Biomedical subjects

Kyung-Jin Kim

Publications and source records attributed to Kyung-Jin Kim.

11 recordsLinked to original sources

PubMed2006

Crystallization and initial crystallographic characterization of the Corynebacterium glutamicum nitrilotriacetate monooxygenase component A.

Safety and environmental concerns have recently dictated the proper disposal of nitrilotriacetate (NTA). Biodegradation of NTA is initiated by NTA monooxygenase, which is composed of two proteins: component A and component B. The NTA monooxygenase component A protein from Corynebacterium glutamicum was crystallized using the sitting-drop vapour-diffusion method in the presence of ammonium sulfate as the precipitant. X-ray diffraction data were collected to a maximum resolution of 2.5 A on a synchrotron beamline. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 111.04, b = 98.51, c = 171.61 A, beta = 101.94 degrees . The asymmetric unit consists of four molecules, corresponding to a packing density of 2.3 A(3) Da(-1). The structure was solved by molecular replacement. Structure refinement is in progress.

Bacterial Proteins↗

PubMed2006

Structural and functional insights into the B30.2/SPRY domain.

The B30.2/SPRY domain is present in approximately 700 eukaryotic (approximately 150 human) proteins, including medically important proteins such as TRIM5alpha and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, we report the crystal structure of an SPRY-SOCS box family protein GUSTAVUS in complex with Elongins B and C, revealing a highly distorted two-layered beta-sandwich core structure of its B30.2/SPRY domain. Ensuing studies identified one end of the beta-sandwich as the surface interacting with an RNA helicase VASA with a 40 nM dissociation constant. The sequence variation in TRIM5alpha responsible for HIV-1 restriction and most of the mutations in Pyrin causing familial Mediterranean fever map on this surface, implicating the corresponding region in many B30.2/SPRY domains as the ligand-binding site. The amino acids lining the binding surface are highly variable among the B30.2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif.

Amino Acid Motifs↗

PubMed2005

The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase.

In many Gram-negative bacteria, including a number of pathogens such as Pseudomonas aeruginosa and Erwinia carotovora, virulence factor production and biofilm formation are linked to the quorum-sensing systems that use diffusible N-acyl-L-homoserine lactones (AHLs) as intercellular messenger molecules. A number of organisms also contain genes coding for lactonases that hydrolyze AHLs into inactive products, thereby blocking the quorum-sensing systems. Consequently, these enzymes attract intense interest for the development of antiinfection therapies. However, the catalytic mechanism of AHL-lactonase is poorly understood and subject to controversy. We here report a 2.0-angstroms resolution structure of the AHL-lactonase from Bacillus thuringiensis and a 1.7-angstroms crystal structure of its complex with L-homoserine lactone. Despite limited sequence similarity, the enzyme shows remarkable structural similarities to glyoxalase II and RNase Z proteins, members of the metallo-beta-lactamase superfamily. We present experimental evidence that AHL-lactonase is a metalloenzyme containing two zinc ions involved in catalysis, and we propose a catalytic mechanism for bacterial metallo-AHL-lactonases.

Bacillus thuringiensis↗

PubMed2005

Crystallization and preliminary crystallographic analysis of Bacillus thuringiensis AHL-lactonase.

The quorum sensing (QS) systems in Gram-negative bacteria are mostly associated with diffusible N-acyl-L-homoserine lactones (AHLs). AHL-degrading enzymes hydrolyze the AHLs into inactive molecules, thereby blocking the QS systems that are closely linked to virulence factor production and biofilm formation. Consequently, these enzymes have recently attracted intense interest for the development of anti-infection therapies for plants and animals. However, despite significant progress in the investigation of AHL-degrading enzymes, no structure is yet available. Accordingly, this study reports on the expression and purification of the AHL-lactonase from Bacillus thuringiensis subsp. kurstaki HD263, as well as the successful crystallization of the enzyme. High-quality native crystals were obtained and a complete data set collected at 2.0 A resolution. The native crystal was found to belong to the space group P2(1)2(1)2(1), with unit cell parameters a=52.7 A, b=55.9 A, and c=74.1 A and one molecule in the asymmetric unit. MAD data were also collected at 2.4 A resolution for a SeMet-substituted crystal.

Bacillus thuringiensis↗

PubMed2005

Highly efficient protein expression and purification using bacterial hemoglobin fusion vector.

