bi300097g_si_001.pdf (60.01 kB)
Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases
journal contribution
posted on 2012-03-13, 00:00 authored by Brianne Sanford, Bach Cao, James M. Johnson, Kurt Zimmerman, Alexander M. Strom, Robyn M. Mueller, Sudeep Bhattacharyya, Karin Musier-Forsyth, Sanchita HatiProlyl-tRNA synthetases (ProRSs) have been shown to activate
both
cognate and some noncognate amino acids and attach them to specific
tRNAPro substrates. For example, alanine, which is smaller
than cognate proline, is misactivated by Escherichia coli ProRS. Mischarged Ala-tRNAPro is hydrolyzed by an editing
domain (INS) that is distinct from the activation domain. It was previously
shown that deletion of the INS greatly reduced cognate proline activation
efficiency. In this study, experimental and computational approaches
were used to test the hypothesis that deletion of the INS alters the
internal protein dynamics leading to reduced catalytic function. Kinetic
studies with two ProRS variants, G217A and E218A, revealed decreased
amino acid activation efficiency. Molecular dynamics studies showed
motional coupling between the INS and protein segments containing
the catalytically important proline-binding loop (PBL, residues 199–206).
In particular, the complete deletion of INS, as well as mutation of
G217 or E218 to alanine, exhibited significant effects on the motion
of the PBL. The presence of coupled dynamics between neighboring protein
segments was also observed through in silico mutations and essential
dynamics analysis. Altogether, this study demonstrates that structural
elements at the editing domain–activation domain interface
participate in coupled motions that facilitate amino acid binding
and catalysis by bacterial ProRSs, which may explain why truncated
or defunct editing domains have been maintained in some systems, despite
the lack of catalytic activity.