Structural studies of PA4608 and C5 protein

Abstract

PA4608 is a single PilZ domain protein from $\emph{Pseudomonas aeruginosa}$ that binds to cyclic dimeric guanosine monophosphate (c-di-GMP). While the monomeric structure of unbound PA4608 has been studied in detail, the molecular details of c-di-GMP binding to this protein are still uncharacterized. Hence, we determined the solution structure of c-di-GMP bound PA4608. We found that PA4608 undergoes conformational changes to expose the c-di-GMP binding site by ejection of the C-terminal $3_10$ helix. An increase in flexibility of the C-terminal tail in the presence of c-di-GMP implies that this region acts as a lid that alternately covers and exposes the hydrophobic surface of the binding site. In addition, mutagenesis and NOE data for PA4608 revealed that conserved residues are in contact with the c-di-GMP. The unique structural characteristics of PA4608, including its monomeric state and its ligand binding characteristics, yield insight into its function as a c-di-GMP receptor. Ribonuclease P is an enzyme which releases the 5’-precursor sequence from immature tRNAs and produces mature tRNAs. RNase P consists of a catalytic RNA subunit and a cofactor protein subunit, and especially for $\emph{ Escherichia coli}$, RNase P is composed of M1 RNA and C5 protein. Although \emph{in vitro} data shows that M1 RNA has catalytic activity at high concentration of magnesium ion without the C5 protein, $\emph{in vivo}$ data indicate that C5 protein is essential and seems to affect the catalytic activity of RNase P. RNase P is categorized to two type - A-type(Ancestral type) and B-type (Bacilus type) - depending on RNA shape. Although the secondary structure of A-type RNase P RNA is different to that of B-type, RNase P protein of A-type and B-type is believed to have similar tertiary structure. The accurate function of the C5 protein in vivo is unknown, but three dimensional structure of C5 protein could help to understand the structural and functional role of C5 protein....