Heung-Soo Lee

Crystal structures of human DJ-1 and Escherichia coli Hsp31, which share an evolutionarily conserved domain.

Human DJ-1 and Escherichia coli Hsp31 belong to ThiJ/PfpI family, whose members contain a conserved domain. DJ-1 is associated with autosomal recessive early onset parkinsonism and Hsp31 is a molecular chaperone. Structural comparisons between DJ-1, Hsp31, and an Archaea protease, a member of ThiJ/PfpI family, lead to the identification of the chaperone activity of DJ-1 and the proteolytic activity of Hsp31. Moreover, the comparisons provide insights into how the functional diversity is realized in proteins that share an evolutionarily conserved domain. On the basis of the chaperone activity the possible role of DJ-1 in the pathogenesis of Parkinsons disease is discussed.

Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature

A large group of hydrolytic enzymes, which contain a conserved stretch of ∼130 amino acids designated the amidase signature (AS) sequence, constitutes a super family that is distinct from any other known hydrolase family. AS family enzymes are widespread in nature, ranging from bacteria to humans, and exhibit a variety of biological functions. Here we report the first structure of an AS family enzyme provided by the crystal structure of malonamidase E2 from Bradyrhizobium japonicum. The structure, representing a new protein fold, reveals a previously unidentified Ser‐cisSer‐Lys catalytic machinery that is absolutely conserved throughout the family. This family of enzymes appears to be evolutionarily distinct but has diverged to acquire a wide spectrum of individual substrate specificities, while maintaining a core structure that supports the catalytic function of the unique triad. Based of the structures of the enzyme in two different inhibited states, an unusual action mechanism of the triad is proposed that accounts for the role of the cis conformation in the triad.

Vapor phase inclusion of ferrocene and its derivative in a microporous metal–organic porous material and its structural characterization by single crystal X-ray diffraction

The inclusion of ferrocene and its derivative in metal-organic porous material MOF-5 is achieved by vapor diffusion; single-crystal X-ray diffraction studies using synchrotron radiation of ferrocene-loaded MOF-5 reveal well-ordered guest molecules packed into the pores.

Methane sorption and structural characterization of the sorption sites in Zn2(bdc)2(dabco) by single crystal X-ray crystallography.

Sorption isotherms of methane in Zn(2)(bdc)(2)(dabco) are measured up to a pressure of 35 bar in the temperature range between 198-296 K. The methane sorption measurements at 296 K showed an uptake of 137 cm(3) cm(-3) at 35 bar. The enthalpy of methane adsorption for Zn(2)(bdc)(2)(dabco) estimated by the virial equation is 13.6 kJ mol(-1) at zero coverage. X-ray structure analysis of methane-adsorbed Zn(2)(bdc)(2)(dabco) by synchrotron radiation at 90 K revealed that methane molecules occupy three independent sorption sites (A, B, and C) with a stoichiometry of Zn(2)(bdc)(2)(dabco) x 6.69 CH(4), which is consistent with the results of the gas sorption measurements at 198 K. In a cavity, eight symmetry-related methane sorption sites A are located near the {Zn(2)(CO(2))(4)} paddle-wheel units, while four symmetry-related methane sorption sites B are near the center of the small windows along the a and b axes. Both A and B sites are half-occupied. Methane molecules occupying sites A are not only in van der Waals contact with the paddle-wheel units, but also interact with the phenyl rings of bdc ligands through partial pi-HC interactions. Methane molecules in B sites interact with the side of the phenyl rings through van der Waals interaction. The site C, located at the center of the cavity, is a secondary sorption site; methane molecules occupying sites C are in van der Waals contact with those in sites A and B.

Crystal structure of bet3 reveals a novel mechanism for Golgi localization of tethering factor TRAPP

Transport protein particle (TRAPP) is a large multiprotein complex involved in endoplasmic reticulum–to–Golgi and intra-Golgi traffic. TRAPP specifically and persistently resides on Golgi membranes. Neither the mechanism of the subcellular localization nor the function of any of the individual TRAPP components is known. Here, the crystal structure of mouse Bet3p (bet3), a conserved TRAPP component, reveals a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Charge-inversion mutations on the flat surface of the highly conserved yeast Bet3p led to conditional lethality, incorrect localization and membrane trafficking defects. A channel-blocking mutation led to similar defects. These data delineate a molecular mechanism of Golgi-specific targeting and anchoring of Bet3p involving the charged surface and insertion of a Golgi-specific hydrophobic moiety into the channels. This essential subunit could then direct other TRAPP components to the Golgi.

Structural Double-Mutant Cycle Analysis of a Hydrogen Bond Network in Ketosteroid Isomerase from Pseudomonas Putida Biotype B.

