Hye-Jin Yoon

Seoul National University, Sŏul, Seoul, South Korea

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Publications (39)247.66 Total impact

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    ABSTRACT: The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an AMP moiety from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. In order to provide missing structural information on the substrate complexes of NaMN AT and to assist structure-based design of specific inhibitors for antibacterial discovery, we have determined the crystal structure of NaMN AT from Pseudomonas aeruginosa in three distinct states, i.e. the NaMN-bound form at 1.7A resolution and ATP-bound form at 2.0A as well as its apo-form at 2.0A. They represent crucial structural information necessary for better understanding of the substrate recognition and the catalytic mechanism. The substrate-unbound and substrate-complexed structures are all in the fully open conformation and there is little conformational change upon binding each of the substrates. Our structures indicate that a conformational change is necessary to bring the two substrates closer together for initiating the catalysis. We suggest that such a conformational change likely occurs only after both substrates are simultaneously bound in the active site.
    Journal of Molecular Biology 09/2005; 351(2):258-65. · 3.91 Impact Factor
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    ABSTRACT: Galectin from an edible fungus Agrocybe cylindracea (ACG) has a strong preference for N-acetylneuraminyl lactose (NeuAcalpha2-3lactose). The sugar recognition mechanism of ACG was explored by the X-ray crystallographic analyses of ligand-free ACG, and its complex with lactose, 3'-sulfonyl lactose and NeuAcalpha2-3lactose. The refined structure shows that ACG is a "proto"-type galectin composed of a beta-sandwich of two antiparallel sheets, each with six strands, in contrast to the five and six strands in animal galectins. ACG dimer in solution was classified as being among the "layer"-type. The carbohydrate recognition domain (CRD) of this galectin is common to those of animal galectins, except for substitution of one residue, Ala64, which corresponds to Asn46 in human galectin 1. A five-residue insertion in ACG at positions 42-46 involving Ser44 and Asn46 modified the architecture of the sugar binding site that contributes sialic acid specificity. Furthermore, it was found that the binding of a sulfate ion near the CRD in the ligand-free form led to a change in the conformation of the loop region caused by main-chain cis/trans transition between Ser44 and Pro45.
    Journal of Molecular Biology 09/2005; 351(4):695-706. · 3.91 Impact Factor
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    ABSTRACT: The bacterial enzyme UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes the first committed step of peptidoglycan biosynthesis, i.e., transfer of enolpyruvate from phosphoenolpyruvate to UDP-N-acetyl-glucosamine. We have overexpressed the enzyme from Haemophilus influenzae in Escherichia coli and crystallized it in the apo-form, as well as in a complex with UDP-N-acetylglucosamine and fosfomycin using ammonium sulfate as the precipitant. X-ray diffraction data from a crystal of the apo-form were collected to 2.8 A resolution at 293 K. The crystal quality was improved by co-crystallization with UDP-N-acetylglucosamine and fosfomycin. X-ray data to 2.2 A have been collected at 100 K from a flash-frozen crystal of the complex. The complex crystals belong to the orthorhombic space group I222 (or I212121) with unit-cell parameters of a = 63.7, b = 124.5, and c = 126.3 A. Assuming a monomer of the recombinant enzyme in the crystallographic asymmetric unit, the calculated Matthews parameter (VM) is 2.71 A3 Da-1 and solvent content is 54.6%.
    Molecules and Cells 07/2005; 19(3):398-401. · 2.21 Impact Factor
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    Proteins Structure Function and Bioinformatics 12/2004; 57(3):639-42. · 3.34 Impact Factor
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    ABSTRACT: Agmatine is the product of arginine decarboxylation and can be hydrolyzed by agmatinase to putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. Besides being an intermediate in polyamine metabolism, recent findings indicate that agmatine may play important regulatory roles in mammals. Agmatinase is a binuclear manganese metalloenzyme and belongs to the ureohydrolase superfamily that includes arginase, formiminoglutamase, and proclavaminate amidinohydrolase. Compared with a wealth of structural information available for arginases, no three-dimensional structure of agmatinase has been reported. Agmatinase from Deinococcus radiodurans, a 304-residue protein, shows approximately 33% of sequence identity to human mitochondrial agmatinase. Here we report the crystal structure of D. radiodurans agmatinase in Mn(2+)-free, Mn(2+)-bound, and Mn(2+)-inhibitor-bound forms, representing the first structure of agmatinase. It reveals the conservation as well as variation in folding, oligomerization, and the active site of the ureohydrolase superfamily. D. radiodurans agmatinase exists as a compact homohexamer of 32 symmetry. Its binuclear manganese cluster is highly similar but not identical to the clusters of arginase and proclavaminate amidinohydrolase. The structure of the inhibited complex reveals that inhibition by 1,6-diaminohexane arises from the displacement of the metal-bridging water.
