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K K Kim

Publications and source records attributed to K K Kim.

At least 91 records · Page 5Linked to original sources
PubMed1995

Crystallization, molecular replacement solution, and refinement of tetrameric beta-amylase from sweet potato.

Sweet potato beta-amylase is a tetramer of identical subunits, which are arranged to exhibit 222 molecular symmetry. Its subunit consists of 498 amino acid residues (Mr 55,880). It has been crystallized at room temperature using polyethylene glycol 1500 as precipitant. The crystals, growing to dimensions of 0.4 mm x 0.4 mm x 1.0 mm within 2 weeks, belong to the tetragonal space group P4(2)2(1)2 with unit cell dimensions of a = b = 129.63 A and c = 68.42 A. The asymmetric unit contains 1 subunit of beta-amylase, with a crystal volume per protein mass (VM) of 2.57 A3/Da and a solvent content of 52% by volume. The three-dimensional structure of the tetrameric beta-amylase from sweet potato has been determined by molecular replacement methods using the monomeric structure of soybean enzyme as the starting model. The refined subunit model contains 3,863 nonhydrogen protein atoms (488 amino acid residues) and 319 water oxygen atoms. The current R-value is 20.3% for data in the resolution range of 8-2.3 A (with 2 sigma cut-off) with good stereochemistry. The subunit structure of sweet potato beta-amylase (crystallized in the absence of alpha-cyclodextrin) is very similar to that of soybean beta-amylase (complexed with alpha-cyclodextrin). The root-mean-square (RMS) difference for 487 equivalent C alpha atoms of the two beta-amylases is 0.96 A. Each subunit of sweet potato beta-amylase is composed of a large (alpha/beta)8 core domain, a small one made up of three long loops [L3 (residues 91-150), L4 (residues 183-258), and L5 (residues 300-327)], and a long C-terminal loop formed by residues 445-493. Conserved Glu 187, believed to play an important role in catalysis, is located at the cleft between the (alpha/beta)8 barrel core and a small domain made up of three long loops (L3, L4, and L5). Conserved Cys 96, important in the inactivation of enzyme activity by sulfhydryl reagents, is located at the entrance of the (alpha/beta)8 barrel.

Amino Acid Sequence↗
PubMed1995

Characterization of human homologue of 4-1BB and its ligand.

The human homologue of 4-1BB (H4-1BB) cDNA was isolated from PMA plus ionomycin-treated human peripheral T-cell cDNA libraries. The amino acid sequence deduced from the nucleotide sequence showed that the protein is composed of 255 amino acids with 2 potential N-linked glycosylation sites. The molecular weight of its protein backbone is calculated to be 27 kDa. The H4-1BB contains features such as signal sequence and transmembrane domain, indicating that it is a receptor protein. This protein showed 60% identity of amino acid sequence to mouse 4-1BB. In the cytoplasmic domain there are 5 regions of amino acid sequences conserved from mouse to human, indicating that these residues might be important in the 4-1BB function. H4-1BB mRNA was detected in unstimulated peripheral blood T cells and was inducible in T-cell lines such as Jurkat and CEM. H4-1BB-AP, a fusion protein between the H4-1BB extracellular domain and alkaline phosphatase, was used to identify the ligand for the H4-1BB. Although the H4-1BB ligand was detected in both T and B cells of human peripheral blood, the ligand was preferentially expressed in primary B cells and B-cell lines. Daudi, a B-cell lymphoma, was one of the B-cell lines that carried a higher number of ligands. Scatchard analysis showed that the Kd = 1.4 x 10(9) M and the number of ligands in Daudi cell was 4.2 x 10(3).

3T3 Cells↗
PubMed1995

An unusual infected hydrocele--a case report.

Of acute scrotal lesions in the neonates, cases needing emergent exploration are quite rare and differential diagnosis of them is not easy. Only a few cases of inflamed hydroceles occurring in young boys have been reported to have been caused by bacterial infection in the literature. We couldn't find any case concerning simultaneous bacterial infection in urine and hydrocele by the same organisms. We present an unusual case of infected hydrocele in a neonate with bacteriuria.

Bacteriuria↗
PubMed1995

Cloning, developmental expression, and evidence for alternative splicing of the murine tuberous sclerosis (TSC2) gene product.