Recently developed bacterial hemoglobin (VHb) fusion expression vector has been widely used for the production of many target proteins due to its distinctive properties of expressing fusion protein with red color which facilitates visualization of the steps in purification, and increasing solubility of the target proteins. However, after intensive use of the vector, several defects have been found. In this report, we present a modified VHb fusion vector (pPosKJ) with higher efficiency, in which most of the defects were eliminated. First, it was found that thrombin protease often digests target protein as well as inserted thrombin cleavage site, so it was replaced by a TEV cleavage site for more specific cleavage of VHb from target protein. Second, a glycine-rich linker sequence was inserted between 6x his-tag and VHb to improve the affinity of 6x his-tag to Ni-NTA resin, resulting in higher purity of eluted fusion protein. Third, EcoRI and XhoI restriction sites located elsewhere in the vector were removed to make these restriction sites available for the cloning of target protein coding genes. A pPosKJ vector was fully examined with an anti-apoptotic BCL-2 family member of Caenorhabditis elegans, CED-9. A C-terminal VHb fusion expression vector (pPosKJC) was also constructed for stable expression of target proteins that may be difficult to express with an N-terminal fusion. Vaccinia-related kinase 1 (VRK1) was also successfully expressed and purified using the vector with high yield. Taken together, we suggest that the VHb fusion vector may be well suited for high-throughput protein expression and purification.

Amino Acid Sequence↗

PubMed2004

Two-promoter vector is highly efficient for overproduction of protein complexes.

The use of bicistronic vectors, which contain two target genes under one promoter, has been the most common practice for the heterologous production of binary protein complexes. The major problem of this method is the much lower expression of the second gene compared with that of the first gene next to the promoter. We tested a simple idea of whether inclusion of an additional promoter in front of the second gene may remove the problem. Compared with bicistronic vectors, corresponding two-promoter vectors yielded four to nine times larger amounts of the complexes between BCL-2 family proteins, BCL-X(L):BAD, BCL-X(L):BIM-S, and CED-9:EGL-1 in bacterial cells as a result of significantly increased expression of the second genes in a manner independent of the order of the target genes. With the two-promoter system, we produced two other complexes in large quantity suitable for extensive crystallization trial. The method does not accompany any technical disadvantages, and represents a significant improvement from the conventional method, which should enjoy wide application for the coexpression of binary or higher order protein complexes by extension.

Circular Dichroism↗

PubMed2003

Fusion protein system designed to provide color to aid in the expression and purification of proteins in Escherichia coli.

We have designed and constructed a new fusion expression vector (pKW32), which contains the His-tagged Vitreoscilla hemoglobin (VHb) coding gene upstream of the multiple cloning site. The pKW32 vector was designed to express target proteins as VHb fusions, which can be purified in one step by affinity chromatography. Due to the color of the heme in VHb, the VHb-fused target proteins have a red color that provides a visual aid for estimating their expression level and solubility. The red color can also be used as a visual marker throughout purification, while the concentration of the fusion protein can be determined by measuring the amount of VHb using carbon monoxide difference spectra. In addition, because of inherently high solubility of VHb, the fusion can increase the solubility of sparingly soluble target proteins. Target proteins can be easily separated from His-tagged VHb due to the presence of a thrombin-cleavage site between them. A mutant VHb, the soluble domain of Vitreoscilla cytochrome bo subunit II, and HIV integrase expressed and purified using the pKW32 system have native function. In addition, the integrase, which is known to be difficult to purify because of low solubility, was purified simply and without solubilizing agents using our system.

Base Sequence↗

PubMed2003

Delta (13)C-urea breath test value is a useful indicator for Helicobacter pylori eradication in patients with functional dyspepsia.

