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Journal of Biochemistry Advance Access published online on March 3, 2008
Journal of Biochemistry, doi:10.1093/jb/mvn033
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© 2008 The Japanese Biochemical Society

Structural bases for the specific interactions between the E2 and E3 components of the Thermus thermophilus 2-oxo acid dehydrogenase complexes

Tadashi Nakai1,*, Seiki Kuramitsu1,2 and Nobuo Kamiya1,3

1 RIKEN SPring-8 Center, Harima Institute, Sayo, Hyogo 679-5148, Japan.
2 Department of Biology, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
3 Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi, Osaka 558-8585, Japan.

*Corresponding author: Dr. Tadashi Nakai, Department of Biochemistry, University of Washington, Box 357742, Seattle, WA 98195-7742, USA; Tel: +1-206-616-4510; Fax: +1-206-685-7002; Email: nakaix{at}u.washington.edu

Received January 7, 2008; Accepted February 13, 2008


  Abstract

Pyruvate dehydrogenase (PDH), branched-chain 2-oxo acid dehydrogenase (BCDH), and 2-oxoglutarate dehydrogenase (OGDH) are multienzyme complexes that play crucial roles in several common metabolic pathways. These enzymes belong to a family of 2-oxo acid dehydrogenase complexes that contain multiple copies of three different components (E1, E2, and E3). For the Thermus thermophilus enzymes, depending on its substrate specificity (pyruvate, branched-chain 2-oxo acid, or 2-oxoglutarate), each complex has distinctive E1 (E1p, E1b, or E1o) and E2 (E2p, E2b, or E2o) components and one of two possible E3 components (E3b and E3o). (The suffixes, p, b, and o identify their respective enzymes, PDH, BCDH, and OGDH.) Our biochemical characterization demonstrates that only three specific E3·E2 complexes can form (E3b·E2p, E3b·E2b, and E3o·E2o). X-ray analyses of complexes formed between the E3 components and the peripheral subunit binding domains (PSBDs), derived from the corresponding E2 binding partners, reveal that E3b interacts with E2p and E2b in essentially the same manner as observed for Geobacillus stearothermophilus E3·E2p. Whereas, E3o interacts with E2o in a novel fashion. The buried intermolecular surfaces of the E3b·PSBDp/b and E3o·PSBDo complexes differ in size, shape, and charge distribution and thus, these differences presumably confer the binding specificities for the complexes.

Key Words: {alpha}-ketoacid dehydrogenase, glycine cleavage system, 2-oxo acid dehydrogenase, protein-protein interaction complex, Thermus thermophilus


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