Tuberous sclerosis (TS) is a genetically heterogeneous disease characterized by the widespread appearance of nonmalignant growths that affect multiple organ systems. A TS disease-determining gene, located at 16p13.3 and designated TSC2, has recently been cloned. In this report, the murine TSC2 homologue was cloned and characterized. cDNA clones encompassing the entire murine TSC2 transcript were isolated. Sequence analysis revealed a high degree of homology between the deduced amino acid sequence of the murine and human gene products. Northern blot surveys demonstrated widespread TSC2 expression which was subject to developmental regulation in a tissue-specific manner. Although high levels of TSC2 transcripts were observed in many adult tissues, protein analyses are required to determine whether functional tuberin protein is synthesized. Reverse transcription-polymerase chain reaction analyses identified at least six regions of alternative splicing, several of which modified putative regulatory motifs in the deduced amino acid structure of the TSC2 protein.

Adult↗
PubMed1994

Crystallization and preliminary X-ray crystallographic study of ribosome-inactivating protein from barley seeds.

Ribosome-inactivating protein from barley seeds has been crystallized using polyethylene glycol as precipitant. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 88.36, b = 62.59, c = 53.18 A and beta = 108.62 degrees. The asymmetric unit contains one molecule of ribosome-inactivating protein with a corresponding crystal volume per protein mass (V(m)) of 2.32 A(3) Da(-1) and a solvent content of 47% by volume. The crystal diffracts to about 2.3 A with X-rays from a rotating-anode source and is very stable in the X-ray beam. X-ray data (nearly complete to 2.4 A Bragg spacing) have been collected from a native crystal.

Journal Article↗
PubMed1994

Tumor suppressor gene expression during normal and pathologic myocardial growth.

Previous studies have identified several host proteins (p53, p107, and p193), which form prominent complexes with SV40 T antigen in transformed cardiomyocytes. Expression of p53 and p107 was monitored during normal and pathologic growth in nontransformed murine myocardium. Both genes were expressed at relatively high levels in embryonic cardiomyocytes. Transcript levels decreased markedly during the process of cardiomyocyte terminal differentiation and were very low or undetectable in adult animals. In contrast, retinoblastoma transcripts were observed at low levels throughout myocardial development. None of the tumor suppressor genes examined were transcriptionally activated during acute myocardial overload or isoproterenol-induced myocardial hypertrophy. The potential role of tumor suppressor gene product expression in myocardial development and pathology is discussed.

Animals↗
PubMed1994

Genomic organization and chromosomal localization of the T-cell antigen 4-1BB.

4-1BB is an inducible T cell surface receptor which belongs to the nerve growth factor receptor superfamily, a group of cysteine-rich cell-surface proteins. 4-1BB is a 30-kDa glycoprotein and exists as both a monomer and a 55-kDa dimer on the T cell surface. Cross-linking 4-1BB with monoclonal antibody resulted in the 2- to 10-fold enhancement of T cell proliferation. We have isolated and characterized 4-1BB genomic clones and have found that the 4-1BB gene contains two different 5' untranslated regions, which are used alternately to form the 4-1BB mRNA. The two 5' UTRs were encoded in the same chromosome and were separated from one another by an intron of approximately 2.5 kb. The entire gene spans approximately 13 kb of mouse chromosome 4. 4-1BB gene consists of 10 exons and 9 introns, in which there are two exons for 5' untranslated regions and 8 exons for coding region. Most of the putative functional domains were encoded by separate exons. 4-1BB extracellular domain contains four potential C6 (CXn C XX C XX CXn C Xn C) motifs, of which the first motif is partial and the third is distinct from those of nerve growth factor receptor or TNF receptor 1. A comparison of exon-intron organization among the genes of the nerve growth factor receptor family indicated that most C6 motif is interrupted by an intron.

Amino Acid Sequence↗
PubMed1994

4-1BB T-cell antigen binds to mature B cells and macrophages, and costimulates anti-mu-primed splenic B cells.

