Acetate is an end product of the energy-yielding metabolism of nearly all fermentative microbes in the domain Bacteria in which acetyl coenzyme A (acetyl-CoA) is converted to acetate by phosphotransacetylase (Pta) (equation 1) and acetate kinase (equation 2) coupled to the synthesis of ATP. Acetate also is the growth substrate for methaneproducing archaea. Thus, acetate is a major intermediate in the global carbon cycle, and acetate conversion to methane is responsible for the majority of biological methane production (7). In Methanosarcina species, Pta and acetate kinase function in the opposite direction to catalyze the ATPdependent activation of acetate to acetyl-CoA for cleavage of the COC bond of acetate by the carbon monoxide dehydrogenase/acetyl-CoA synthase, which releases the methyl group for eventual reduction to methane.The kinetic and catalytic mechanisms of acetate kinase are well characterized; however, Pta has been studied in considerably less detail, although the enzyme from the fermentative anaerobe Clostridium kluyveri was purified in the early 1950s (35). Kinetic analyses of Ptas from C. kluyveri and Veillonella alcalescens have suggested that rather than a ping-pong mechanism, the mechanism likely proceeds through formation of a ternary complex (20,28). In a reexamination of the C. kluyveri Pta workers attempted to detect an acetyl-enzyme intermediate; however, no isotope exchange from labeled acetyl phosphate into either acetyl-CoA or inorganic phosphate was observed in the absence of free CoA, and attempts to isolate an acetyl-Pta intermediate were unsuccessful, which is consistent with a ternary complex mechanism (9). Although numerous genetic and physiological studies have continued to demonstrate the universal function of Pta in acetate metabolism in diverse microbes (1,4,6,8,15,17,24,25,27,30,32,38), mechanistic analyses of the enzyme were abandoned until there was an investigation of Pta from the archaeon Methanosarcina thermophila, which obtains energy for growth by converting acetate to methane (22).Cloning of the gene and heterologous expression of Pta from M. thermophila allowed the large-scale production of protein required for structural studies, biochemical analyses, and the use of site-specific replacement to analyze the function of specific residues (22). Cys 312 was predicted to be present in the active site, although it is not essential for catalysis (31). Arg 87 and Arg 133 were proposed to interact with the 3Ј and 5Ј phosphate groups of CoA, respectively (12), while Arg 310 was found to be essential for catalysis, although its role was not defined further (31). In spite of the insight gained from the site-specific replacement studies, key questions remained. The architecture of the active site was unknown, and, other than the residues * Corresponding author. Mailing address for Hermann Schindelin: Department of Biochemistry, Center for Structural Biology, SUNY Stony Brook, Stony Brook, NY 11794-5115.