Ken Hirotsu

Enantioselective Single-Crystal-to-Single-Crystal Photodimerization of Coumarin and Thiocoumarin in Inclusion Complexes with Chiral Host Compounds.

An intermolecular enantioselective photoreaction by a single-crystal-to-single-crystal transformation has been carried out for the first time, as is evident from X-ray structure analysis and X-ray powder diffractometric studies. This reaction, the dimerization of the title compound to cyclobutane derivative 1 (X=O, S), provides a good example for studying the mechanism of topochemical reactions in the crystal.

Crystal Structure of a Homolog of Mammalian Serine Racemase from Schizosaccharomyces pombe

d-Serine is an endogenous coagonist for the N-methyl-d-aspartate receptor and is involved in excitatory neurotransmission in the brain. Mammalian pyridoxal 5′-phosphate-dependent serine racemase, which is localized in the mammalian brain, catalyzes the racemization of l-serine to yield d-serine and vice versa. The enzyme also catalyzes the dehydration of d- and l-serine. Both reactions are enhanced by Mg·ATP in vivo. We have determined the structures of the following three forms of the mammalian enzyme homolog from Schizosaccharomyces pombe: the wild-type enzyme, the wild-type enzyme in the complex with an ATP analog, and the modified enzyme in the complex with serine at 1.7, 1.9, and 2.2 Å resolution, respectively. On binding of the substrate, the small domain rotates toward the large domain to close the active site. The ATP binding site was identified at the domain and the subunit interface. Computer graphics models of the wild-type enzyme complexed with l-serine and d-serine provided an insight into the catalytic mechanisms of both reactions. Lys-57 and Ser-82 located on the protein and solvent sides, respectively, with respect to the cofactor plane, are acid-base catalysts that shuttle protons to the substrate. The modified enzyme, which has a unique “lysino-d-alanyl” residue at the active site, also exhibits catalytic activities. The crystal-soaking experiment showed that the substrate serine was actually trapped in the active site of the modified enzyme, suggesting that the lysino-d-alanyl residue acts as a catalytic base in the same manner as inherent Lys-57 of the wild-type enzyme.

Single-Crystal-to-Single-Crystal Enantioselective [2+2] Photodimerization of Coumarin, Thiocoumarin and Cyclohex-2-enone in the Inclusion Complexes with Chiral Host Compounds

Abstract Single-crystal-to-single-crystal enantioselective [2+2] photodimerization reactions of coumarin (1a), thiocoumarin (1b) and cyclohex-2-enone (2) were found to proceed efficiently in inclusion complexes with (R,R)-(−)-trans-bis(hydroxydiphenylmethyl)-2,2-dimethyl-1,3-dioxacyclopentane (3a), (R,R)-(−)-trans-2,3-bis(hydroxydiphenylmethyl)-1,4-dioxaspiro[4.4]nonane (3b), and (−)-1,4-bis[3-(o-chlorophenyl)-3-hydroxy-3-phenylprop-1-ynyl]benzene (4), respectively. Through these reactions, (−)-anti-head-to-head dimer 6a, (+)-anti-head-to-head dimer 6b and (−)-syn-trans dimer 10 were obtained in 100, 100 and 48% ee, respectively.

Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin.

This study presents the first three-dimensional structures of human cytosolic branched-chain aminotransferase (hBCATc) isozyme complexed with the neuroactive drug gabapentin, the hBCATc Michaelis complex with the substrate analog, 4-methylvalerate, and the mitochondrial isozyme (hBCATm) complexed with gabapentin. The branched-chain aminotransferases (BCAT) reversibly catalyze transamination of the essential branched-chain amino acids (leucine, isoleucine, valine) to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. The cytosolic isozyme is the predominant BCAT found in the nervous system, and only hBCATc is inhibited by gabapentin. Pre-steady state kinetics show that 1.3 mm gabapentin can completely inhibit the binding of leucine to reduced hBCATc, whereas 65.4 mm gabapentin is required to inhibit leucine binding to hBCATm. Structural analysis shows that the bulky gabapentin is enclosed in the active-site cavity by the shift of a flexible loop that enlarges the active-site cavity. The specificity of gabapentin for the cytosolic isozyme is ascribed at least in part to the location of the interdomain loop and the relative orientation between the small and large domain which is different from these relationships in the mitochondrial isozyme. Both isozymes contain a CXXC center and form a disulfide bond under oxidizing conditions. The structure of reduced hBCATc was obtained by soaking the oxidized hBCATc crystals with dithiothreitol. The close similarity in active-site structures between cytosolic enzyme complexes in the oxidized and reduced states is consistent with the small effect of oxidation on pre-steady state kinetics of the hBCATc first half-reaction. However, these kinetic data do not explain the inactivation of hBCATm by oxidation of the CXXC center. The structural data suggest that there is a larger effect of oxidation on the interdomain loop and residues surrounding the CXXC center in hBCATm than in hBCATc.

