13 results on '"Kyeong Kyu Kim"'
Search Results
2. Crystal structure of carbohydrate esterase SmAcE1 from Sinorhizobium meliloti
- Author
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Changsuk Oh, Truc Kim, T. Doohun Kim, and Kyeong Kyu Kim
- Subjects
Inorganic Chemistry ,Structural Biology ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry - Published
- 2021
3. Crystal structure analysis of c4763, a uropathogenicEscherichia coli-specific protein
- Author
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Doyoun Kim, Jongkeun Choi, Hun Kim, and Kyeong Kyu Kim
- Subjects
Models, Molecular ,Recombinant Fusion Proteins ,Protein subunit ,Amino Acid Motifs ,Molecular Sequence Data ,Biophysics ,Gene Expression ,Sequence alignment ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,Protein Structure, Secondary ,Research Communications ,Microbiology ,Kluyveromyces ,Plasmid ,Bacterial Proteins ,Structural Biology ,Escherichia coli ,Genetics ,medicine ,Urea ,Uropathogenic Escherichia coli ,Cloning, Molecular ,Gene ,Kluyveromyces lactis ,biology ,Allophanate Hydrolase ,Condensed Matter Physics ,biology.organism_classification ,Protein Structure, Tertiary ,Protein Subunits ,Structural Homology, Protein ,Protein Multimerization ,Crystallization ,Sequence Alignment ,Function (biology) ,Plasmids ,Protein Binding - Abstract
Urinary-tract infections (UTIs), which are some of the most common infectious diseases in humans, can cause sepsis and death without proper treatment. Therefore, it is necessary to understand their pathogenicity for proper diagnosis and therapeutics. UropathogenicEscherichia coli, the major causative agents of UTIs, contain several genes that are absent in nonpathogenic strains and are therefore considered to be relevant to UTI pathogenicity. c4763 is one of the uropathogenicE. coli-specific proteins, but its function is unknown. To investigate the function of c4763 and its possible role in UTI pathogenicity, its crystal structure was determined at a resolution of 1.45 Å by a multiple-wavelength anomalous diffraction method. c4763 is a homodimer with 129 residues in one subunit that contains a GGCT-like domain with five α-helices and seven β-strands. c4763 shows structural similarity to the C-terminal domain of allophanate hydrolase fromKluyveromyces lactis, which is involved in the degradation of urea. These results suggest that c4763 might be involved in the utilization of urea, which is necessary for bacterial survival in the urinary tract. Further biochemical and physiological investigation will elucidate its functional relevance in UTIs.
- Published
- 2015
4. Structural and functional characterization of an Isd-type haem-degradation enzyme fromListeria monocytogenes
- Author
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Thao, Duong, Kwangsu, Park, Truc, Kim, Sung Wook, Kang, Myong-Joon, Hahn, Myung Joon, Hahn, Hye Yeon, Hwang, Inae, Jang, Han Bin, Oh, and Kyeong Kyu, Kim
- Subjects
Oxygenase ,Molecular Sequence Data ,Human pathogen ,Heme ,Crystallography, X-Ray ,medicine.disease_cause ,Catalysis ,chemistry.chemical_compound ,Listeria monocytogenes ,Structural Biology ,polycyclic compounds ,medicine ,Humans ,Amino Acid Sequence ,chemistry.chemical_classification ,Biliverdin ,biology ,Chemistry ,Biliverdine ,digestive, oral, and skin physiology ,General Medicine ,Monooxygenase ,biology.organism_classification ,Enzyme ,Biochemistry ,Mutagenesis, Site-Directed ,Oxygenases ,Bacteria ,Function (biology) ,Bacterial Outer Membrane Proteins - Abstract
Bacterial pathogens have evolved diverse types of efficient machinery to acquire haem, the most abundant source of iron in the human body, and degrade it for the utilization of iron. Gram-positive bacteria commonly encode IsdG-family proteins as haem-degrading monooxygenases.Listeria monocytogenesis predicted to possess an IsdG-type protein (Lmo2213), but the residues involved in haem monooxygenase activity are not well conserved and there is an extra N-terminal domain in Lmo2213. Therefore, its function and mechanism of action cannot be predicted. In this study, the crystal structure of Lmo2213 was determined at 1.75 Å resolution and its haem-binding and haem-degradation activities were confirmed. Structure-based mutational and functional assays of this protein, designated as an Isd-typeL. monocytogeneshaem-degrading enzyme (Isd-LmHde), identified that Glu71, Tyr87 and Trp129 play important roles in haem degradation and that the N-terminal domain is also critical for its haem-degrading activity. The haem-degradation product of Isd-LmHde is verified to be biliverdin, which is also known to be the degradation product of other bacterial haem oxygenases. This study, the first structural and functional report of the haem-degradation system inL. monocytogenes, sheds light on the concealed haem-utilization system in this life-threatening human pathogen.
