JB Accepts, published online ahead of print on 21 December 2007

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J. Bacteriol. doi:10.1128/JB.01469-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways

Chen Yang, Dmitry A. Rodionov, Irina A. Rodionova, Xiaoqing Li, and Andrei L. Osterman^*

From the Burnham Institute for Medical Research, La Jolla, California 92037, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China, Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia, Fellowship for Interpretation of Genomes, Burr Ridge, Illinois 60527

^* To whom correspondence should be addressed. Email: osterman{at}burnham.org.

Members of a novel Glycerate-2-kinase family (GK-II) were tentatively identified in a broad range of species, including eukaryotes, archaea, and many bacteria that lack a canonical enzyme of the GarK family (GK-I). A recently reported 3D structure of GK-II from Thermotoga maritima (TM1585, 2b8n) revealed a new fold distinct from other known kinase families. Here we verified the enzymatic activity of TM1585, assessed its kinetic characteristics, and used directed mutagenesis to confirm the essential role of the two active site residues Lys-47 and Arg-325. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria, and in particular in T. maritima. Comparative analysis of 400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of T. maritima, a three-step serine degradation pathway was inferred based on tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively) that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution.

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