Dae Sil Lee

Bio: Dae Sil Lee is an academic researcher from Korea Research Institute of Bioscience and Biotechnology. The author has contributed to research in topics: DNA polymerase & Xylose isomerase. The author has an hindex of 11, co-authored 24 publications receiving 951 citations.

Crystal structure of Thermus aquaticus DNA polymerase

Abstract: THE DNA polymerase from Thermus aquaticus (Taq polymerase), famous for its use in the polymerase chain reaction, is homologous to Eschenchia coli DNA polymerase I (pol I) (ref. 1). Like pol I, Taq polymerase has a domain at its amino terminus (residues 1-290) that has 5' nuclease activity and a domain at its carboxy terminus that catalyses the polymerase reaction. Unlike pol I, the intervening domain in Taq polymerase has lost the editing 3′-5′ exonuclease activity. Although the structure of the Klenow fragment of pol I has been known for ten years2, that of the intact pol I has proved more elusive. The structure of Taq polymerase determined here at 2.4 A resolution shows that the structures of the polymerase domains of the thermostable enzyme and of the Klenow fragment are nearly identical, whereas the catalytically critical carboxylate residues that bind two metal ions are missing from the remnants of the 3′-5′-exonuclease active site of Taq polymerase. The first view of the 5′ nuclease domain, responsible for excising the Okazaki RNA in lagging-strand DNA replication, shows a cluster of conserved divalent metal-ion-binding carboxylates at the bottom of a cleft. The location of this 5′-nuclease active site some 70 A from the polymerase active site in this crystal form highlights the unanswered question of how this domain works in concert with the polymerase domain to produce a duplex DNA product that contains only a nick.

Antibacterial activity of [10]-gingerol and [12]-gingerol isolated from ginger rhizome against periodontal bacteria.

Abstract: Ginger (Zingiber officinale Roscoe) has been used widely as a food spice and an herbal medicine. In particular, its gingerol-related components have been reported to possess antimicrobial and antifungal properties, as well as several pharmaceutical properties. However, the effective ginger constituents that inhibit the growth of oral bacteria associated with periodontitis in the human oral cavity have not been elucidated. This study revealed that the ethanol and n-hexane extracts of ginger exhibited antibacterial activities against three anaerobic Gram-negative bacteria, Porphyromonas gingivalis ATCC 53978, Porphyromonas endodontalis ATCC 35406 and Prevotella intermedia ATCC 25611, causing periodontal diseases. Thereafter, five ginger constituents were isolated by a preparative high-performance liquid chromatographic method from the active silica-gel column chromatography fractions, elucidated their structures by nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry and their antibacterial activity evaluated. In conclusion, two highly alkylated gingerols, [10]-gingerol and [12]-gingerol effectively inhibited the growth of these oral pathogens at a minimum inhibitory concentration (MIC) range of 6-30 microg/mL. These ginger compounds also killed the oral pathogens at a minimum bactericidal concentration (MBC) range of 4-20 microg/mL, but not the other ginger compounds 5-acetoxy-[6]-gingerol, 3,5-diacetoxy-[6]-gingerdiol and galanolactone.

Application of rpoB and Zinc Protease Gene for Use in Molecular Discrimination of Fusobacterium nucleatum Subspecies

Abstract: Fusobacterium nucleatum is classified into five subspecies that inhabit the human oral cavity (F. nucleatum subsp. nucleatum, F. nucleatum subsp. polymorphum, F. nucleatum subsp. fusiforme, F. nucleatum subsp. vincentii, and F. nucleatum subsp. animalis) based on several phenotypic characteristics and DNA-DNA hybridization patterns. However, the methods for detecting or discriminating the clinical isolates of F. nucleatum at the subspecies levels are laborious, expensive, and time-consuming. Therefore, in this study, the nucleotide sequences of the RNA polymerase β-subunit gene (rpoB) and zinc protease gene were analyzed to discriminate the subspecies of F. nucleatum. The partial sequences of rpoB (approximately 2,419 bp), the zinc protease gene (878 bp), and 16S rRNA genes (approximately 1,500 bp) of the type strains of five subspecies, 28 clinical isolates of F. nucleatum, and 10 strains of F. periodonticum (as a control group) were determined and analyzed. The phylogenetic data showed that the rpoB and zinc protease gene sequences clearly delineated the subspecies of F. nucleatum and provided higher resolution than the 16S rRNA gene sequences in this respect. According to the phylogenetic analysis of rpoB and the zinc protease gene, F. nucleatum subsp. vincentii and F. nucleatum subsp. fusiforme might be classified into a single subspecies. Five clinical isolates could be delineated as a new subspecies of F. nucleatum. The results suggest that rpoB and the zinc protease gene are efficient targets for the discrimination and taxonomic analysis of the subspecies of F. nucleatum.

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Abstract: Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282--283, Bioinformatics, 18, 77--82) describing an ultrafast protein sequence clustering program called cd-hit. This program can efficiently cluster a huge protein database with millions of sequences. However, the applications of the underlying algorithm are not limited to only protein sequences clustering, here we present several new programs using the same algorithm including cd-hit-2d, cd-hit-est and cd-hit-est-2d. Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets. All these programs can handle huge datasets with millions of sequences and can be hundreds of times faster than methods based on the popular sequence comparison and database search tools, such as BLAST. Availability: http://cd-hit.org Contact: [email protected]

Recent Advances in Zinc Enzymology

Abstract: Zinc enzymology is, compared to some other current areas of metallobiochemistry, a maturing field, but in addition to further developments of structure-function relationships it has also provided a number of surprising new results and ideas in the last few years. In fact, the number of studies makes it impossible to provide a comprehensive review of the recent literature on zinc enzymology here, and the authors therefore focus on those zinc enzymes for which structure-function relationships are possible on the basis of structural and biochemical data. This means that, with a few exceptions, only zinc enzymes for which NMR or crystal structures are available are included here. Another seemingly simple, yet experimentally sometimes complex issue concerns the choice of which metalloenzyme is a zinc enzyme. Since there is in principle no difference in chemical catalysis by low-affinity compared to high-affinity metal sites, some of these enzymes are also included in this article, especially if they are or have been discussed as zinc enzymes, or are active with zinc. 552 refs.

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution

Abstract: DNA polymerases change their specificity for nucleotide substrates with each catalytic cycle, while achieving error frequencies in the range of 10−5to 10−6. Here we present a 2.2 A crystal structure of the replicative DNA polymerase from bacteriophage T7 complexed with a primer–template and a nucleoside triphosphate in the polymerase active site. The structure illustrates how nucleotides are selected in a template-directed manner, and provides a structural basis for a metal-assisted mechanism of phosphoryl transfer by a large group of related polymerases.

DNA replication fidelity.

Abstract: DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases. Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity. These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments. We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment.