Abstract
The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational changes involving an opening-closing motion of the nucleotide-binding domain (NBD) and a swiveling motion of the central domain (CD). However, why PPDK is active only in a dimeric form and to what extent an alternate binding change mechanism could underlie this fact has remained elusive. We performed unbiased molecular dynamics simulations, configurational free energy computations, and rigidity analysis to address this question. Our results support the hypothesis that PPDK dimerization influences the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains. Such an influence would be a prerequisite for an alternate binding change mechanism to occur. To the best of our knowledge, this is the first time that a possible explanation has been suggested as to why only dimeric PPDK is active.
Highlights
Pyruvate phosphate dikinase (PPDK) is a key enzyme in the cellular energy metabolism that catalyzes the ATP
The temporal separation of the partial reactions is mirrored by a spatial separation of reaction centers[6, 7]: PPDK consists of three domains, an N-terminal nucleotide-binding domain (NBD), the location of partial reaction (1), a C-terminal PEP/pyruvate-binding domain (PBD), the location of partial reaction (2), and a central domain (CD), the location of H456 (Fig. 1a)
Our computations support the hypothesis that PPDK dimerization does influence the opening-closing motion of the NBDs, and that this influence is mediated via the CDs of both chains
Summary
Pyruvate phosphate dikinase (PPDK) is a key enzyme in the cellular energy metabolism that catalyzes the ATP-. Structural clustering of the PPDK structures reveals two principal movements (Supplementary Fig. S1): First, the NBD, which consists of three subdomains forming the ATP-grasp motif[15], shows an opening-closing motion assumed to be associated with ATP binding[13]. Our calculations revealed an intramolecular coupling between the CD motion and the opening-closing motion of the NBD, which was corroborated by the comparative analysis of available PPDK crystal structures[8]. The distinct conformational states of the NBD of 5JVJ have led to the hypothesis that PPDK employs an alternate binding change mechanism[8] ( termed reciprocating mechanism stressing its processivity19) similar to ATP synthase[20, 21] or bacterial ATP-dependent DNA helicases[22]. No further detailed insights if and how such an alternate
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