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Journal of Bacteriology, August 2004, p. 5129-5137, Vol. 186, No. 15
0021-9193/04/$08.00+0     DOI: 10.1128/JB.186.15.5129-5137.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

The Phosphoenolpyruvate Carboxylase from Methanothermobacter thermautotrophicus Has a Novel Structure

University of Illinois at Urbana-Champaign, Urbana, Illinois,¹ Virginia Bioinformatics Institute,² Departments of Biochemistry,³ Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia⁴

Received 9 February 2004/ Accepted 29 April 2004

In Methanothermobacter thermautotrophicus, oxaloacetate synthesis is a major and essential CO₂-fixation reaction. This methanogenic archaeon possesses two oxaloacetate-synthesizing enzymes, pyruvate carboxylase and phosphoenolpyruvate carboxylase. The phosphoenolpyruvate carboxylase from this organism was purified to homogeneity. The subunit size of this homotetrameric protein was 55 kDa, which is about half that of all known bacterial and eukaryotic phosphoenolpyruvate carboxylases (PPCs). The NH₂-terminal sequence identified this enzyme as the product of MTH943, an open reading frame with no assigned function in the genome sequence. A BLAST search did not show an obvious sequence similarity between MTH943 and known PPCs, which are generally well conserved. This is the first report of a new type of phosphoenolpyruvate carboxylase that we call PpcA ("A" for "archaeal"). Homologs to PpcA were present in most archaeal genomic sequences, but only in three bacterial (Clostridium perfringens, Oenococcus oeni, and Leuconostoc mesenteroides) and no eukaryotic genomes. PpcA was the only recognizable oxaloacetate-producing enzyme in Methanopyrus kandleri, a hydrothermal vent organism. Each PpcA-containing organism lacked a PPC homolog. The activity of M. thermautotrophicus PpcA was not influenced by acetyl coenzyme A and was about 50 times less sensitive to aspartate than the Escherichia coli PPC. The catalytic core (including His¹³⁸, Arg⁵⁸⁷, and Gly⁸⁸³) of the E. coli PPC was partly conserved in PpcA, but three of four aspartate-binding residues (Lys⁷⁷³, Arg⁸³², and Asn⁸⁸¹) were not. PPCs probably evolved from PpcA through a process that added allosteric sites to the enzyme. The reverse is also equally possible.

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