- Published
- 2014
5. Characterization, crystallization and preliminary X-ray diffraction analysis of an (S)-specific esterase (pfEstA) fromPseudomonas fluorescensKCTC 1767: enantioselectivity for potential industrial applications
- Author
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T. Doohun Kim, Seulgi Kim, Tri Duc Ngo, and Kyeong Kyu Kim
- Subjects
Stereochemistry ,Molecular Sequence Data ,Biophysics ,Sequence alignment ,Pseudomonas fluorescens ,Biology ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,Esterase ,Substrate Specificity ,law.invention ,Hydrolysis ,Bacterial Proteins ,Structural Biology ,law ,Consensus Sequence ,Genetics ,Consensus sequence ,medicine ,Amino Acid Sequence ,Crystallization ,Escherichia coli ,Peptide sequence ,Esterases ,Stereoisomerism ,Condensed Matter Physics ,biology.organism_classification ,Crystallization Communications ,Sequence Alignment - Abstract
The structures and reaction mechanisms of enantioselective hydrolases, which can be used in industrial applications such as biotransformations, are largely unknown. Here, the X-ray crystallographic study of a novel (S)-specific esterase (pfEstA) fromPseudomonas fluorescensKCTC 1767, which can be used in the production of (S)-ketoprofen, is described. Multiple sequence alignments with other hydrolases revealed thatpfEstA contains a conserved Ser67 within the S-X-X-K motif as well as a highly conserved Tyr156. Recombinant protein containing an N-terminal His tag was expressed inEscherichia coli, purified to homogeneity and characterized using SDS–PAGE, MALDI-TOF MS and enantioselective analysis.pfEstA was crystallized using a solution consisting of 1 Msodium citrate, 0.1 MCHES pH 9.5, and X-ray diffraction data were collected to a resolution of 1.9 Å with anRmergeof 7.9%. The crystals ofpfEstA belonged to space groupP212121, with unit-cell parametersa= 65.31,b= 82.13,c = 100.41 Å, α = β = γ = 90°.
