Suk-Youl Park

High-resolution structure of ybfF from Escherichia coli K12: a unique substrate-binding crevice generated by domain arrangement

Esterases are one of the most common enzymes and are involved in diverse cellular functions. ybfF protein from Escherichia coli (Ec_ybfF) belongs to the esterase family for the large substrates, palmitoyl coenzyme A and malonyl coenzyme A, which are important cellular intermediates for energy conversion and biomolecular synthesis. To obtain molecular information on ybfF esterase, which is found in a wide range of microorganisms, we elucidated the crystal structures of Ec_ybfF in complexes with small molecules at resolutions of 1.1 and 1.68 A, respectively. The structure of Ec_ybfF is composed of a globular alpha/beta hydrolase domain with a three-helical bundle cap, which is linked by a kinked helix to the alpha/beta hydrolase domain. It contains a catalytic tetrad of Ser-His-Asp-Ser with the first Ser acting as a nucleophile. The unique spatial arrangement and orientation of the helical cap with respect to the alpha/beta hydrolase domain form a substrate-binding crevice for large substrates. The helical cap is also directly involved in catalysis by providing a substrate anchor, viz., the conserved residues of Arg123 and Tyr208. The high-resolution structure of Ec_ybfF shows that the inserted helical bundle structure and its spatial orientation with respect to the alpha/beta hydrolase domain are critical for creating a large inner space and constituting a specific active site, thereby providing the broad substrate spectrum toward large biomolecules.

Structures of iron-dependent alcohol dehydrogenase 2 from Zymomonas mobilis ZM4 with and without NAD+ cofactor.

The ethanologenic bacterium Zymomonas mobilis ZM4 is of special interest because it has a high ethanol yield. This is made possible by the two alcohol dehydrogenases (ADHs) present in Z. mobilis ZM4 (zmADHs), which shift the equilibrium of the reaction toward the synthesis of ethanol. They are metal-dependent enzymes: zinc for zmADH1 and iron for zmADH2. However, zmADH2 is inactivated by oxygen, thus implicating zmADH2 as the component of the cytosolic respiratory system in Z. mobilis. Here, we show crystal structures of zmADH2 in the form of an apo-enzyme and an NAD+–cofactor complex. The overall folding of the monomeric structure is very similar to those of other functionally related ADHs with structural variations around the probable substrate and NAD+ cofactor binding region. A dimeric structure is formed by the limited interactions between the two subunits with the bound NAD+ at the cleft formed along the domain interface. The catalytic iron ion binds near to the nicotinamide ring of NAD+, which is likely to restrict and locate the ethanol to the active site together with the oxidized Cys residue and several nonpolar bulky residues. The structures of the zmADH2 from the proficient ethanologenic bacterium Z. mobilis, with and without NAD+ cofactor, and modeling ethanol in the active site imply that there is a typical metal-dependent catalytic mechanism.

The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity

Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is located close to the probable DNA-binding site for translocation, which is far from the NTD nucleolytic core. Comparison of relative domain arrangements with other functionally related ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that a linker helix connecting two RDs and an extended region within the nuclease domain may play a central role in switching the DNA translocation into the restriction activity.

Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals

Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals Suk-Youl Park, Woo-Ram Lee, Suk-Chan Lee, Myung-Hee Kwon, Yong-Sung Kim, and Jeong-Sun Kim* 1Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Korea 2Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea 3Department of Genetic Engineering, Sungkyunkwan University, Suwon 440-746, Korea 4Department of Microbiology, Ajou Medical School, Suwon 443-749, Korea

Crystal structure of the transcriptional activator HlyU from Vibrio vulnificus CMCP6.

MINT‐7710072, MINT‐7710086: HlyU_Vv (uniprotkb:Q8DES3) and HlyU_Vv (uniprotkb:Q8DES3) bind (MI:0407) by X‐ray crystallography (MI:0114)

Crystal structure of Cmr5 from Pyrococcus furiosus and its functional implications

pfCmr5 and pfCmr4 bind by ion exchange chromatography (View interaction)

Precise manipulation of a microrobot in the pulsatile flow of human blood vessels using magnetic navigation system

This paper proposes a method to precisely manipulate a microrobot in the pulsatile flow that simulates the flow characteristics of human blood vessels by utilizing the electromagnetic transfer function of a magnetic navigation system (MNS). The frequency response characteristics of the MNS were utilized so that the input voltages in each coil can precisely generate the required time-varying magnetic force of a microrobot. An experiment which successfully anchoring a microrobot in a pulsatile flow was conducted to verify the proposed method.

A study on the moving mechanism for flower robot

As a service robot, we proposed a flower robot which has several functions, such as moving mechanism, sensing ability, and home appliance functions. Among the various functions, the moving function of the flower robot is very important function. The moving flower robot can be divided as a flower, a stem and leaves. We tried to mimic the blooming of flower, the swaying of the stem and the stirring of the leaves in the wind. For the actuation of the flower robot, we used micromotors and tendon mechanisms. From the motions of the flower, the stem and the leaves, the desired target positions are decided. In addition, based on inverse kinematics and trajectory generations, the overall control system for the moving flower robot is constructed. Through the various experiments, the performances of each part of the flower robot are verified and the characteristics are discussed.

Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016.

In multifunctional type I restriction enzymes, active methyltransferases (MTases) are constituted of methylation (HsdM) and specificity (HsdS) subunits. In this study, the crystal structure of a putative HsdM subunit from Vibrio vulnificus YJ016 (vvHsdM) was elucidated at a resolution of 1.80 Å. A cofactor-binding site for S-adenosyl-L-methionine (SAM, a methyl-group donor) is formed within the C-terminal domain of an α/β-fold, in which a number of residues are conserved, including the GxGG and (N/D)PP(F/Y) motifs, which are likely to interact with several functional moieties of the SAM methyl-group donor. Comparison with the N6 DNA MTase of Thermus aquaticus and other HsdM structures suggests that two aromatic rings (Phe199 and Phe312) in the motifs that are conserved among the HsdMs may sandwich both sides of the adenine ring of the recognition sequence so that a conserved Asn residue (Asn309) can interact with the N6 atom of the target adenine base (a methyl-group acceptor) and locate the target adenine base close to the transferred SAM methyl group.

Full wave finite-difference time-domain study of lossless acoustic bipolar cylindrical cloak with compressed geometry and complementary media

Full-wave finite-difference time-domain analysis of a lossless acoustic cloak with complementary media is studied for bipolar cylindrical geometry. The material parameters for the acoustic cloak are obtained by comparing two-dimensional Maxwells equations in the transverse magnetic polarization and acoustic field equations for general curvilinear coordinates. The permittivity and permeability tensors for the corresponding electromagnetic fields are then obtained by using an effective medium approach in general relativity. The complementary media cancels the phase vectors across the boundaries of the illuminated acoustic waves. It is shown that for the lossless cloak the broadband and illumination direction independent cloaking can be achieved with the proposed structure.