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Journal of Bacteriology, March 2008, p. 1773-1782, Vol. 190, No. 5
0021-9193/08/$08.00+0     doi:10.1128/JB.01469-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways{triangledown} ,{dagger}

Chen Yang,1,2,{ddagger} Dmitry A. Rodionov,1,3,{ddagger} Irina A. Rodionova,1 Xiaoqing Li,1 and Andrei L. Osterman1,4*

Burnham Institute for Medical Research, La Jolla, California 92037,1 Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China,2 Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia,3 Fellowship for Interpretation of Genomes, Burr Ridge, Illinois 605274

Received 11 September 2007/ Accepted 16 December 2007

Members of a novel glycerate-2-kinase (GK-II) family were tentatively identified in a broad range of species, including eukaryotes and archaea and many bacteria that lack a canonical enzyme of the GarK (GK-I) family. The recently reported three-dimensional structure of GK-II from Thermotoga maritima (TM1585; PDB code 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 analyses 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 the 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.

* Corresponding author. Mailing address: Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037. Phone: (858) 646-3100. Fax: (858) 795-5249. E-mail: osterman{at}burnham.org

{triangledown} Published ahead of print on 21 December 2007.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

{ddagger} C.Y. and D.A.R. contributed equally to this work.

Journal of Bacteriology, March 2008, p. 1773-1782, Vol. 190, No. 5
0021-9193/08/$08.00+0     doi:10.1128/JB.01469-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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