1CVJ,2K8G,4F02,4F25


Conserved Protein Domain Family
RRM2_I_PABPs

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cd12379: RRM2_I_PABPs 
Click on image for an interactive view with Cn3D
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins
This subfamily corresponds to the RRM2 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 mammalian, such as ovary and testis. It may play an important role in germ cell development. 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: 409813
Aligned: 51 rows
Threshold Bit Score: 123.068
Created: 13-Sep-2011
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
RNA binding
Conserved site includes 12 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        97 GVGNIFIKNLDKsIDNKALYDTFSaFGNILSCKVVcde-ngsKGYGFVHFETqeAAERAIEKMNGMll----ndRKVFVG 171 human
3123239      166 GTGNVFIKNLDPaIDNKALHDTFSaFGKILSCKVAvdelgnaKGYGFVHFDSveSANAAIEHVNGMll----ndKKVYVG 241 fission yeast
Q05196       144 GKGNVFIKNLDAsIDNKALYETFSsFGTILSCKVAmdvvgrsKGYGFVQFEKeeTAQAAIDKLNGMll----ndKQVFVG 219 thale cress
AAC39368     112 GVGNIFIKNLDKtIDAKALHDTFSaFGKILSCKVAtdangvsKGYGFVHFEDqaAADRAIQTVNQKki----egKIVYVA 187 Chlamydomonas r...
EDQ91621      94 GAGNIFIKNLNKeIDNKALYDTFSaFGTILSCKVAadekgesRGYGFVHFEKeeDAQKAIDTVNGKml----lkQVVTVT 169 Monosiga brevic...
P04147       124 GSGNIFIKNLHPdIDNKALYDTFSvFGDILSSKIAtdengksKGFGFVHFEEegAAKEAIDALNGMll----ngQEIYVA 199 Saccharomyces c...
XP_002774026 120 GNANVFVKNLDKtIDNKALYDTFSlFGNILSCKVAtdddgksRGYGFVHFENdeSAHKAITKLNGMmi----geKAVYVG 195 Perkinsus marin...
GAB69072     102 GAGNIFVKNLDKsIDNKALFDTFSmFGNILSCKVAtdefgksKSYGFVHYEDeeSAKEAIEKVNGIql----gsKNVYVG 177 Plasmodium cyno...
EAN76907     107 GSGNIFVKNLKEeVDSRELSLIFKkFGEILSCKVMddesgksRGYGFVHFKDddAAKAAIEKMNGDkehadadkAALYVA 186 Trypanosoma bru...
NP_188259    110 GFANLYVKNLDSsITSSCLERMFCpFGSILSCKVVeen-gqsKGFGFVQFDTeqSAVSARSALHGSmv----ygKKLFVA 184 thale cress
Feature 1        #
1CVJ_A       172 R 172 human
3123239      242 H 242 fission yeast
Q05196       220 H 220 thale cress
AAC39368     188 P 188 Chlamydomonas reinhardtii
EDQ91621     170 K 170 Monosiga brevicollis MX1
P04147       200 P 200 Saccharomyces cerevisiae S288c
XP_002774026 196 P 196 Perkinsus marinus ATCC 50983
GAB69072     178 H 178 Plasmodium cynomolgi strain B
EAN76907     187 N 187 Trypanosoma brucei TREU927
NP_188259    185 K 185 thale cress

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