Conserved Protein Domain Family
RRM3_I_PABPs

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cd12380: RRM3_I_PABPs 
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins
This subfamily corresponds to the RRM3 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 an 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. 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 mammalian, 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 the 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: 409814
Aligned: 40 rows
Threshold Bit Score: 122.668
Created: 13-Sep-2011
Updated: 25-Oct-2021
Structure
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Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Q9H361       190 FPNVYIKNFGEDmDDERLKDLFGKFGpALSVKVMTDe-sGKSKGFGFVSFErHEDAQKAVDEMNGKEl-nGKQIYVGRAQ 267 human
P21187       182 FTNVYVKNFTEDfDDEKLKEFFEPYGkITSYKVMSKe-dGKSKGFGFVAFEtTEAAEAAVQALNGKDmgeGKSLYVARAQ 260 fruit fly
NP_001088471 180 FNNIYVKNFPPEtDDEKLKEMFTEFGeIKSACVMKDs-eGKSKGFGFVCYLnPEHAEAAVAAMHGKEi-gGRSLYASRAQ 257 African clawed ...
NP_611924    202 FKNLYVKNLSEEfTEQHLREMFEPYGrITSHKLMLDe-eGRSRRFGFVAYEnPQSALAAVIGLHGKQlgdNKFLYVARAL 280 fruit fly
AEW42987     190 FNNVYIKNFGDElDDDKIRELFDPFGkIISAKVMTDe-iGKSRGFGFVSYEePEAAEKAVDNLNGMElggGKVLYAGRAQ 268 Haliotis divers...
VDL26462      17 FSNCYVKNFSADlDDQGLKELFEEFGeIKSACVMKDe-sGNSKGFGFVCFSnTDSAEAAVNAMNNKEi-nGQKLYVNRAQ 94  Hymenolepis dim...
AAC39368     202 YTNVFVKNLPADiGDDELGKMATEHGeITSAVVMKDd-kGGSKGFGFINFKdAESAAKCVEYLNEREm-sGKTLYAGRAQ 279 Chlamydomonas r...
Q05196       238 FTNVYVKNLPKEiTDDELKKTFGKYGdISSAVVMKDq-sGNSRSFGFVNFVsPEAAAVAVEKMNGISl-gEDVLYVGRAQ 315 thale cress
EFN52098     218 FTNVFVKNLDEAvSDDEVKAMFAEHGtVNSCIIMRDd-eGKSKGFGFINFEePEQAASAVQALNGKDv-nCKELYVGRAQ 295 Chlorella varia...
XP_004349052 223 FTNVFVKNLPEDtTDAALNDMFSKFGkITSVVIMKSsddDKSKGFGFVCYEkVEDAQAAVNALNGTEl-aGKTLFVARAQ 301 Capsaspora owcz...
Q9H361       268 KK 269 human
P21187       261 KK 262 fruit fly
NP_001088471 258 RK 259 African clawed frog
NP_611924    281 SK 282 fruit fly
AEW42987     269 KK 270 Haliotis diversicolor
VDL26462      95 SK 96  Hymenolepis diminuta
AAC39368     280 KK 281 Chlamydomonas reinhardtii
Q05196       316 KK 317 thale cress
EFN52098     296 KK 297 Chlorella variabilis
XP_004349052 302 KK 303 Capsaspora owczarzaki ATCC 30864
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