    Journal of Biological Chemistry 12/2004; 279(48):50505-13. · 4.65 Impact Factor
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    ABSTRACT: Monodehydroascorbate (MDA) radical reductase (EC 1.6.5.4) is an FAD enzyme that catalyzes the univalent reduction of MDA radical to ascorbate using NAD(P)H as an electron donor. The recombinant MDA reductase from cucumber was crystallized using polyethylene glycol 6000 as a precipitant. The crystals belong to space group P2(1), with unit-cell parameters a = 60.8, b = 138.6, c = 61.7 A, beta = 114.5 degrees, and contained two molecules per asymmetric unit. The Matthews coefficient (VM) and the solvent content are 2.46 A3 Da(-1) and 50.0%, respectively. Diffraction data were collected to a resolution of 2.4 A at 100 K using Cu Kalpha radiation with a multi-wire area detector and gave a data set with an overall Rsym of 10.0% and a completeness of 92.5%.
    Acta Crystallographica Section D Biological Crystallography 09/2004; 60(Pt 8):1498-9. · 14.10 Impact Factor
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    ABSTRACT: The enzyme nicotinic acid mononucleotide adenylyltransferase (NaMN AT; EC 2.7.7.18) is essential for the synthesis of nicotinamide adenine dinucleotide and is a potential target for antibiotics. It catalyzes the transfer of an adenyl group from ATP to nicotinic acid mononucleotide to form nicotinic acid adenine dinucleotide. NaMN AT from Pseudomonas aeruginosa was overexpressed in Escherichia coli and crystallized at 291 K using 100 mM bis-Tris propane pH 7.0, 700 mM trisodium citrate and 15%(v/v) glycerol. X-ray diffraction data have been collected to 1.70 A. The crystals are tetragonal, belonging to space group P4(1)22 (or P4(3)22), with unit-cell parameters a = b = 65.02, c = 109.80 A. The presence of one monomer in the asymmetric unit gives a reasonable V(M) of 2.15 A(3) Da(-1), with a solvent content of 42.7%.
    Acta Crystallographica Section D Biological Crystallography 06/2004; 60(Pt 5):948-9. · 14.10 Impact Factor
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    ABSTRACT: Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate to chorismate in the shikimate pathway, which represents an attractive target for discovering antimicrobial agents and herbicides. Chorismate serves as a common precursor for the synthesis of aromatic amino acids and many aromatic compounds in microorganisms and plants. Chorismate synthase requires reduced FMN as a cofactor but the catalyzed reaction involves no net redox change. Here, we have determined the crystal structure of chorismate synthase from Helicobacter pylori in both FMN-bound and FMN-free forms. It is a tetrameric enzyme, with each monomer possessing a novel "beta-alpha-beta sandwich fold". Highly conserved regions, including several flexible loops, cluster together around the bound FMN to form the active site. The unique FMN-binding site is formed largely by a single subunit, with a small contribution from a neighboring subunit. The isoalloxazine ring of the bound FMN is significantly non-planar. Our structure illuminates the essential functional roles played by the cofactor.
    Journal of Molecular Biology 03/2004; 336(4):903-15. · 3.91 Impact Factor
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    ABSTRACT: The RecR protein plays a key role in the RecFOR pathway of recombination, which is necessary for the repair of ssDNA gaps. RecR from Deinococcus radiodurans has been overexpressed in Escherichia coli and crystallized at 297 K using polyethylene glycol 1000 as a precipitant. X-ray diffraction data to 2.90 A resolution have been collected at 100 K using Cu Kalpha X-rays from a mercury-soaked crystal. The crystal belongs to space group C222(1), with unit-cell parameters a = 106.96, b = 122.25, c = 156.01 A. The asymmetric unit contains four monomers of RecR, with a crystal volume per protein weight (V(M)) of 2.57 A(3) Da(-1) and a solvent content of 51.0%.
    Acta Crystallographica Section D Biological Crystallography 03/2004; 60(Pt 2):379-81. · 14.10 Impact Factor
