Structural Insights into the Mechanism of Phosphoenolpyruvate Carboxykinase Catalysis

Abstract

Mammalian PEPCK2 catalyzes the reversible formation of PEP from OAA and GTP (or ITP) in a divalent cation-dependent reaction (Scheme 1), as was elegantly discussed in the first minireview of this series on PEPCK (1). SCHEME 1. PEPCK-catalyzed interconversion of OAA and PEP. In this third minireview, high-resolution crystal structures of mammalian PEPCK are examined to gain insights into the mechanism of PEPCK catalysis, including the reaction's reversibility and nucleotide specificity. Regarding reaction reversibility, PEPCK is responsible for regeneration of the high-energy phosphoryl donor PEP from the unstable, activated β-keto acid OAA. When coupled with pyruvate carboxylase, PEPCK reverses the essentially irreversible formation of pyruvate and ATP from PEP and ADP in the glycolytic reaction catalyzed by pyruvate kinase. As illustrated (Fig. 1), PEPCK could achieve this feat by stabilizing the inherently unstable enolate form of pyruvate generated by decarboxylation of OAA (Scheme 1). Stabilization of this intermediate would reduce the energetic cost for phosphoryl transfer by ∼30 kJ mol−1 relative to direct reversal of the pyruvate kinase-catalyzed reaction. An energetic driving force for the pyruvate kinase reaction is the favorable tautomerization of the high-energy enol to its corresponding keto form; in contrast, by stabilizing the enolate, PEPCK could prevent its energetically favorable protonation and tautomerization, allowing phosphoryl transfer to occur. Thus, by stabilizing this intermediate in a high-energy state, the PEPCK reaction would be energetically rendered freely reversible; the crystal structures that will be described indicate that PEPCK does, in fact, stabilize the enolate intermediate. FIGURE 1. Diagram representing the reaction coordinates for the pyruvate kinase-catalyzed (A) and PEPCK-catalyzed (B) reactions. The standard free energy values given are approximate values based upon the average values from a number of literature sources. The ... The recent structures of PEPCK from human, rat, and chicken (2–5), the enzymes from Trypanosoma cruzi (6), Anaerobiospirillum succiniciproducens (7), and Corynebacterium glutamicum (8), and earlier work on the isozyme from Escherichia coli (9–13) illustrate that the active-site residues and architecture are well conserved, despite what is rather poor overall sequence homology when comparing members of the ATP- and GTP-dependent families.3 As detailed in this minireview, the cationic environment of the active site, dominated by the juxtaposition of two divalent metal ions and the positioning of lysine and arginine residues, is well suited to allow for the stabilization of the enolate intermediate discussed above and to facilitate phosphoryl transfer. An informative aspect of the PEPCK-catalyzed reaction revealed by the recent structural data on the GTP-dependent isozyme from rat is the illumination of the previously unappreciated role of conformational changes occurring in the active site during the catalytic cycle (5). The most prevalent mobile feature illustrated by the structural work is a 10-residue Ω-loop lid domain whose closure is potentially capable of protecting the enolate intermediate (Fig. 2) (2–5). A similar domain is present in ATP-dependent PEPCK, as represented by the E. coli enzyme, which was the first PEPCK to be structurally characterized (9). The structural data on PEPCK demonstrate that only upon closure of the lid domain are the substrates positioned correctly for catalysis to occur (5). Furthermore, another loop domain, the ubiquitous P-loop or kinase-1a motif in the GTP-dependent PEPCKs, also shows dynamic behavior, adapting various conformations correlated with substrate binding. The potential role of the dynamic P-loop in catalysis is of interest because it contains a reactive cysteine residue that is conserved in all GTP-dependent PEPCKs and whose specific modification has been known for 2 decades to result in the inactivation of the enzyme (14, 15). As described below, recent structural work characterizing the low-energy conformational states that define the reaction coordinate of the enzyme-catalyzed reaction (2–5, 16), considered together with previous biochemical studies, has allowed a relatively detailed picture of the mechanism of catalysis utilized by PEPCK to emerge. Both the role of the positively charged active site and the important conformational changes occurring within that site are discussed in the context of an integrated mechanism for PEPCK-mediated catalysis. FIGURE 2. Crystallographic images defining the chemical reaction path of PEPCK-mediated conversion of OAA to PEP. A schematic drawing to aid in the interpretation of the structural data is presented on the right-hand side of each panel. In the left-hand images, ...