Solution structure of the dimerization domain of ribosomal protein P2 provides insights for the structural organization of eukaryotic stalk

Abstract

The lateral stalk of ribosome is responsible for kingdom-specific binding of translation factors and activation of GTP hydrolysis that drives protein synthesis. In eukaryotes, the stalk is composed of acidic ribosomal proteins P0, P1 and P2 that constitute a pentameric P-complex in 1: 2: 2 ratio. We have determined the solution structure of the N-terminal dimerization domain of human P2 (NTD-P2), which provides insights into the structural organization of the eukaryotic stalk. Our structure revealed that eukaryotic stalk protein P2 forms a symmetric homodimer in solution, and is structurally distinct from the bacterial counterpart L12 homodimer. The two subunits of NTD-P2 form extensive hydrophobic interactions in the dimeric interface that buries 2400 Å2 of solvent accessible surface area. We have showed that P1 can dissociate P2 homodimer spontaneously to form a more stable P1/P2 1 : 1 heterodimer. By homology modelling, we identified three exposed polar residues on helix-3 of P2 are substituted by conserved hydrophobic residues in P1. Confirmed by mutagenesis, we showed that these residues on helix-3 of P1 are not involved in the dimerization of P1/P2, but instead play a vital role in anchoring P1/P2 heterodimer to P0. Based on our results, models of the eukaryotic stalk complex were proposed.

Disruption of the ribosomal P complex leads to stress-induced autophagy

“…3 Though the precise biological functions of RPLP proteins are still unclear, it is known that all RPLP proteins contain a conserved motif at the C terminus that is involved in the recruitment of both translation factors and ribosome-inactivation proteins to the ribosomal stalk. RPLP0, RPLP1, and RPLP2 also have their own specific characteristics on both expression profiling and amino acid composition analysis compared with the major RP proteins.…”

Erythrocytic Stage-dependent Regulation of Oligomerization of Plasmodium Ribosomal Protein P2

“…By homology modeling, a structural model of P1/P2 dimerization domain was proposed and this model predicted that helix-3 of P1 is not involved in P1/P2 dimerization, but plays an important role in formation of the P-complex (25). The hetero-oligomerization of P1/P2 proteins have been reported earlier, and these appear to be precursors to the pentameric ribosomal P-protein complex (26).…”

“…The structure of the N-terminal dimerization domain of human P2 protein was determined recently by NMR (25). By homology modeling, a structural model of P1/P2 dimerization domain was proposed and this model predicted that helix-3 of P1 is not involved in P1/P2 dimerization, but plays an important role in formation of the P-complex (25).…”

The acidic ribosomal protein P2 fromEuplotes octocarinatusis phosphorylated at its N-terminal domain

“…They form a pentameric complex (1:2:2 ratio) and play a crucial role in the interaction with translation factors (Lee et al 2010(Lee et al , 2012. In eukaryotic systems, three functional domains may be recognized in the P family protein's primary structure (Tchorzewski 2002).…”

“…In eukaryotic systems, three functional domains may be recognized in the P family protein's primary structure (Tchorzewski 2002). First, the hydrophobic N-terminal domain is known to be responsible for P1/P2 dimerization and for anchoring them into a ribosomal particle through the ribosomal protein P0 (Tchorzewski et al 2000;Gonzalo and Reboud 2003;Naganuma et al 2007;Lee et al 2010Lee et al , 2012. Second, the central region of the protein consists of a very flexible hinge structure that is rich in alanine, glycine, and proline residues, therefore it has a wide range of movement.…”