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    ABSTRACT: The enzyme HemK (or PrmC) is one of the first identified methyltransferases that modify glutamine. It methylates the highly conserved GGQ motif in class I release factors (RF1 and RF2) in Escherichia coli. HemK from Thermotoga maritima was over-expressed and crystallized in the presence of S-adenosylmethionine at 296 K using ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.5 A resolution from a native crystal. The crystal is orthorhombic, belonging to the space group I222 (or I2(1)2(1)2(1)), with unit-cell parameters of a = 104.24, b = 118.73, and c = 146.62 A. Two (or three) monomers of recombinant HemK are likely to be present in the crystallographic asymmetric unit, giving a V(M) of 3.62 A3 Da(-1) (or 2.41 A3 Da(-1)), with a solvent content of 62.7% (or 44.0%).
    Molecules and Cells 11/2003; 16(2):266-9. · 2.21 Impact Factor
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    ABSTRACT: tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L- methionine (AdoMet) to G(37) within a subset of bacterial tRNA species, which have a G residue at the 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. Here we report four crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy and phosphate, and as an apo form. This first structure of TrmD indicates that it functions as a dimer. It also suggests the binding mode of G(36)G(37) in the active site of TrmD and the catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows structural similarity to trp repressor. We propose a plausible model for the TrmD(2)-tRNA(2) complex, which provides insights into recognition of the general tRNA structure by TrmD.
    The EMBO Journal 07/2003; 22(11):2593-603. · 9.82 Impact Factor
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    ABSTRACT: Acetohydroxy acid isomeroreductase (AHIR) is a key enzyme in the biosynthesis of branched-chain amino acids. We have determined the first crystal structure of a class I AHIR from Pseudomonas aeruginosa at 2.0 A resolution. Its dodecameric architecture of 23 point group symmetry is assembled of six dimeric units and dimerization is essential for the formation of the active site. The dimeric unit of P.aeruginosa AHIR partially superimposes with a three-domain monomer of spinach AHIR, a class II enzyme. This demonstrates that the so-called plant-specific insert in the middle of spinach AHIR is structurally and functionally equivalent to the C-terminal alpha-helical domain of P.aeruginosa AHIR, and the C-terminal alpha-helical domain was duplicated during evolution from the shorter, class I AHIRs to the longer, class II AHIRs. The dimeric unit of P.aeruginosa AHIR possesses a deep figure-of-eight knot, essentially identical with that in the spinach AHIR monomer. Thus, our work lowers the likelihood of the previous proposal that "domain duplication followed by exchange of a secondary structure element can be a source of such a knot in the protein structure" being correct.
    Journal of Molecular Biology 05/2003; 328(2):505-15. · 3.91 Impact Factor
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    ABSTRACT: The enzyme 3-deoxy-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase; CKS) catalyzes the activation of 3-deoxy-manno-octulosonate (KDO) by forming CMP-KDO. It is essential for the biosynthesis of lipopolysaccharides in Gram-negative bacteria and is a potential target for the discovery of antibacterial agents. L-CKS from Haemophilus influenzae was overexpressed with a C-terminal hexahistidine tag in Escherichia coli and crystallized in the presence of the substrate KDO at 297 K using PEG 4000 as a precipitant and ethylene glycol as an additive. The diffraction limit and spot shape of the native crystal could be improved significantly by dehydration/annealing. X-ray diffraction data were collected to 2.5 A resolution from a native crystal. The crystals are orthorhombic, belonging to the space group P2(1)2(1)2(1), with unit-cell parameters a = 48.6, b = 83.1, c = 117.3 A. The presence of two monomers of recombinant L-CKS in the crystallographic asymmetric unit gives a reasonable V(M) of 2.05 A(3) Da(-1), with a solvent content of 40.0%.
    Acta Crystallographica Section D Biological Crystallography 02/2003; 59(Pt 1):180-2. · 14.10 Impact Factor
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    ABSTRACT: The enzyme tRNA(m(1)G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) specifically to guanosine at position 37 within a subset of tRNA species in bacteria. The modified guanosine is next to the anticodon and is important for the maintenance of the correct reading frame during translation. TrmD from Haemophilus influenzae with both N- and C-terminal tags was overexpressed in Escherichia coli and crystallized at 297 K using sodium acetate as a precipitant. Native X-ray diffraction data were collected to 1.85 A resolution. The crystals are rhombohedral, belonging to the space group R32, with unit-cell parameters a = b = 98.05, c = 176.79 A, alpha = beta = 90, gamma = 120 degrees. The presence of one monomer of recombinant TrmD in the crystallographic asymmetric unit gives a V(M) of 3.07 A(3) Da(-1) and a solvent content of 59.9%.
