• BMB Reports
• /
• v.32 no.6
• /
• pp.547-553
• /
• 1999

Aminoacyl-tRNA synthetases are essential enzymes catalyzing the attachment of specific amino acids to cognate tRNAs. In the present work, the substrate analogue L-methionine hydroxamate was used to identify functional residues located in the active site of the E. coli methionyl-tRNA synthetase (MetRS). This compound inhibited bacteria, yeast, and human MetRS activities to a similar degree, suggesting a conserved active site structure and mechanism between MetRSs of different phylogenetic domains. Mutants of the E. coli MetRS resistant to methionine hydroxamate were also isolated. These mutants contained a substitution either at T10, Y15, or Y94. These residues are highly conserved among the different MetRSs and the mutants showed decreased aminoacylation activity, suggesting their functional and structural significances. The putative roles of these residues are discussed on a structural basis.

• Molecules and Cells
• /
• v.26 no.3
• /
• pp.228-235
• /
• 2008

Thiol-dependent redox systems are involved in regulation of diverse biological processes, such as response to stress, signal transduction, and protein folding. The thiol-based redox control is provided by mechanistically similar, but structurally distinct families of enzymes known as thiol oxidoreductases. Many such enzymes have been characterized, but identities and functions of the entire sets of thiol oxidoreductases in organisms are not known. Extreme sequence and structural divergence makes identification of these proteins difficult. Thiol oxidoreductases contain a redox-active cysteine residue, or its functional analog selenocysteine, in their active sites. Here, we describe computational methods for in silico prediction of thiol oxidoreductases in nucleotide and protein sequence databases and identification of their redox-active cysteines. We discuss different functional categories of cysteine residues, describe methods for discrimination between catalytic and noncatalytic and between redox and non-redox cysteine residues and highlight unique properties of the redox-active cysteines based on evolutionary conservation, secondary and three-dimensional structures, and sporadic replacement of cysteines with catalytically superior selenocysteine residues.

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.281-283
• /
• 2002

S-modulin in frog or its bovine homologue, recoverin, is a 26 kDa EF-hand $Ca^{2+}$-binding protein found in rod photoreceptors. The $Ca^{2+}$ -bound form of S-modulin binds to rhodopsin kinase (Rk) and inhibits its activity. Through this regulation, S-modulin is believed to modulate the light-sensitivity of a rod. In the present study, we tried to identify the interaction site of the $Ca^{2+}$ -bound form of S-modulin to Rk. First, we mapped roughly the interaction regions by using partial peptides of S-modulin. The result suggested that a specific region near the amino terminus is the interaction site of S- modulin. We then identified the essential amino acid residues in this region by using S-modulin mutant proteins: four amino acid residues were suggested to interact with Rk. These residues are located in a small closed pocket in the $Ca^{2+}$-free, inactive form of S-modulin, but exposed to the surface of the molecules in the $Ca^{2+}$ -bound, active form of S-modulin. Two additional amino acid residues were found to be crucial for the $Ca^{2+}$ -dependent conformational changes of S-modulin. The present study firstly identified the functional site of S-modulin, a member of a neuronal calcium sensor protein family.in family..

• BMB Reports
• /
• v.31 no.3
• /
• pp.258-263
• /
• 1998

Acetolactate synthase (ALS) is the common enzyme in the biosynthetic pathways leading to leucine, valine, and isoleucine. Tobacco ALS was expressed in E. coli and purified to homogeneity. The recombinant tobacco ALS was inactivated by thiol-specific reagents, N-ethylmaleimide (NEM) and 5,5'-dithio-bis-(2-nitrobenzoic acid) (DTNB). Inactivation of the ALS by NEM followed pseudo-first order kinetics and was first order with respect to the modifier. The substrate pyruvate protected the enzyme against the inactivation by NEM and DTNB. Extrapolation to complete inactivation of the enzyme by DTNB showed modification of approximately 2 out of 4 total cysteinyl residues (or 2 cysteinyl and 1 cysteinyl residues), with approximately 1 residue protected by pyruvate. The tobacco ALS was also inactivated by the tryptophanspecific reagent, N-bromosuccinimide (NBS), and was similarly protected by pyruvate. The kinetics of the inactivation was first-order with respect to NBS. The present data suggest that cysteinyl and tryptophanyl residues play a key role in the catalytic function of the enzyme.

• Journal of Microbiology
• /
• v.44 no.1
• /
• pp.50-53
• /
• 2006

Cys-29 and Cys-251 of Streptomyces albus valine dehydrogenase(ValDH) were highly conserved in the corresponding region of $NAD(P)^+$-dependent amino acid dehydroganase sequences. To ascertain the functional role of these cysteine residues in S. albus ValDH, site-directed mutagenesis was performed to change each of the two residues to serine. Kinetic analyses of the enzymes mutated at Cys-29 and Cys-251 revealed that these residues are involved in catalysis. We also constructed mutant ValDH by substituting valine for leucine at 305 by site-directed mutagenesis. This residue was chosen, because it has been proposed to be important for substrate discrimination by phenylalanine dehydrogenase (PheDH) and leucine dehydrogenase (LeuDH). Kinetic analysis of the V305L mutant enzyme revealed that it is involved in the substrate binding site. However it displayed less activity than the wild type enzyme toward all aliphatic and aromatic amino acids tested.

• Animal Bioscience
• /
• v.34 no.2
• /
• pp.265-275
• /
• 2021

Objective: The study developed mushroom stalk residues as feed additives in the broiler diet for improving the growth performance and immunity of broilers as well as to increase the value of mushroom stalk residues. Methods: In total, 300 ROSS 308 broilers were randomly allocated into fifteen pens with five dietary treatments: i) control, basal diet; ii) CMWM, supplemented with 1% Cordyceps militaris waster medium (CM); iii) CMPE, supplemented with 0.5% CM+0.5% Pleurotus eryngii stalk residue (PE); iv) CMPS, supplemented with 0.5% CM+0.5% Pleurotus sajorcaju stalk residue (PS); v) CMFV, supplemented with 0.5% CM+0.5% Fammulina velutipes stalk residue (FV). Results: The chemical analysis results showed that CM extracts, PE extracts, PS extracts, and FV extracts contain functional components such as polysaccharides and phenols and have both 2, 2-diphenyl-1-picryl-hydrazyl-hydrate scavenging and Ferrous scavenging capacities. The group CMWM saw increased body weight gain and feed conversion rate and the promotion of jejunum villus growth, but there is no significant difference in the intestinal bacteria phase. Antioxidant genes in the nuclear factor (erythroid-derived 2)-like 2 (Nrf2)- antioxidant responsive element pathway among the groups are significantly higher than that of the control group, especially in group CMWM. Conclusion: The mushroom stalk residues have antioxidant functional components, can improve the intestinal health and body weight gain of chickens, and can activate the antioxidant pathway of Nrf2 to increase the heme oxygenase-1 expression. The treatment with 1% CM was the most promising as a feed additive.

• Journal of Plant Biotechnology
• /
• v.1 no.1
• /
• pp.13-19
• /
• 1999

The visco-elastic properties of gluten are major determinants of the processing properties of doughs. These visco-elastic properties are strongly influenced by the ratio of monomeric and polymeric proteins and the size distribution of the polymeric proteins, which make up the gluten fraction of the dough. Recent studies have revealed that other features, such as the number of the cysteine residues of the HMW-GS, also play an important role in determining the functional characteristics. To modify the processing properties at molecular level, the relationship between the structure of molecules and dough properties has to be understood. In order to explore the relationships between individual proteins and dough properties, we have developed procedures for incorporating bacterially expressed proteins into doughs, and measuring their functional properties in small-scale equipment. A major problem in investigating the structure/function relationships of individual seed storage proteins is to obtain sufficient amounts of pure polypeptides from the complex families of proteins expressed in the endosperm. Therefore, we have established a simplified model system in which we produce specific protein genes through bacterial expression and test their functional properties in smallscale apparatus after incorporation into base flour. An S poor protein gene has been chosen as a template gene. This template gene has been modified using standard recombinant DNA techniques in order to test the effects of varying the number and position of cysteine residues, and the size of the protein. Doughs have been mixed in small scale apparatus and characterized with respect to their polymeric composition and their functional properties, including dough mixing, extensibility and small scale bating. We conclude that dough characteristics can be manipulated in a predictable manner by altering the cysteine residues and the size of high molecular weight glutenins.

• BMB Reports
• /
• v.32 no.2
• /
• pp.181-188
• /
• 1999

4-Aminobutyrate aminotransferase plays an essential role in the 4-aminobutyric acid shunt, converting 4-aminobutyrate to succinic semialdehyde. Recombinant 4-aminobutyrate aminotransferases were overexpressed as their catalytically active forms in E. coli by coproduction with thioredoxin and their solubilities were also dramatically increased. In order to study the structural and functional aspects of the C-terminal domain of brain 4-aminobutyrate aminotransferase, we have constructed a C-terminal mutant of pig brain 4-aminobutyrate aminotransferase and analyzed the functional and structural roles of C-terminal amino acids residues on the enzyme. The deletion of five amino-acid residues from C-terminus did not interfere with the kinetic parameters and functional properties of the enzyme. Also, the deletion did not affect the dimeric structure of the protein aligned along the subunit interface at neutral pH. However, the deletion of the C-terminal region of the protein changed the stability of its dimeric structure at acidic pH. The dissociation of the enzyme acidic, facilitated by the deletion of five amino acids from C-terminus, abolished the catalytic activity.

• The Korean Journal of Physiology and Pharmacology
• /
• v.22 no.1
• /
• pp.91-99
• /
• 2018

Protein phosphatase 1 (PP1) is involved in various signal transduction mechanisms as an extensive regulator. The PP1 catalytic subunit (PP1c) recognizes and binds to PP1-binding consensus residues (FxxR/KxR/K) in NBCe1-B. Consequently, we focused on identifying the function of the PP1-binding consensus residue, $^{922}FMDRLK^{927}$, in NBCe1-B. Using site-directed mutagenesis and co-immunoprecipitation assays, we revealed that in cases where the residues were substituted (F922A, R925A, and K927A) or deleted (deletion of amino acids 922-927), NBCe1-B mutants inhibited PP1 binding to NBCe1-B. Additionally, by recording the intracellular pH, we found that PP1-binding consensus residues in NBCe1-B were not only critical for NBCe1-B activity, but also relevant to its surface expression level. Therefore, we reported that NBCe1-B, as a substrate of PP1, contains these residues in the C-terminal region and that the direct interaction between NBCe1-B and PP1 is functionally critical in controlling the regulation of the ${HCO_3}^-$ transport. These results suggested that like IRBIT, PP1 was another novel regulator of ${HCO_3}^-$ secretion in several types of epithelia.

• Journal of Environmental Health Sciences
• /
• v.30 no.4
• /
• pp.308-313
• /
• 2004

Native and acetylated soybean protein with acetylation percentage of $25\%$ were incubated with glucose to induce Maillard reaction. Acetylation of ${\varepsilon}$-amino group of lysine residues changed the conformation of soybean protein. The direct uv spectrum of native and acetylated soybean protein showed conformational changes with accessibility of tyrosine and tryptophan residues increased. Acetylation suppressed Maillard reaction between soybean protein and glucose. Acetylated soybean protein showed improved water sorption, fat binding, foam formation, and emulsion activity of the protein, but depressed brown pigment development and trypsin digestion. Thus aceylation prevented deterioration of certain functional characteristics that occurred during storage, besides causing functional characteristics to be improved on its own.