- Published
- 2012
6. Structures ofStaphylococcus aureuspeptide deformylase in complex with two classes of new inhibitors
- Author
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Sang Jae Lee, Seung-Jae Lee, Seung Kyu Lee, Hye-Jin Yoon, Hyung Ho Lee, Kyeong Kyu Kim, Bong Jin Lee, Byung Il Lee, and Se Won Suh
- Subjects
Models, Molecular ,Staphylococcus aureus ,Protein Conformation ,Klebsiella pneumoniae ,Biology ,Crystallography, X-Ray ,medicine.disease_cause ,Amidohydrolases ,Haemophilus influenzae ,Peptide deformylase ,Minimum inhibitory concentration ,Structural Biology ,Streptococcus pneumoniae ,medicine ,Humans ,Enzyme Inhibitors ,Respiratory Tract Infections ,chemistry.chemical_classification ,General Medicine ,Staphylococcal Infections ,Antimicrobial ,biology.organism_classification ,Anti-Bacterial Agents ,Enzyme ,chemistry ,Biochemistry ,Moraxella catarrhalis - Abstract
Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse-hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory-tract infections, such as Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae, and leading nosocomial pathogens such as Staphylococcus aureus and Klebsiella pneumoniae with a minimum inhibitory concentration (MIC) in the range 0.1-0.8 mg ml(-1). Interestingly, the reverse-hydroxamate/nonpeptide compounds showed a 250-fold higher antimicrobial activity towards S. aureus, although the four compounds showed similar K-i values against S. aureus PDF enzymes, with Ki values in the 11-85 nM range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of S. aureus PDF in complex with the four inhibitors were determined at resolutions of 1.90-2.30 angstrom. The inhibitor-bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn2+ ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse-hydroxamate inhibitors) appears to be correlated to S. aureus inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.
- Published
- 2012
7. Crystallization and diffraction analysis of Sm23: an SGNH-family arylesterase fromSinorhizobium meliloti1021
- Author
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Heejin Hwang, T. Doohun Kim, So-Hyun Park, Sung-Soo Kim, Tri Duc Ngo, and Kyeong Kyu Kim
- Subjects
Stereochemistry ,Biophysics ,Crystal structure ,Biology ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,law.invention ,Arylesterase ,chemistry.chemical_compound ,Structural Biology ,law ,Genetics ,medicine ,Crystallization ,Escherichia coli ,Sinorhizobium meliloti ,Mycobacterium smegmatis ,Condensed Matter Physics ,biology.organism_classification ,Magnesium formate ,chemistry ,Crystallization Communications ,Antigens, Helminth ,Recombinant DNA - Abstract
Industrial demand for active biocatalysts with desirable biochemical properties is constantly increasing and the discovery and characterization of novel esterases is potentially useful for industrial processes. Here, X-ray crystallographic studies of an (R)-specific SGNH arylesterase (Sm23) from Sinorhizobium meliloti 1021 are reported. The recombinant protein was expressed in Escherichia coli with a His tag and purified to homogeneity. Sm23 was crystallized using 0.2 M magnesium formate as a precipitant and X-ray diffraction data were collected to a resolution of 2.2 Å with an R(merge) of 6.9%. The crystals of SM23 belonged to the I-centred tetragonal space group I4(1)22, with unit-cell parameters a = b = 126.6, c = 190.9 Å. A molecular-replacement solution was obtained using the crystal structure of arylesterase from Mycobacterium smegmatis as a template.
- Published
- 2011
8. Purification, crystallization and preliminary crystallographic analysis of Est-Y29: a novel oligomeric β-lactamase
- Author
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Sangbum Joo, Kyeong Kyu Kim, Yeon-Woo Ryu, Sung-Soo Kim, Sangyoung Yoon, Seung-Bum Kim, Jongkook Moon, and T. Doohun Kim
- Subjects
medicine.drug_class ,Chemistry ,Antibiotics ,Cephalosporin ,Biophysics ,Pathogenic bacteria ,Crystallography, X-Ray ,Condensed Matter Physics ,medicine.disease_cause ,Biochemistry ,beta-Lactamases ,law.invention ,Crystallography ,Protein structure ,Crystallization Communications ,Structural Biology ,law ,Genetics ,medicine ,Recombinant DNA ,High incidence ,Crystallization ,Protein Structure, Quaternary ,Escherichia coli - Abstract
beta-Lactam antibiotics such as penicillins and cephalosporins have a four-atom ring as a common element in their structure. The beta-lactamases, which catalyze the inactivation of these antibiotics, are of great interest because of their high incidence in pathogenic bacteria. A novel oligomeric class C beta-lactamase (Est-Y29) from a metagenomic library was expressed, purified and crystallized. The recombinant protein was expressed in Escherichia coli with an N-terminal 6xHis tag and purified to homogeneity. EstY-29 was crystallized and X-ray intensity data were collected to 1.49 A resolution using synchrotron radiation.
