• BMB Reports
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• 제32권4호
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• pp.414-418
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• 1999

A novel gene for malonyl-CoA decarboxylase was discovered in the mat operon, which encodes a set of genes involved in the malonate metabolism of Rhizobium trifolii (An and Kim, 1998). The subunit mass determined by SDS-PAGE was 53 kDa, which correspond to the deduced mass from the sequence data. The molecular mass of the native enzyme determined by field flow fractionation was 208 kDa, indicating that R. trifolii malonyl-CoA decarboxylase is homotetrameric. R. trifolii malonyl-CoA decarboxylase converted malonyl-CoA to acetyl-CoA with a specific activity of 100 unit/mg protein. Methylmalonyl-CoA was decarboxylated with a specific activity of 0.1 unit/mg protein. p-Chloromercuribenzoate inhibited this enzyme activity, suggesting that thiol group(s) is(are) essential for this enzyme catalysis. Database analysis showed that malonyl-CoA decarboxylase from R. trifolii shared 32.7% and 28.1% identity in amino acid sequence with those from goose and human, respectively, and it would be located in the cytoplasm. However, there is no sequence homology between this enzyme and that from Saccharopolyspora erythreus, suggesting that malonyl-CoA decarboxylases from human, goose, and R. trifolii are in the same class, whereas that from S. erythreus is in a different class or even a different enzyme, methylmalonyl-CoA decarboxylase. According to the homology analysis, Cys-214 among three cysteine residues in the enzyme was found in the homologous region, suggesting that the cysteine was located at or near the active site and plays a critical role in catalysis.

• Archives of Pharmacal Research
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• 제25권1호
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• pp.11-24
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• 2002

The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

• Bulletin of the Korean Chemical Society
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• 제24권1호
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• pp.65-69
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• 2003

The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthiocholine(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. [Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477- 10482] The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site.

• Bulletin of the Korean Chemical Society
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• 제31권12호
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• pp.3543-3548
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• 2010

A kinetic study on nucleophilic displacement reactions of 2-pyridyl X-substituted benzoates 1a-e with potassium ethoxide (EtOK) in anhydrous ethanol is reported. Plots of pseudo-first-order rate constants ($k_{obsd}$) vs. $[EtOK]_o$ exhibit upward curvature. The $k_{obsd}$ value at a fixed $[EtOK]_o$ decreases steeply upon addition of 18-crown-6-ether (18C6) to the reaction mixture up to [18C6]/$[EtOK]_o$ = 1 and then remains nearly constant thereafter. In contrast, $k_{obsd}$ increases sharply upon addition of LiSCN or KSCN. Dissection of $k_{obsd}$ into $k_{EtO^-}$ and $k_{EtOM}$ has revealed that ion-paired EtOK is more reactive than dissociated $EtO^-$, indicating that $K^+$ ion acts as a Lewis acid catalyst. Hammett plots for the reactions of 1a-e with dissociated $EtO^-$ and ion-paired EtOK result in excellent linear correlation with $\rho$ values of 3.01 and 2.67, respectively. The $k_{EtOK}/k_{EtO^-}$ ratio increases as the substituent X in the benzoyl moiety becomes a stronger electron-donating group. $K^+$ ion has been concluded to catalyze the current reaction by stabilizing the transition state through formation of a 6-membered cyclic complex.

• 대한화학회지
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• 제41권4호
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• pp.205-209
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• 1997

신경수초 염기성 단백질(MBP)에 대한 탈인산화의 자리 특이성에 대한 연구를 시험관에서 수행하였다. MBP에서 인산화된 자리를 알아내기 위해서 MBP를 단백질 키나제 C로 인산화 시키고 단백질 탈인산화 효소 PP2A로 탈인산화시켰다. 인산화된 MBP는 트립신으로 잘라내어서 역상 HPLC 크로마토그래피로 펩티드 조각들을 분리하였다. 각 조각들을 섬광 계측한 후 일부 펩티드의 아미노산 서열을 결정하였다. 일곱 개의 방사능을 보이는 펩티드 조각이 검출되었으며 두번째 조각($P_2$)의 $Ser^{55}$에 해당하는 아미노산이 인산화 반응에 가장 큰 민감도를 보였다. 그러나 탈인산화는 다섯번째 고작($P_5$)의 인산이 가장 잘 방출되는 것으로 나타났다. 이 결과는 MBP가 단백질 탈인산화 반응에 적절한 기질임을 보여주고 있다.

