Takao Matsuzaki

Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution.

The crystal structure of RNase H from Escherichia coli has been determined by the multiple isomorphous replacement method, and refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.196 at 1.48 A resolution. In the final structure, the root-mean-square (r.m.s.) deviation for bond lengths is 0.017 A, and for angle distances 0.036 A. The structure is composed of a five-stranded beta-sheet and five alpha-helices, and reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intermolecular residues. The refined structure allows an explanation of the particular interactions between the basic protrusion, consisting of helix alpha III and the following loop, and the remaining major domain. The beta-sheet, alpha II, alpha III and alpha IV form a central hydrophobic cleft that contains all six tryptophan residues, and presumably serves to fix the orientation of the basic protrusion. Two parallel adjacent helices, alpha I and alpha IV, are associated with a few triads of hydrophobic interactions, including many leucine residues, that are similar to the repeated leucine motif. The well-defined electron density map allows detailed discussion of amino acid residues likely to be involved in binding a DNA/RNA hybrid, and construction of a putative model of the enzyme complexed with a DNA/RNA hybrid oligomer. In this model, a protein region, from the Mg(2+)-binding site to the basic protrusion, covers roughly two turns of a DNA/RNA hybrid double helix. A segment (11-23) containing six glycine residues forms a long loop between the beta A and beta B strands. This loop, which protrudes into the solvent region, lies on the interface between the enzyme and a DNA/RNA hybrid in the model of the complex. The mean temperature factors of main-chain atoms show remarkably high values in helix alpha III that constitutes the basic protrusion, suggesting some correlation between its flexibility and the nucleic acid binding function. The Mg(2+)-binding site, surrounded by four invariant acidic residues, can now be described more precisely in conjunction with the catalytic activity. The arrangement of molecules within the crystal appears to be dominated by the cancelling out of a remarkably biased charge distribution on the molecular surface, which is derived in particular from the separation between the acidic Mg(2+)-binding site and the basic protrusion.

Keramamine-A and -B, novel antimicrobial alkaloids from the Okinawan marine sponge Pellina sp.

Abstract Keramamine-A and -B, two new β-carboline alkaloids with a 13 membered ring have been isolated from the Okinawan marine sponge Pellina sp. as antimicrobial substances and the structures of keramamine-A and -B have been determined by X-ray analysis and by spectral and chemical means, respectively.

The Translin Ring Specifically Recognizes DNA Ends at Recombination Hot Spots in the Human Genome

We previously showed that consensus sequences exist at the chromosomal breakpoints in lymphoid malignancies and that these sequences are specifically recognized by a novel DNA binding protein, Translin. In the present study, the native form of Translin was established to be a ring-shaped structure by electron microscopy and crystallographic studies. It was also determined that this multimeric Translin formed by the subunits is responsible for its binding to target sequences situated only at single-stranded DNA ends. Furthermore, DNA-damaging reagents were found to initiate a signaling pathway for the active nuclear transport of Translin. The results support the hypothesis that staggered breaks occur at recombination hot spots and Translin has a pivotal function in recognition of the generated single-stranded DNA ends.

Ca-antagonistic substance from soft coral of the genusSarcophyton

A 14-membered ring diterpenoid named cembrane, possessing Ca-antagonistic action on the isolated rabbit aorta, has been isolated from a soft coral of the genusSarcophyton, and its structure established by X-ray and spectroscopic data.

Hexacarbonylbis(tricyclopentylphosphine)dirhodium and hexacarbonylbis(triisopropylphosphine)dirhodium from a catalytic system for syngas conversion to ethylene glycol

Two dimeric rhodium compounds, [Rh(CO) 3 P(c-C 5 H 9 ) 3 ] 2 ( 1 ) and [Rh)CO) 3 P(i-Pr) 3 ] 2 ( 2 ) have been isolated from the catalytic reaction mixtures of syngas conversion to ethylene glycol, and their molecular structures without a bridging carbonyl were determined by single crystal X-ray diffraction studies.

Structure and stereochemistry of brianolide, a new antiinflammatory diterpenoid from the Okinawan gorgonianBriareum sp.

Brianolide (1), a new antiinflammatory diterpenoid of the briarein class, possessing a β substituent at C-12 (R), has been isolated from the Okinawan gorgonianBriareum sp. Its structure has been established from spectral data in conjunction with a single crystal X-ray analysis.

Piscicidal cis-clerodane diterpenes from Solidago altissima L: absolute configurations of 5α,10α-cis-clerodanes

Abstract From Solidago altissima L. (Compositae), a new 5α, 10α-cis-clerodane diterpene (Solidagolactone VIII) and known solidagolactones were isolated as piscicidal constituents. The structures of the constituents including absolute configurations were determined, and a revised structure was given to solidagolactone VII.

Crystallization and preliminary X-ray investigation of six new crystal forms of ribonuclease U2 from Ustilago sphaerogena

Abstract Ribonuclease (RNase) U 2 is a purine-specific endoribonuclease secreted by Ustilago sphaerogena . In addition to type I and II crystals, six new crystal types of III, IV, V, VI, VII, and VIII have been obtained with the hanging-drop vapor-diffusion method. Type III and IV crystals were grown from ammonium sulfate solutions of pH 4.5. Type V is from an ammonium sulfate solution containing zinc chloride. Type VI is from a 2-methyl-2,4-pentanediol solution containing manganese chloride. Type VII of a complex with adenosine-2′-monophosphate and type VIII of a complex with adenosine-3′-monophosphate are from polyethylene glycol 8000 solutions containing calcium acetate. These types of crystals suggest polymorphic nature in crystallization of RNase U 2 . Three-dimensional structure determinations of these new crystals are in progress, with the molecular replacement method by use of the structure of the type II crystal.

Naphthoquinone methide type near-i.r. dye: the properties and structure of 4-(2′-acetylamino-4′-diethylaminophenylimino)-1,4-dihydronaphthylidene- malononitrile

The introduction of an acetylamino group at the 2′-position in the aniline ring of a naphthoquinone methide dye produced a red shift with a large increase in the molecular extinction coefficient in CHCI3 solution, and an intramolecular ring-closure reaction of the compound under alkaline conditions gave a new blue dye; the stereochemistry of this chromophoric system was determined by X-ray analysis.

Mechanisms of the selective inhibition of thrombin, factor xa, plasmin and trypsin

Abstract The three-dimensional structures of bovine trypsin-inhibitor complexes were determined by X-ray analysis. The selective inhibition of thrombin, factor Xa, plasmin and trypsin exhibited by arginine and lysine derivatives was clearly explained based on the structures and the homology in the amino acid sequences of these enzymes. The differences in the sequences at the positions corresponding to I1e-63, Leu-99 and Ser-190 of trypsin were shown to give each enzyme different binding affinity toward the inhibitors and result in the selective inhibition. This study provides design strategies for enzyme specific inhibitors and suggestions for site-directed mutagenesis experiments.