Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8

Hiroaki Sakai1, Marina N. Vassylyeva1, 2, Takanori Matsuura1, Shun-ichi Sekine2, 3, Kazumi Gotoh4, Makoto Nishiyama4, Takaho Terada1, 2, Mikako Shirouzu1, 2, Seiki Kuramitsu2, Dmitry G. Vassylyev2, 3 and Shigeyuki Yokoyama1, 2, 3, 5

1RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
2Structurome Group, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
3Cellular Signaling Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan
4Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
5Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan

J. Mol. Biol. 332(3), 729-740 (2003)

The thermophilic bacterium Thermus thermophilus synthesizes lysine through the α-aminoadipate pathway, which uses α-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of α-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0 Å and 2.38 Å resolutions, respectively. LysX is composed of three α+β domains, each composed of a four to five-stranded β-sheet core flanked by α-helices. The C-terminal and central domains form an ATP-grasp fold, which is responsible for ATP binding. LysX has two flexible loop regions, which are expected to play an important role in substrate binding and protection. In spite of the low level of sequence identity, the overall fold of LysX is surprisingly similar to that of other ATP-grasp fold proteins, such as D-Ala:D-Ala ligase, PurT-encoded glycinamide ribonucleotide transformylase, glutathione synthetase, and synapsin I. In particular, they share a similar spatial arrangement of the amino acid residues around the ATP-binding site. This observation strongly suggests that LysX is an ATP-utilizing enzyme that shares a common evolutionary ancestor with other ATP-grasp fold proteins possessing a carboxylate-amine/thiol ligase activity.

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MATSUURA Takanori (Please change the mark “%” to “@”)

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