Hiroaki Sakai

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

The thermophilic bacterium Thermus thermophilus synthesizes lysine through the alpha-aminoadipate pathway, which uses alpha-aminoadipate as a biosynthetic intermediate of lysine. LysX is the essential enzyme in this pathway, and is believed to catalyze the acylation of alpha-aminoadipate. We have determined the crystal structures of LysX and its complex with ADP at 2.0A and 2.38A resolutions, respectively. LysX is composed of three alpha+beta domains, each composed of a four to five-stranded beta-sheet core flanked by alpha-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.

Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8

Ribosomal protein L27 is located near the peptidyltransferase center at the interface of ribosomal subunits, and is important for ribosomal assembly and function. We report the crystal structure of ribosomal protein L27 from Thermus thermophilus HB8, which was determined by the multiwavelength anomalous dispersion method and refined to an R‐factor of 19.7% (Rfree = 23.6%) at 2.8 Å resolution. The overall fold is an all β‐sheet hybrid. It consists of two sets of four‐stranded β‐sheets formed around a well‐defined hydrophobic core, with a highly positive charge on the protein surface. The structure of ribosomal protein L27 from T. thermophilus HB8 in the RNA‐free form is investigated, and its functional roles in the ribosomal subunit are discussed.

Crystallization and preliminary X‐ray diffraction analysis of ribosomal protein L11 methyltransferase from Thermus thermophilus HB8

Ribosomal proteins are subjected to a variety of post-translational modifications, of which methylation is the most frequently found in all three kingdoms of life. PrmA is the only bacterial enzyme identified to date that catalyzes the methylation of a ribosomal protein. It is responsible for the introduction of nine methyl groups into the N-terminal domain of ribosomal protein L11. The PrmA protein from Thermus thermophilus HB8 was crystallized and a preliminary X-ray diffraction analysis was performed. A cryocooled crystal diffracted X-rays beyond 1.9 A using synchrotron radiation.

Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8.

The gene encoding LysX, an essential component of the lysine-biosynthesis pathway in Thermus thermophilus (molecular weight approximately equal 31,000 Da), was cloned and expressed and the purified protein was crystallized by the hanging-drop vapour-diffusion technique in two different space groups, C2 (unit-cell parameters a = 124.7, b = 51.4, c = 103.6 A, beta = 122.8 degrees ) and R3 (a = b = 122.6, c = 97.6 A). Crystals improved by macroseeding diffracted to beyond 2.3 and 3 A resolution for the C2 and R3 crystal forms, respectively. Complete diffraction data sets were collected for the C2 and R3 crystal forms at 2.5 and 3.1 A resolution, respectively. Crystals of selenomethionine-containing LysX protein were obtained by cross-microseeding, using the native microcrystals as a seed. Structure determination is now in progress.