• Bulletin of the Korean Chemical Society
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• v.21 no.12
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• pp.1217-1221
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• 2000

L-alanine dehydrogenase from Bacillus subtilis exhibits allosteric kinetic properties in the presence of $ZN^{2+}$. $ZN^{2+}$ induces the binding of substrate (L-alanine) to be cooperative at pH 8.0. The effect of pH variation between pH 7.0 and pH 10.0 on the inhibition by $ZN^{2+}$ correlates with the pH effect on the $K_m$ values for L-alanine within these pH range indicating that $ZN^{2+}$ and substrate compete for the same site. No such cooperativity is induced by $ZN^{2+}$ when the reaction is carried out at pH 10. At this higher pH, $ZN^{2+}$ binds with the enzyme with lower affinity and noncompetitive with respect to L-alanine. Inhibition of L-alanine dehydrogenase by $ZN^{2+}$ depends on the ionic strength. Increase in KCI concentration reduced the inhibition, but allosteric property in $ZN^{2+}$ binding is conserved. A model for the regulatory mechanism of L-alanine dehydrogenase as a noncooperative substrate-cooperative cofactor allosteric enzyme, which is compatible in both concerted and the sequential allosteric mechanism, is proposed.

• Journal of the Korean Chemical Society
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• v.68 no.1
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• pp.32-39
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• 2024

Glycerol dehydrogenase (GlyDH) plays a crucial role in the glycerol metabolism pathway by catalyzing the oxidation of glycerol to dihydroxyacetone (DHA). Previous studies of GlyDH have predominantly focused on unraveling the structural features of the active site and its binding interactions with ligand. However, the structural details of GlyDH in complex with both NAD⁺ and the substrate bound have remained elusive. In this study, we present the crystal structures of Klebsiella pneumoniae GlyDH (KpGlyDH) in the absence and presence of NAD⁺ at a resolution of 2.1 Å. Notably, both structures reveal the binding of the substrate, ethylene glycol, to the zinc ion. Interestingly, a significant change in the coordination number of the zinc ion is observed, with three in the absence of NAD⁺ and four in its presence. These findings shed light on the structural aspects of GlyDH and its interactions with NAD⁺ and the substrate.

• 한국생물공학회:학술대회논문집
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• 2003.10a
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• pp.716-716
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• 2003

• Journal of Integrative Natural Science
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• v.6 no.4
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• pp.234-243
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• 2013

N-terminal kinase-like (NTKL) protein was initially identified as a protein binding to protein kinase B (PKB, also known as Akt). Though NTKL-BP1 (NTKL-binding protein 1) has been identified as an NTKL binding protein, its functions related to binding have not yet been elucidated. Here, a new alternative spliced variant of NTKL and its association with integrin ${\beta}1$ is described, in addition to the kinase activity of NTKL and its substrate candidates. Although the phosphorylation of the candidates must be further confirmed using other experimental methods, the observation that NTKL can phosphorylate ROCK1, DYRK3, and MST1 indicates that NTKL may act as a signaling protein to regulate actin assembly, cell migration, cell growth, and to facilitate differentiation and development in an integrin-associated manner.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.144-148
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• 2018

Catalytic enzyme Pyrazinamidase (PncA) from Mycobacterium tuberculosis can hydrolyze substrate pyrazinamide (PZA) to pyrazoic acid (POA) as active form of compound. Using NMR spectroscopy, pH-dependent catalytic properties were monitored including metal binding mode during converting PZA to POA. There seems to be a conformational change through zinc binding in active site from the perturbation of peak intensities in series of 2D HSQC spectra the conformation changes through zinc binding.

• BMB Reports
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• v.29 no.6
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• pp.519-524
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• 1996

Peptidylprolyl cis-trans isomerase (PPlase) catalyzes the cis-trans isomerization of prolyl peptide and facilitates the folding of cellular proteins and peptides. PPlase consists of two distinct immunophilins, each specifically binding to the immunosupressive drug cyclosporin A (CsA) or FK506, respectively. A PPlase was isolated and partially purified from porcine spleen. The molecular weight of porcine spleen PPlase was determined to be ~14,000 on the basis of SDS-PAGE. The purified enzyme was strongly inhibited by FK506, but not by CsA. The inhibition constant and the true concentration of enzyme preparations were determined by active site titration using the tight binding inhibitor FK506: $K_{i}=18.7$ nM and $E_{t}=172$ nM. The equilibrium ratio of conformer. [cis]/[trans], of prolyl peptide substrates (N-Suc-Ala-Xaa-Pro-Phe-p-NA) in anhydrous trifluoroethanol/LiCl solvent system varied from 0.24 to 0.85 depending on the nature of Xaa. Overall. in this solvent-salt system, the populations of the cis conformer of substrates in equilibrium are higher than in an aqueous solution so that the substantial error caused by high background absorption can be reduced. The reactivities of porcine spleen PPlase are shown to be highly sensitive to changes in the structure of substrates. Thus, $k_{cat}/K_m$ value for the most reactive substrate (Xaa Leu) is $4.007+10^{6}M^{1}s^{1}$ and, is 2,636 fold higher than that for the least reactive peptide substrate tested, Xaa=Glu.