    Acta Crystallographica Section D Biological Crystallography 02/2003; 59(Pt 1):183-4. · 14.10 Impact Factor
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    ABSTRACT: Peptide deformylase (PDF) from the pathogenic bacterium Pseudomonas aeruginosa has been overexpressed in Escherichia coli and crystallized in the presence of its inhibitor actinonin at 297 K using polyethylene glycol (PEG) 4000 as a precipitant. The diffraction limit and the spot shape of the crystals could be slightly improved by the crystal annealing/dehydration procedure. X-ray diffraction data to 1.85 A have been collected using synchrotron radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 68.75, b = 74.46, c = 77.18 A. The asymmetric unit contains two subunits of peptide deformylase, with a corresponding crystal volume per protein mass (V(M)) of 2.45 A(3) Da(-1) and a solvent content of 49.8%.
    Acta Crystallographica Section D Biological Crystallography 11/2002; 58(Pt 10 Pt 2):1874-5. · 14.10 Impact Factor
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    ABSTRACT: beta-Xylosidases are involved in the breakdown of xylans into xylose and belong to either family 39 or 43 of the glycosyl hydrolases. At present, no structural information is available for any member of these families. beta-Xylosidase from the thermophilic anaerobe Thermoanaerobacterium saccharolyticum, a member of glycosyl hydrolase family 39, has been crystallized at 296 K using the hanging-drop vapour-diffusion method. The crystal diffracts to 2.4 A resolution with synchrotron X-rays and belongs to space group P4(1)2(1)2 (or P4(3)2(1)2), with unit-cell parameters a = b = 92.75, c = 241.37 A. The asymmetric unit contains two monomers of the recombinant enzyme, giving a corresponding V(M) of 2.21 A(3)Da(-1) and a solvent content of 44.3%.
    Acta Crystallographica Section D Biological Crystallography 04/2002; 58(Pt 3):531-2. · 14.10 Impact Factor
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    ABSTRACT: A 260-residue protein (FabG3) encoded by the Rv2002 gene of Mycobacterium tuberculosis shows amino-acid sequence similarity to beta-ketoacyl carrier protein (ACP) reductase, FabG. A soluble mutant (I6T/V47M/T69M) was produced by the green fluorescent protein-based directed-evolution method. It was crystallized at 296 K using the hanging-drop vapour-diffusion method. The diffraction quality of the crystal improved significantly after annealing/dehydration. X-ray diffraction data were collected to 1.8 A resolution using synchrotron radiation. The crystal belongs to the space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 70.38, c = 148.93 A. The asymmetric unit contains two subunits, with a corresponding V(M) of 1.90 A(3) Da(-1) and a solvent content of 35.3%.
    Acta Crystallographica Section D Biological Crystallography 03/2002; 58(Pt 2):303-5. · 14.10 Impact Factor
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    ABSTRACT: The enzyme tRNA(m1G37)methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (AdoMet) specifically to guanosine at position 37 within a subset of tRNA species in bacteria. The modified guanosine is next to the anticodon and is important for the maintenance of the correct reading frame during translation. TrmD from Haemophilus influenzae with both N- and C-terminal tags was overexpressed in Escherichia coli and crystallized at 297 K using sodium acetate as a precipitant. Native X-­ray diffraction data were collected to 1.85 Å resolution. The crystals are rhombohedral, belonging to the space group R32, with unit-cell parameters a = b = 98.05, c = 176.79 Å, α = β = 90, γ = 120°. The presence of one monomer of recombinant TrmD in the crystallographic asymmetric unit gives a VM of 3.07 Å3 Da−1 and a solvent content of 59.9%.
    Acta Crystallographica Section D Biological Crystallography 01/2002; 59(1):183-184. · 12.67 Impact Factor
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    ABSTRACT: Arabidopsis thaliana P1 protein was crystallized using the hanging drop vapor-diffusion method in 0.1 M piperazine-1,4-bis(2-ethanesulfonic acid) buffer, containing 14% polyethylene glycol 6000 and 0.2 M magnesium acetate at pH 6.5 and 20°C. The crystals are orthorhombic and belong to the space group P212121 with unit cell dimensions of a=49.8, b=122.4 and c=149.9 Å. The diffraction data up to 2.9 Å were collected by a multiwire area detector.
    Biochimica et Biophysica Acta 08/2000; · 4.66 Impact Factor

Publication Stats

278 Citations
247.66 Total Impact Points

Institutions

  • 2002–2014
    • Seoul National University
      • • Department of Chemistry
      • • Division of Chemistry and Molecular Engineering
      Sŏul, Seoul, South Korea
  • 2010–2012
    • Kookmin University
      • Department of Bio and Nano Chemistry
      Seoul, Seoul, South Korea
  • 2000
    • Kyoto University
      Kioto, Kyōto, Japan