Molecular Mechanism of ATP Hydrolysis in an ABC Transporter

Abstract

Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO42– as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H2PO4–. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg2+ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved.

Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway

“…[20][21][22][23][24][25] Recent state-of-theart studies have already calculated potentials of mean force with high-level hybrid-meta Hamiltonians, even though the size of the QM region is still reduced and the MD time, despite being remarkable, is still smaller than the timescale of many enzyme structural uctuations, due to insurmountable CPU limitations. 26 In these excellent studies, the effects of conformational diversity are accounted for implicitly, through the sampling made in each point along the reaction coordinate, and thus not used to gain understanding of the nature of the uctuations in the interactions that stabilize the transition structures, which is the major purpose of this study and other studies of this kind.…”

Omnipresent Maxwell's demons orchestrate information management in living cells

“…Some transporters have NBDs that do not have similar abilities in binding and hydrolysing ATP. Furthermore, the fact that the interface of the NBD dimer consists of two ATPbinding pockets denotes different functions for the two NBDs in the transport cycle (Priess et al, 2018). Recent structural and biochemical data suggest that it is ATP binding and formation of a compact dimer in a 'tense' form, rather than ATP hydrolysis, that provides the 'power stroke' that will result in transport.…”

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

“…The mechanism of ATP hydrolysis in CFTR is not precisely known, but studies of ATP hydrolysis on the MalK dimer and on the B 12 vitamin importer BtuCD conclude that the presence of a water molecule between ATP and the catalytic glutamate is essential for ATP hydrolysis, regardless of the proposed mechanism. [65][66][67][68] Jones et al also defined geometric criteria for assessing hydrolysiscompetent conformations, based on Sav1866 MD simulations, such as distances and angles between the catalytic residues and the water molecule, as well as the coordination between a backbone carbonyl group from the D-loop and the catalytic water. 69 Other groups have also defined similar criteria involving the D-loop coordination.…”