• Parasites, Hosts and Diseases
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• v.53 no.3
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• pp.335-339
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• 2015

Cryptosporidium andersoni ATP-binding cassette (CaABC) is an important membrane protein involved in substrate transport across the membrane. In this research, the nucleotide binding domain (NBD) of CaABC gene was amplified by PCR, and the eukaryotic expression vector of pEGFP-C1-CaNBD was reconstructed. Then, the recombinant plasmid of pEGFP-C1-CaNBD was transformed into the mouse intestinal epithelial cells (IECs) to study the iron transportation function of CaABC. The results indicated that NBD region of CaABC gene can significantly elevate the transport efficiency of $Ca^{2+}$, $Mg^{2+}$, $K^+$, and $HCO_3{^-}$ in IECs (P<0.05). The significance of this study is to find the ATPase inhibitors for NBD region of CaABC gene and to inhibit ATP binding and nutrient transport of CaABC transporter. Thus, C. andersoni will be killed by inhibition of nutrient uptake. This will open up a new way for treatment of cryptosporidiosis.

• Reproductive and Developmental Biology
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• v.30 no.3
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• pp.169-174
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• 2006

To search of a new porcine pheromonal odorants, the comparative molecular similarity indices analysis(CoMSIA) between porcine odorant binding protein(pOBP) as receptor and ligands of green odorants 2-(Cyclohexyloxy)tetrahydrofurane derivatives as substrate molecule were conducted and disscused quantitatively. In the optimized CoMSIA model(I-AI) with chirality($I:\;C_{1'}(R),\;C_2(S)$) in substrate molecules and atom based fit alignment(AE) of the odorants the statistical PLS results showed the best predictability of the binding affinities based on the LOO cross-validated value ${r^2}_{cv.}\;(q^2=0.856)$ and non cross-validated conventional coefficient(${r^2}_{ncv.}=0.964)$). The structural distinctions of the highest active molecules were able to understand from the interaction between pOBP and green odorants in the contour maps with CoMSIA model.

• BMB Reports
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• v.34 no.3
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• pp.194-200
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• 2001

Secreted arginase from Evernia prunastri thallus has been purified 616-fold from the incubation medium. Purified arginase was resolved as only one peak in a capillary electrophoresis with a pI value of 5.35. The protein contained high amounts of acidic amino acids, such as Asx and Glx, and a relatively high quantity of Ser and Gly. The molecular mass of native, purified arginase was estimated as about 26 kDa by SE-HPLC. Substrate saturated kinetic showed a typical Michaelis-Menten relationship with a K_m value of 3.3 mM L-arginine. Atranorin behaved as a mixed activator of the enzyme (apparent $K_m$ = 0.96 mM); whereas evernic and usnic acid were revealed as non competitive inhibitors (apparent $K_m$ values were 3.16 mM and 3.05 mM, respectively). Kinetics of atranorin binding indicated that saturation was reached from 0.18 ${\mu}mol$ of the total atranorin and the occurrence of multiple sites for the ligand. This agrees with a possible aggregation of several enzyme subunits during the interaction process. A value of binding sites of about 12 was obtained. The binding of evernic acid was saturated from 23 nmol of total phenol. The number of binding sites was about 5. The loss of the binding ability of evernic acid could be interpreted as a single negative cooperatively. Usnic acid behaves in a similar way to evernic acid, although the binding saturation occurs at $0.14\;{\mu}moles$ of the ligand. This binding appears to be unspecific, and has 28 usnic acid binding sites to the protein.

• Molecules and Cells
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• v.39 no.3
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• pp.211-216
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• 2016

CYP107W1 from Streptomyces avermitilis is a cytochrome P450 enzyme involved in the biosynthesis of macrolide oligomycin A. A previous study reported that CYP107W1 regioselectively hydroxylated C12 of oligomycin C to produce oligomycin A, and the crystal structure of ligand free CYP107W1 was determined. Here, we analyzed the structural properties of the CYP107W1-oligomycin A complex and characterized the functional role of the Trp178 residue in CYP107W1. The crystal structure of the CYP107W1 complex with oligomycin A was determined at a resolution of $2.6{\AA}$. Oligomycin A is bound in the substrate access channel on the upper side of the prosthetic heme mainly by hydrophobic interactions. In particular, the Trp178 residue in the active site intercalates into the large macrolide ring, thereby guiding the substrate into the correct binding orientation for a productive P450 reaction. A Trp178 to Gly mutation resulted in the distortion of binding titration spectra with oligomycin A, whereas binding spectra with azoles were not affected. The Gly178 mutant's catalytic turnover number for the 12-hydroxylation reaction of oligomycin C was highly reduced. These results indicate that Trp178, located in the open pocket of the active site, may be a critical residue for the productive binding conformation of large macrolide substrates.