Survey on the PABC recognition motif PAM2.
The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for the PABC domain. This domain is contained in homologs of the poly(A)-binding protein PABP and the ubiquitin-protein ligase HYD. Despite the importance of the PAM2 motif, a comprehensive analysis of its occurrence in different proteins has been missing. Using iterated sequence profile searches, we obtained an extensive list of proteins carrying the PAM2 motif. We discuss their functional context and domain architecture, which often consists of RNA-binding domains. Our list of PAM2 motif proteins includes eukaryotic homologs of eRF3/GSPT1/2, PAIP1/2, Tob1/2, Ataxin-2, RBP37, RBP1, Blackjack, HELZ, TPRD, USP10, ERD15, C1D4.14, and the viral protease P29. The identification of the PAM2 motif in as yet uncharacterized proteins can give valuable hints with respect to their cellular function and potential interaction partners and suggests further experimentation. It is also striking that the PAM2 motif appears to occur solely outside globular protein domains.
Albrecht
Mario
M
Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, Saarbrücken 66123, Germany. mario.albrecht@mpi-sb.mpg.de
Lengauer
Thomas
T
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000067528:Ataxins; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry; D030562:Databases, Protein; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins; D009696:Nucleic Acids / Q000378:metabolism; D010448:Peptide Initiation Factors / Q000737:chemistry; D010454:Peptide Termination Factors / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment
D000067528:Ataxins; D002352:Carrier Proteins; D009419:Nerve Tissue Proteins; D009696:Nucleic Acids; D010448:Peptide Initiation Factors; D010454:Peptide Termination Factors; D011506:Proteins; C087971:peptide-chain-release factor 3