast
Q1ZXC2       265 DP 266 Dictyostelium discoideum AX4
XP_002782349 127 DP 128 Perkinsus marinus ATCC 50983
XP_002294914  88 DP 89  Thalassiosira pseudonana CCMP1335
EEY61004     124 DP 125 Phytophthora infestans T30-4
GAB69072      95 DP 96  Plasmodium cynomolgi strain B
P04147       117 DP 118 Saccharomyces cerevisiae S288c

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