3PKN

Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)

Summary for 3PKN

• Entry DOI: 10.2210/pdb3pkn/pdb
• Descriptor: Polyadenylate-binding protein 1, La-related protein 4, SULFATE ION, ... (5 entities in total)
• Functional Keywords: all helical domain, protein binding, la-related protein 4
• Biological source: Homo sapiens (human); More
• Cellular location: Cytoplasm: P11940
• Total number of polymer chains: 2
• Total formula weight: 11186.60

Authors

Xie, J.,Kozlov, G.,Gehring, K. (deposition date: 2010-11-11, release date: 2011-01-12, Last modification date: 2023-09-06)

Primary citation

Yang, R.,Gaidamakov, S.A.,Xie, J.,Lee, J.,Martino, L.,Kozlov, G.,Crawford, A.K.,Russo, A.N.,Conte, M.R.,Gehring, K.,Maraia, R.J.
La-Related Protein 4 Binds Poly(A), Interacts with the Poly(A)-Binding Protein MLLE Domain via a Variant PAM2w Motif, and Can Promote mRNA Stability.
Mol.Cell.Biol., 31:542-556, 2011

PubMed Abstract: The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.

PubMed: 21098120
DOI: 10.1128/MCB.01162-10

Experimental method

X-RAY DIFFRACTION (1.8 Å)