KSI (ketosteroid isomerase) catalyses an allylic isomerization reaction at a diffusion-controlled rate. A hydrogen bond network, Asp(99).Water(504).Tyr(14).Tyr(55).Tyr(30), connects two critical catalytic residues, Tyr(14) and Asp(99), with Tyr(30), Tyr(55) and a water molecule in the highly apolar active site of the Pseudomonas putida KSI. In order to characterize the interactions among these amino acids in the hydrogen bond network of KSI, double-mutant cycle analysis was performed, and the crystal structure of each mutant protein within the cycle was determined respectively to interpret the coupling energy. The DeltaDeltaG(o) values of Y14F/D99L (Tyr(14)-->Phe/Asp(99)-->Leu) KSI, 25.5 kJ/mol for catalysis and 28.9 kJ/mol for stability, were smaller than the sums (i.e. 29.7 kJ/mol for catalysis and 34.3 kJ/mol for stability) for single mutant KSIs respectively, indicating that the effect of the Y14F/D99L mutation was partially additive for both catalysis and stability. The partially additive effect of the Y14F/D99L mutation suggests that Tyr(14) and Asp(99) should interact positively for the stabilization of the transition state during the catalysis. The crystal structure of Y14F/D99L KSI indicated that the Y14F/D99L mutation increased the hydrophobic interaction while disrupting the hydrogen bond network. The DeltaDeltaG(o) values of both Y30F/D99L and Y55F/D99L KSIs for the catalysis and stability were larger than the sum of single mutants, suggesting that either Tyr(30) and Asp(99) or Tyr(55) and Asp(99) should interact negatively for the catalysis and stability. These synergistic effects of both Y30F/D99L and Y55F/D99L mutations resulted from the disruption of the hydrogen bond network. The synergistic effect of the Y55F/D99L mutation was larger than that of the Y30F/D99L mutation, since the former mutation impaired the proper positioning of a critical catalytic residue, Tyr(14), involved in the catalysis of KSI. The present study can provide insight into interpreting the coupling energy measured by double-mutant cycle analysis based on the crystal structures of the wild-type and mutant proteins.

The crystalline-state photochromism, thermochromism and X-ray structural characterization of a new spiroxazine

Abstract A new spiroxazine 4 was found to be photochromic and thermochromic both in solution and in the crystalline state. X-ray crystallography was used to determine that the molecules of the spiroxazine were arranged in a monoclinic (C2) crystallographic system. Intermolecular hydrogen bonds, together with interlayer, aromatic π–π stacking interactions, stabilize the molecular conformation and packing in the crystal structure.

High-pressure growth of fluorine-free SmFeAsO1−x superconducting single crystals

Fluorine-free SmFeAsO1?x single crystals of a nominal composition with x = 0.15 were grown under the pressure of 3.3?GPa and at 1350?1450??C by using the self-flux method. Plate-shaped crystals of a few?200??m in lateral size were obtained. The resistively determined superconducting transition of a single crystal was at about 53.5?K, with a narrow resistive transition width of 0.5?K. The detailed crystal structure was analyzed by using synchrotron-irradiated x-ray diffractometry and high-resolution scanning transmission electron microscopy. A sharp transition, a low residual resistivity, and a large residual resistivity ratio indicate the high quality of our single crystals. The temperature and magnetic field dependences of the magnetization also confirmed the absence of extrinsic impurity phases.

The conserved cis-Pro39 residue plays a crucial role in the proper positioning of the catalytic base Asp38 in ketosteroid isomerase from Comamonas testosteroni.

KSI (ketosteroid isomerase) from Comamonas testosteroni is a homodimeric enzyme that catalyses the allylic isomerization of Delta5-3-ketosteroids to their conjugated Delta4-isomers at a reaction rate equivalent to the diffusion-controlled limit. Based on the structural analysis of KSI at a high resolution, the conserved cis-Pro39 residue was proposed to be involved in the proper positioning of Asp38, a critical catalytic residue, since the residue was found not only to be structurally associated with Asp38, but also to confer a structural rigidity on the local active-site geometry consisting of Asp38, Pro39, Val40, Gly41 and Ser42 at the flexible loop between b-strands B1 and B2. In order to investigate the structural role of the conserved cis-Pro39 residue near the active site of KSI, Pro39 was replaced with alanine or glycine. The free energy of activation for the P39A and P39G mutants increased by 10.5 and 16.7 kJ/mol (2.5 and 4.0 kcal/mol) respectively, while DG(U)H2O (the free-energy change for unfolding in the absence of urea at 25.00+/-0.02 degrees C) decreased by 31.0 and 35.6 kJ/mol (7.4 and 8.5 kcal/mol) respectively, compared with the wild-type enzyme. The crystal structure of the P39A mutant in complex with d-equilenin [d-1,3,5(10),6,8-estrapentaen-3-ol-17-one], a reaction intermediate analogue, determined at 2.3 A (0.23 nm) resolution revealed that the P39A mutation significantly disrupted the proper orientations of both d-equilenin and Asp38, as well as the local active-site geometry near Asp38, which resulted in substantial decreases in the activity and stability of KSI. Upon binding 1-anilinonaphthalene-8-sulphonic acid, the fluorescence intensities of the P39A and P39G mutants were increased drastically, with maximum wavelengths blue-shifted upon binding, indicating that the mutations might alter the hydrophobic active site of KSI. Taken together, our results demonstrate that the conserved cis-Pro39 residue plays a crucial role in the proper positioning of the critical catalytic base Asp38 and in the structural integrity of the active site in KSI.

Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis

Crystal structure and domain characterization of ScpB from Mycobacterium tuberculosis Jeong-Sun Kim, Sujin Lee, Beom Sik Kang, Myung Hee Kim, Heung-Soo Lee, and Kyung-Jin Kim* 1Department of Chemistry, Chonnam National University, Gwangju, 500-757, Korea 2 Beamline Division, Pohang Accelerator Laboratory, Pohang, Kyungbuk 790-784, Korea 3 School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, Korea 4 Systems Microbiology Research Center, Korea Research Institute of Biosciences and Biotechnology, Yusung, Daejon 305-806, Korea