- Published
- 2009
9. Crystallization and preliminary X-ray studies of SdiA fromEscherichia coli
- Author
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Lan Dao Ngoc Nguyen, Dong Young Kim, Chun-ai Wu, Kyeong Kyu Kim, and Neratur Krishnappagowda Lokanath
- Subjects
genetic structures ,Cell division ,Operon ,Biophysics ,Biology ,Crystallography, X-Ray ,medicine.disease_cause ,Biochemistry ,law.invention ,Plasmid ,X-Ray Diffraction ,Structural Biology ,law ,Escherichia coli ,Genetics ,medicine ,Receptor ,Escherichia coli Proteins ,food and beverages ,biochemical phenomena, metabolism, and nutrition ,Condensed Matter Physics ,Recombinant Proteins ,Quorum sensing ,Crystallization Communications ,Conjugation, Genetic ,Trans-Activators ,Recombinant DNA ,bacteria ,Crystallization ,Plasmids - Abstract
SdiA enhances cell division by regulating the ftsQAZ operon in Escherichia coli as a transcription activator. In addition, SdiA is suggested to play a role in detecting quorum signals that emanate from other species. It is therefore a homologue of LuxR, a cognate quorum-sensing receptor that recognizes a quorum signal and activates the quorum responses. To elucidate the role of SdiA and its functional and structural relationship to LuxR, structural studies were performed on E. coli SdiA. Recombinant SdiA was overexpressed, purified and crystallized at 287 K using the hanging-drop vapour-diffusion method. X-ray diffraction data from a native crystal were collected with 99.7% completeness to 2.7 A resolution with an R(merge) of 6.0%. The crystals belong to the hexagonal space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 130.47, c = 125.23 A.
- Published
- 2007
10. Crystallization and preliminary X-ray crystallographic study of UDP-glucose pyrophosphorylase (UGPase) fromHelicobacter pylori
- Author
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Kyeong Kyu Kim, Se Won Suh, Young-Hyun Han, Hun Kim, Chun Ai Wu, Sung Chul Ha, Dong Young Kim, and Chun-Sang Kim
- Subjects
Ammonium sulfate ,Helicobacter pylori ,UTP-Glucose-1-Phosphate Uridylyltransferase ,biology ,UTP—glucose-1-phosphate uridylyltransferase ,Metabolite ,X-ray ,General Medicine ,Crystallography, X-Ray ,biology.organism_classification ,law.invention ,chemistry.chemical_compound ,Metabolic pathway ,Crystallography ,chemistry ,Biochemistry ,Structural Biology ,law ,Orthorhombic crystal system ,Crystallization - Abstract
UDP-glucose pyrophosphorylase (UGPase) catalyzes the synthesis of UDP-glucose, an essential metabolite in all living organisms. An X-ray crystallographic study of UGPase from Helicobacter pylori has been performed in order to elucidate its role in the regulation of this important metabolic pathway. UGPase was crystallized from 0.1 M sodium acetate trihydrate pH 4.6, 2.0 M ammonium sulfate and 0.1 M guanidine-HCl. According to diffraction data collected at a resolution of 2.9 A using a synchrotron-radiation source, the crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 91.47, b = 98.61, c = 245.70 A, alpha = beta = gamma = 90.0 degrees.