4-1BB is expressed on activated murine T cells and may function as an accessory signaling molecule during T-cell activation. To identify putative 4-1BB ligands, a fusion protein consisting of the extracellular domain of 4-1BB fused to human placental alkaline phosphatase (4-1BB-AP) was constructed. Alkaline phosphatase activity could then be used as an indicator of the relative amount of bound 4-1BB. These studies indicated that 4-1BB-AP specifically bound to the surface of various mature B and macrophage cell lines. 4-1BB-AP bound at low levels to T cell lines (non-activated and anti-CD3-activated), pre-B-cell lines, and an immature macrophage cell line. 4-1BB-AP did not bind to a glial tumor cell line, HeLa cells, or COS cells. In addition, 4-1BB-AP bound at higher levels to F(ab')2 anti-mu-activated primary B cells compared to anti-CD3-activated primary T cells. Scatchard analysis indicated that the A20 B cell lymphoma expressed 3680 binding sites per cell with a Kd of 1.86 nM. Affinity cross-linking studies demonstrated that a major cell surface species of 120 kDa bound to 4-1BB-AP; 4-1BB-AP also bound to a minor species of approximately 60 kDa. The addition of paraformaldehyde-fixed SF21 cells expressing recombinant 4-1BB synergized with F(ab')2 anti-mu in inducing splenic B cell proliferation suggesting that 4-1BB may function as a regulator of B cell growth.

Animals↗
PubMed1994

Crystallization and preliminary X-ray crystallographic analysis of phospholipid transfer protein from maize seedlings.

Phospholipid transfer protein from maize seedlings has been crystallized using trisodium citrate as precipitant. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1) with unit cell dimensions of a = 24.46 A, b = 49.97 A, and c = 69.99 A. The presence of one molecule in the asymmetric unit gives a crystal volume per protein mass (Vm) of 2.36 A3/Da and a solvent content of 48% by volume. The X-ray diffraction pattern extends at least to 1.6 A Bragg spacing when exposed to both CuK alpha and synchrotoron X-rays. A set of X-ray data to approximately 1.9 A Bragg spacing has been collected from a native crystal.

Amino Acid Sequence↗
PubMed1994

Functional analysis of T-cell antigen 4-1BB in activated intestinal intra-epithelial T lymphocytes.

The 4-1BB antigen has been recently demonstrated to be a 30 kDa inducible T-cell antigen and is expressed on the cell surface of activated splenic T cells and thymocytes. This novel T-cell antigen also associates physically with the T cell-specific protein tyrosine kinase, p56lck. We show here that the inducible T-cell antigen 4-1BB is expressed on activated intestinal intra-epithelial T lymphocytes (IEL). After activation, or in the presence of IL-2, the activated IELs showed higher levels of 4-1BB. Functional studies revealed that the activated IELs triggered with anti-4-1BB monoclonal antibody could enhance the level of IEL cytotoxicity against anti-CD3-secreting hybridoma cells. Cross-linking of anti-4-1BB antibody also enhanced the proliferation of IELs. These results suggest that the inducible antigen 4-1BB has broad biological functions which not only play a role in activated splenic T cells and thymocytes but also in the mucosal immune system.

Animals↗
PubMed1994

Characterization of mouse Pmel 17 gene and silver locus.

Pmel 17 cDNA clones, isolated from wild-type and si/si murine melanocytes, were sequenced and compared. A single nucleotide (A) insertion was found in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus and to extend the Pmel 17 protein by 12 residues. The mutation was confirmed by the sequence of the PCR-amplified genomic region including the mutation site. Silver Pmel 17 was not recognized by antibodies directed toward the C-terminal amino acids of wild-type Pmel 17, indicating a defect in this region. These results indicate that silver Pmel 17 protein has a major defect at the carboxyl terminus.

Amino Acid Sequence↗
PubMed1993

Cloning and sequence analysis of the gene encoding the crystalline surface layer protein of Rickettsia typhi.

The nucleotide sequence of the gene (slpT) encoding the crystalline surface layer protein (SLP) of Rickettsia typhi was determined. The slpT gene consists of 4935 bp coding for a 1645-amino-acid (aa) protein containing a predicted signal peptide at the N terminus. The size of the predicted SLP exceeds the observed size (135 kDa) on SDS-PAGE. The N-terminal aa sequence of the 32-kDa protein of R. typhi reported by Hackstadt et al. [Infect. Immun. 60 (1992) 159-165] was found in the C-terminal portion of the deduced aa sequence, suggesting that the product of slpT is processed into the mature SLP and the 32-kDa protein.

Amino Acid Sequence↗
PubMed1993

Crystallization and preliminary X-ray crystallographic analysis of the protease inhibitor ecotin.