Synthesis and structures of E- and Z-phosphaethylenes

Abstract The X-ray analyses of sterically protected E- and Z-2-phenyl-1-(2,4,6-tri-t-butylphenyl) phosphaethylenes (E-1 and Z-1) were carried out and the structures in the crystal are discussed.

X-Ray structure of the α-cyclodextrin–ferrocene (2 : 1) inclusion compound

The crystal structure of the α-cyclodextrin–ferrocene (2 : 1) inclusion compound has been determined by an X-ray analysis which shows that the ferrocene molecule with approximate D5d symmetry is encapsulated by the dimer of the α-cyclodextrins in a tail-to-tail orientation and inclined by 42° relative to the six-fold axes of the α-cyclodextrins of the dimer.

A mixed valence binuclear complex of vanadium(IV) and vanadium(V). X-Ray crystal structure of (NH4)3[V2O3(nitrotriacetate)2]·3H2O

A deep blue mixed valence complex [VO(nta)–O–VO(nta)]3–(nta = nitrilotriacetate) was found to be in equilibrium with [VIVO(nta)(H2O)]– and [VVO2(nta)]2– in aqueous solution; the crystal structure of its ammonium salt trihydrate has been determined.

The Novel Substrate Recognition Mechanism Utilized by Aspartate Aminotransferase of the Extreme Thermophile Thermus thermophilus HB8

Aspartate aminotransferase (AspAT) is a unique enzyme that can react with two types of substrate with quite different properties, acidic substrates, such as aspartate and glutamate, and neutral substrates, although the catalytic group Lys-258 acts on both types of substrate. The dynamic properties of the substrate-binding site are indispensable to the interaction with hydrophobic substrates (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55–63). AspATs from various organisms are classified into two subgroups, Ia and Ib. The former includes AspATs fromEscherichia coli and higher eukaryotes, whereas the latter includes those from Thermus thermophilus and many prokaryotes. The AspATs belonging to subgroup Ia each have an Arg-292 residue, which interacts with the distal carboxyl groups of dicarboxylic (acidic) substrates, but the functionally similar residue of subgroup Ib AspATs has not been identified. In view of the x-ray crystallographic structure of T. thermophilus AspAT, we expected Lys-109 to be this residue in the subgroup Ib AspATs and constructed K109V and K109S mutants. Replacing Lys-109 with Val or Ser resulted in loss of activity toward acidic substrates but increased that toward the neutral substrate, alanine, considerably. These results indicate that Lys-109 is a major determinant of the acidic substrate specificity of subgroup Ib AspATs. Kinetic analysis of the interactions with neutral substrates indicated that T. thermophilusAspAT is subject to less steric hindrance and its substrate-binding pocket has a more flexible conformation than E. coli AspAT. A flexible active site in the rigid T. thermophilus AspAT molecule may explain its high activity even at room temperature.

Unusual Disordered Crystal Structure of a Racemate Exhibiting a Novel Enantiomeric Resolution: Preferential Enrichment

Simple recrystallization of racemic (±)-NC leads to preferential enrichment of one enantiomer in the mother liquor, which allows the efficient resolution of the two enantiomers. In the unique disordered crystal structure of the racemate, the two enantiomers form centrosymmetric dimers as the major component.

The crystal structure of pyroglutamyl peptidase I from Bacillus amyloliquefaciens reveals a new structure for a cysteine protease

BACKGROUND The N-terminal pyroglutamyl (pGlu) residue of peptide hormones, such as thyrotropin-releasing hormone (TRH) and luteinizing hormone releasing hormone (LH-RH), confers resistance to proteolysis by conventional aminopeptidases. Specialized pyroglutamyl peptidases (PGPs) are able to cleave an N-terminal pyroglutamyl residue and thus control hormonal signals. Until now, no direct or homology-based three-dimensional structure was available for any PGP. RESULTS The crystal structure of pyroglutamyl peptidase I (PGP-I) from Bacillus amyloliquefaciens has been determined to 1.6 A resolution. The crystallographic asymmetric unit of PGP-I is a tetramer of four identical monomers related by noncrystallographic 222 symmetry. The protein folds into an alpha/beta globular domain with a hydrophobic core consisting of a twisted beta sheet surrounded by five alpha helices. The structure allows the function of most of the conserved residues in the PGP-I family to be identified. The catalytic triad comprises Cys144, His168 and Glu81. CONCLUSIONS The catalytic site does not have a conventional oxyanion hole, although Cys144, the sidechain of Arg91 and the dipole of an alpha helix could all stabilize a negative charge. The catalytic site has an S1 pocket lined with conserved hydrophobic residues to accommodate the pyroglutamyl residue. Aside from the S1 pocket, there is no clearly defined mainchain substrate-binding region, consistent with the lack of substrate specificity. Although the overall structure of PGP-I resembles some other alpha/beta twisted open-sheet structures, such as purine nucleoside phosphorylase and cutinase, there are important differences in the location and organization of the active-site residues. Thus, PGP-I belongs to a new family of cysteine proteases.