- Published
- 2004
11. Purification, crystallization and preliminary X-ray studies of ClpX fromHelicobacter pylori
- Author
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Dong Young Kim, Young-Hyun Han, Dong Ryoung Kim, Kyeong Kyu Kim, Chun Ai Wu, and Sung Chul Ha
- Subjects
medicine.medical_treatment ,Protein subunit ,Crystallography, X-Ray ,medicine.disease_cause ,law.invention ,Structural Biology ,law ,medicine ,Molecule ,Cloning, Molecular ,Crystallization ,Escherichia coli ,Heat-Shock Proteins ,Adenosine Triphosphatases ,Protease ,Helicobacter pylori ,biology ,Hexagonal crystal system ,Chemistry ,Escherichia coli Proteins ,Endopeptidase Clp ,General Medicine ,biology.organism_classification ,Biochemistry ,Chaperone (protein) ,Solvents ,biology.protein ,ATPases Associated with Diverse Cellular Activities ,Molecular Chaperones - Abstract
ClpX, a member of the HSP (heat-shock protein) 100 family, functions as a molecular chaperone and is a regulatory subunit of the ClpXP protease. To understand the chaperone and regulatory mechanisms of ClpX, Helicobacter pylori ClpX has been overexpressed in Escherichia coli and crystallized at 295 K using (NH(4))(2)HPO(4) as precipitant. X-ray diffraction data have been collected to 2.6 A resolution using a synchrotron-radiation source. The crystals belong to the hexagonal space group P6(5) or P6(1), with unit-cell parameters a = b = 78.52 (04), c = 131.51 (09) A, alpha = beta = 90, gamma = 120 degrees. The crystallographic asymmetric unit contains one molecule of ClpX, with a corresponding V(M) of 2.78 A(3) Da(-1) and a solvent content of 55.8%.
- Published
- 2003
12. Crystallization and preliminary X-ray diffraction analysis ofSaccharomyces cerevisiaeYgr203p, a homologue of Acr2 arsenate reductase
- Author
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Hyun Kyu Song, J.H. Cho, B.M. Kim, Kyeong Kyu Kim, Se Won Suh, Seung-Je Cho, Jinho Moon, Young Sil Kim, and Jae Young Lee
- Subjects
Saccharomyces cerevisiae Proteins ,Arsenate Reductases ,Genetic Vectors ,Phosphatase ,Saccharomyces cerevisiae ,Ion Pumps ,Crystallography, X-Ray ,medicine.disease_cause ,law.invention ,Fungal Proteins ,Multienzyme Complexes ,Structural Biology ,law ,medicine ,cdc25 Phosphatases ,Crystallization ,Escherichia coli ,Adenosine Triphosphatases ,Fungal protein ,Sequence Homology, Amino Acid ,biology ,Arsenite Transporting ATPases ,General Medicine ,biology.organism_classification ,Recombinant Proteins ,Yeast ,Molecular Weight ,Crystallography ,Arsenate reductase ,Orthorhombic crystal system - Abstract
Ygr203p, a 148-residue protein encoded by the ygr203w gene of Saccharomyces cerevisiae, is a homologue of the yeast Acr2 arsenate reductase encoded by the acr2 (or ypr200c) gene. It also shows significant sequence similarity to the human cell-cycle control Cdc25 phosphatase family. It has been overexpressed in soluble form in Escherichia coli with a His(6) tag at its C-terminus. The recombinant protein has been crystallized at 296 K using sodium chloride as precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 40.48, b = 50.95, c = 91.95 A. The asymmetric unit contains a monomer, giving a crystal volume per protein mass (V(m)) of 2.61 A(3) Da(-1) and a solvent content of 53.8%. The crystals diffract to better than 1.9 A resolution with Cu Kalpha X-rays. They are therefore suitable for high-resolution structure determination.
- Published
- 2000
13. Structural and functional characterization of an Isd-type haem-degradation enzyme fromListeria monocytogenes. Corrigendum
- Author
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Thao Duong, Kwangsu Park, Truc Kim, Sung Wook Kang, Myong-Joon Hahn, Hye-Yeon Hwang, Inae Jang, Han Bin Oh, and Kyeong Kyu Kim
- Subjects
Structural Biology ,General Medicine - Abstract
The author list in Duonget al.[(2014).Acta Cryst.D70, 615–626] is corrected.
- Published
- 2014
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