BACKGROUND: Eradication of Helicobacter pylori is not routinely recommended for the symptomatic relief and the prevention of gastric cancer in patients with functional dyspepsia. The present study investigated a useful indicator of H. pylori eradication in such patients by determining the optimal cutoff value of a 13C-urea breath test (UBT). METHODS: One hundred dyspeptic patients participated in the study. Dyspepsia was scored, and a 13C-UBT administered. A level of delta 13C-UBT of>4 per thousand was diagnosed as H. pylori-positive. After the stomach was endoscopically sprayed with phenol red, biopsy specimens were taken from the antrum, body and cardia of the stomach for the assessment of H. pylori density, and activity (neutrophil infiltration) and degree (lymphocyte infiltration) of gastritis. RESULTS: Correlation between delta 13C-UBT and dyspepsia score was not found. Delta 13C-UBT significantly correlated with H. pylori density score in the total stomach (r = 0.53, P < 0.0001), neutrophil (r = 0.34, P = 0.0005) and lymphocyte score (r = 0.69, P < 0.0001). Twenty-six of the 100 subjects had a neutrophil score of >or=4, lymphocyte score of >or=4, and H. pylori score of >or=4. Their 95% confidence interval of mean was 58.2 per thousand, which reflects moderate to marked acute and chronic gastritis, and dense H. pylori colonization. CONCLUSIONS: The 13C-UBT is a reliable semiquantitative test to assess H. pylori density and the activity and degree of gastritis. It is proposed that H. pylori eradication therapy might be beneficial for patients with functional dyspepsia with a delta 13C-UBT of >58.2 per thousand.

Adult↗

PubMed2003

Isolation, sequencing, and characterization of the cytochrome bo operon from Vitreoscilla.

The entire operon encoding the sodium pumping cytochrome bo from the bacterium Vitreoscilla was isolated and sequenced, and this sequence was analyzed by blast and hydropathy plots. There are fairly similar phylogenetic relationships which apply to all five proteins, but overall greater similarity to members of the gamma subdivision than the beta subdivision of the Proteobacteria. Hydropathy plots of all five Cyo proteins show near identity with those of the corresponding E. coli subunits, indicating that the similarity extends from sequence to structure. The operon appears to have a typical Shine-Dalgarno sequence, an E. coli-like promoter, and several possible binding sites for regulatory proteins. The Vitreoscilla Cyo B subunit (the probable Na+ pump) is almost identical to E. coli Cyo B at 18 key amino acids; thus, there are no obvious changes in Vitreoscilla Cyo B that hint at the details of its Na+ pumping ability.

Bacterial Proteins↗

PubMed2002

Vitreoscilla hemoglobin binds to subunit I of cytochrome bo ubiquinol oxidases.

The bacterium, Vitreoscilla, can induce the synthesis of a homodimeric hemoglobin under hypoxic conditions. Expression of VHb in heterologous bacteria often enhances growth and increases yields of recombinant proteins and production of antibiotics, especially under oxygen-limiting conditions. There is evidence that VHb interacts with bacterial respiratory membranes and cytochrome bo proteoliposomes. We have examined whether there are binding sites for VHb on the cytochrome, using the yeast two-hybrid system with VHb as the bait and testing every Vitreoscilla cytochrome bo subunit as well as the soluble domains of subunits I and II. A significant interaction was observed only between VHb and intact subunit I. We further examined whether there are binding sites for VHb on cytochrome bo from Escherichia coli and Pseudomonas aeruginosa, two organisms in which stimulatory effects of VHb have been observed. Again, in both cases a significant interaction was observed only between VHb and subunit I. Because subunit I contains the binuclear center where oxygen is reduced to water, these data support the function proposed for VHb of providing oxygen directly to the terminal oxidase; it may also explain its positive effects in Vitreoscilla as well as in heterologous organisms.

Bacterial Proteins↗

PubMed2002

Comparative analysis of sequences expressed during the liquid-cultured mycelia and fruit body stages of Pleurotus ostreatus.

To characterize genes involved in fruit body development, two complementary DNA (cDNA) libraries were constructed from RNA isolated from liquid-cultured mycelia and fruit bodies of Pleurotus ostreatus. Using single-pass sequencing of cDNA clones, 952 and 1069 expressed sequence tags (ESTs) were generated from liquid-cultured mycelia and fruit body cDNA library, respectively. A BLASTX search revealed that 390 of the liquid-cultured mycelia ESTs (41%) and 531 of the fruit body ESTs (50%) showed significant similarity to protein sequences described in the nonredudant database (E values < or =1 x 10(-5)). When liquid-cultured mycelia and fruit body ESTs were compared by the SeqMan II program, among the total of 2021 ESTs, 1256 ESTs were unigenes, and 66 unigenes (5.3%) were commonly expressed during both stages. The functional catalogs of the ESTs were made by comparison with functionally identified Saccharomyces cerevisiae genes. Liquid-cultured mycelium ESTs were compared with fruit body ESTs and changes of the expressed genes during fruit body development were analyzed.

Culture Media↗