Ecotin, a novel serine protease inhibitor isolated from Escherichia coli, has been crystallized using polyethylene glycol 1500 as the precipitating agent. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell parameters of a = 39.22 A, b = 84.86 A, and c = 98.74 A. The asymmetric unit contains one dimeric molecule of ecotin, with a crystal volume per protein mass (Vm) of 2.55 A3/Da and a solvent content of 51.8% by volume. The crystals diffract to at least 2.2 A using a conventional X-ray source, and X-ray data have been collected to 2.7 A Bragg spacing from a native crystal.

Bacterial Proteins↗
PubMed1993

Inducible T cell antigen 4-1BB. Analysis of expression and function.

4-1BB is an inducible receptor-like protein expressed in both cytolytic and Th cells. Optimal induction of 4-1BB mRNA in T cells required both PMA and ionomycin stimulation, indicating that protein kinase C activation and increases in intracellular Ca2+ were required for its expression. 4-1BB was categorized as an early activation gene since the protein synthesis inhibitor, cycloheximide, blocked the induction of 4-1BB mRNA. A rat mAb, 53A2, was generated against recombinant soluble 4-1BB and was used to characterize this molecule. 4-1BB is a 30-kDa glycoprotein and appears to exist as both a monomer and a 55-kDa dimer on the cell surface of a T cell clone. The 4-1BB protein may be post-translationally modified since its predicted backbone is 25 kDa. FACS analysis indicated that 4-1BB was inducible and expressed on the cell surface of activated splenic T cells and thymocytes. Cross-linking of 4-1BB on anti-CD3-stimulated T cells with 53A2 resulted in a dramatic enhancement of T cell proliferation. This suggests that 4-1BB may function as an accessory signaling molecule during T cell activation.

Amino Acid Sequence↗
PubMed1993

Crystallization and preliminary X-ray crystallographic analysis of alpha-amylase from Bacillus subtilis.

Large crystals of alpha-amylase from Bacillus subtilis have been obtained at room temperature using polyethylene glycol 6000 as precipitant. They grow to typical dimensions of 0.25 mm x 0.3 mm x 2.0 mm in five days. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 85.46 A, b = 166.5 A and c = 332.7 A. The asymmetric unit seems to contain eight molecules of alpha-amylase, with crystal volume per protein mass (Vm) of 2.69 A3/Da and solvent content of 54.3% by volume. Despite a very long c-axis, the crystals diffracted to about 2.2 A Bragg spacing using the rotating anode X-rays and were resistant to damage by X-rays. Thus they are suitable for structure determination by X-ray methods at high resolution. X-ray diffraction data have been collected to 3.4 A Bragg spacing from a native crystal.

Bacillus subtilis↗
PubMed1993

Crystallization and preliminary X-ray crystallographic analysis of probable amylase/protease inhibitor-B from rice seeds.

Large crystals of probable amylase/protease inhibitor-B have been grown at room temperature from ammonium sulfate solution. The crystals grow within five days to dimensions of 0.6 mm x 0.6 mm x 0.6 mm. They diffract to at least 1.7 A upon exposure to synchrotron X-rays. The crystals belong to the space group P4(1)2(1)2 (or P4(3)2(1)2) with unit cell dimensions of a = 38.02 A and c = 98.98 A. The presence of one molecule per asymmetric unit gives the unit cell volume per protein mass (Vm) of 1.99 A3/Da and the solvent fraction of 38.2% by volume. X-ray data have been collected to 2.0 A Bragg spacing from native crystals.

Crystallization↗
PubMed1993

Crystallization and preliminary X-ray crystallographic analysis of arylesterase from Pseudomonas fluorescens.

Large crystals of arylesterase from Pseudomonas fluorescens have been grown at room temperature using ammonium sulfate as a precipitant. They grow to dimensions of 0.7 x 0.7 x 0.6 mm3 within a month. The crystals belong to the trigonal space group P3(1) (or P3(2)), with unit cell dimensions of a = 147.12 A and c = 131.08 A. The asymmetric unit seems to contain six molecules of dimeric arylesterase, with corresponding crystal volume per protein mass (VM) of 2.53 A3/Da and solvent fraction of 51.5% by volume. The crystals diffract to at least 2.2 A Bragg spacing when exposed to X-rays from a rotating-anode source. X-ray data have been collected to 2.9 A Bragg spacing from native crystals.

Carboxylic Ester Hydrolases↗