Crystal structures and evolutionary relationship of two different lipoamide dehydrogenases (E3s) from Thermus thermophilus

Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan* RIKEN Harima Institute/SPring-8, Hyogo 679-5148, Japan** Iwaki-Meisei University, Iwaki, Japan***
â—‹Hiroshi Kondo* Ella Czarina Magat Juan* M. Tofazzal Hossain* Wataru Adachi* Tadashi Nakai** Nobuo Kamiya** Ryoji Masui** Seiki Kuramitsu** Kaoru Suzuki*** Takeshi Sekiguchi*** Akio Takenaka*

2-Oxoglutarate dehydrogenase complex (OGDC) and pyruvate dehydrogenase complex (PDC) have similar architectures composed of three proteins, E1, E2 and E3, in which E1 and E2 are substrate-specific while E3 is the common component. However, the E3 gene is classified into either E3o or E3p type, depending on the organisms. Recently, it has been found that a few of organisms possess two E3 genes. They correspond to E3o and E3p, which may bind to the cognate complexes. To compare the two structures, the crystal structures of E3o and E3p from Thermus thermophilus have been determined at 1.7 and 1.6 Å resolutions, respectively. The structures of the active sites are highly conserved between the two E3s. Several differences occur on surface residues, which form flexible loops that may be in contact with the different core architectures of the complexes. Ultracentrifugation experiments of E2o and E2p indicate that the cores of OGDC and PDC in Thermus thermophilus are cubic (432 symmetry, 24E1:24E2:12E3 composition) and icosahedral (532 symmetry, 60E1:60E2:24E3 composition), respectively. These structural features are similar to those of eucaryotes and Gram-positive prokaryotes, but different from those of Gram-negative prokaryotes where both OGDC and PDC are cubic. We propose that an ancestor operon with a cubic symmetry carrying a set of E1, E2 and E3 genes may have taken the following evolutionary steps: (1) duplication to generate two operons, (2a) disappearance of one of the E3 genes in either operon, or (2b) transformation of the architecture in one of the operons into the icosahedral form, and (3) disappearance of one of the E3 genes in the operon with a cubic architecture.