ct200387u_si_001.pdf (1.06 MB)
Unidirectional Mechanistic Valved Mechanisms for Ammonia Transport in GatCAB
journal contribution
posted on 2012-02-14, 00:00 authored by Jiyoung Kang, Shigehide Kuroyanagi, Tomohiro Akisada, Yohsuke Hagiwara, Masaru TatenoGlutamine amidotransferase CAB (GatCAB), a crucial enzyme
involved
in translational fidelity, catalyzes three reactions: (i) the glutaminase
reaction to yield ammonia (NH3 or NH4+) from glutamine, (ii) the phosphorylation of Glu-tRNAGln, and (iii) the transamidase reaction to convert the phosphorylated
Glu-tRNAGln to Gln-tRNAGln. In the crystal structure
of GatCAB, the two catalytic centers are far apart, and the presence
of a hydrophilic channel to transport the molecules produced by the
reaction (i) was proposed. We investigated the transport mechanisms
of GatCAB by molecular dynamics (MD) simulations and free energy (PMF)
calculations. In the MD simulations (in total ∼1.1 μs),
the entrance of the previously proposed channel is closed, as observed
in the crystal structure. Instead, a novel hydrophobic channel has
been identified in this study: Since the newly identified entrance
opened and closed repeatedly in the MD simulations, it may act as
a gate. The calculated free energy difference revealed the significant
preference of the newly identified gate/channel for NH3 transport (∼104-fold). In contrast, with respect
to NH4+, the free energy barriers are significantly
increased for both channels due to tight hydrogen-bonding with hydrophilic
residues, which hinders efficient transport. The opening of the newly
identified gate is modulated by Phe206, which acts as a “valve”.
For the backward flow of NH3, our PMF calculation revealed
that the opening of the gate is hindered by Ala207, which acts as
a mechanistic “stopper” against the motion of the “valve”
(Phe206). This is the first report to elucidate the detailed mechanisms
of unidirectional mechanistic valved transport inside proteins.