• Bulletin of the Korean Chemical Society
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• 제33권8호
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• pp.2724-2730
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• 2012

A new heterogeneous acidic catalyst was successfully prepared by impregnation of silica (Aerosil 300) by an acidic ionic liquid, named 1-(4-sulfonic acid)butylpyridinium hydrogen sulfate [$PYC_4SO_3H$][$HSO_4$], and characterized using FT-IR spectroscopy, the $N_2$ adsorption/desorption analysis (BET), thermal analysis (TG/DTG), and X-ray diffraction (XRD) techniques. The amount of loaded acidic ionic liquid on Aerosil 300 support was determined by acid-base titration. This new solid acidic supported heterogeneous catalyst exhibits excellent activity in the synthesis of 2-aryl-2,3-dihydroquinazolin-4(1H)-ones by cyclocondensation reaction of 2-aminobenzamide with aromatic aldehydes under solvent-free conditions and the desired products were obtained in very short reaction times with high yields. This catalyst has the advantages of an easy catalyst separation from the reaction medium and lower problems of corrosion. Recycling of the catalyst and avoidance of using harmful organic solvent are other advantages of this simple procedure.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVI)
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• pp.402-406
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• 2005

Lipomyces starkeyi produces a novel glucanhydrolase containing endo-dextranase and ${\alpha}-amylase$ activities. A cDNA from L. starkeyi encoding a dextranase was isolated and characterized. The 2,052 kb cDNA fragment (lsd1) carrying dextranase gene showed one open reading frame (ORF) composed of 1,824 bp flanked by a 41 bp 5'-UTR and a 184 bp 3'-UTR including a poly(A) tail of 27 bp. The ORF encodes for a 608 amino acid with a predicted molecular mass of 67.6 kDa. There was 77% deduced amino acid sequence identity between the LSD1 dextranase and the dextranase from Penicillium minioluteum. The primary structure of the dextranase from L. starkeyi has distant similarity with enzymes belonging to glycosyl hydrolase family 49. The lsd1 protein was expressed in the Saccharmyces cerevisiae under control of GAL1 promoter and active dextranase was produced.

• BMB Reports
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• 제28권3호
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• pp.204-209
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• 1995

The pH dependence of kinetic parameters in the amination direction of the aspartase from Hafnia alvei has been determined. The V/K for fumarate is bell shaped with pK values of 6.4 and 8.7. The maximum velocity for fumarate is also bell shaped with pK values of 7.2 and 9.1. The pH dependence of 1/K, for potassium (competitive inhibitor of ammonia) decreases at low pH with pK 7.6. Together with data [Yoon and Cook (1994) Korean J. Biochem. 27, 1-5] on the deamination direction of the aspartase, these results are consistent with two enzyme groups which are necessary for catalysis. An enzymatic group that must be deprotonated has been identified. Another enzyme group must be protonated for substrate binding. Both the general base and general acid group are in a protonation state opposite that in which they started when aspartate was bound. A proton is abstracted from C-3 of the monoanionic form of L-aspartate by an enzyme general base with, a pK of 6.3~6.6 in the absence and presence of $Mg^{2+}$ Ammonia is then expelled with the assistance of a general acid group giving $NH_{4+}$ as the product.

• Journal of Microbiology and Biotechnology
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• 제10권4호
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• pp.559-563
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• 2000

A dextransucrase gene (dsrB742) that expresses a dextransucrase to synthesize mostly ${\alpha}-1{\rightarrow}6$ linked dextran with a low amount (3-5%) of ${\alpha}-1{\rightarrow}3$ branching was cloned and sequenced from Leuconostoc mesenteroides B-742CB. The 6.1-kb PstI fragments were ligated with pGEM-3Zf(-) and transformed into E. coli $DH5{\alpha}$. The recombinant clone (pDSRB742) synthesized dextran on an agar plate containing 2% (w/v) sucrose. The dextran synthesized was hydrolyzed with Penicillium endo-dextranase. The hydrolyzate was composed of glucose, isomaltose, isomaltotriose, and branced pentasaccharide. The nucleotide sequence of dsrB742 showed one open reading frame (ORF) composed of 4,524 bp encoding dextrasnsucrase. The deduced amino acid sequence revealed a calculated molecular mass of 168.6 kDa. It also showed an activity band of 184 kKa on a non-denaturing SDS-PAGE (10%). The amino acid sequence of DSRB742 exhibited a 50% similarity with DSRA from L. mesenteroides B-1299, a 70% similarity with DSRS from L. mesenteroides B-512 (F, FMCM) and a 45-56% similarity with Streptococcal GTFs.

• Bulletin of the Korean Chemical Society
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• 제32권2호
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• pp.656-658
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• 2011

A green and efficient method for the synthesis of 3,4-dihydropyrimidin-2(1H)-ones and -thiones through one-pot three-component reaction of ethyl acetoacetate, an aryl aldehyde, and urea or thiourea in acetonitrile using silica gel-supported polyphosphoric acid (PPA-$SiO_2$) as catalyst is described. Compared to the classical Biginelli reaction conditions, the present methodology offers several advantages such as high yields, relatively short reaction times, mild reaction condition and a recyclable catalyst with a very easy work up.