QM/MM Study of the Reaction Mechanism of the Carboxyl Transferase Domain of Pyruvate Carboxylase from Staphylococcus aureus

Biochemistry ◽  
2014 ◽  
Vol 53 (27) ◽  
pp. 4455-4466 ◽  
Author(s):  
Xiang Sheng ◽  
Yongjun Liu
Keyword(s):  
Staphylococcus Aureus ◽  
Reaction Mechanism ◽  
Pyruvate Carboxylase

Kinetic and Thermodynamic Analysis of Acetyl-CoA Activation of Staphylococcus aureus Pyruvate Carboxylase

Biochemistry ◽  
2017 ◽  
Vol 56 (27) ◽  
pp. 3492-3506 ◽  
Author(s):  
Lauren E. Westerhold ◽  
Lance C. Bridges ◽  
Saame Raza Shaikh ◽  
Tonya N. Zeczycki
Keyword(s):  
Staphylococcus Aureus ◽  
Thermodynamic Analysis ◽  
Pyruvate Carboxylase ◽  
Acetyl Coa ◽  
Kinetic And Thermodynamic Analysis

scholarly journals Structural and functional studies of SAV0551 from Staphylococcus aureus as a chaperone and glyoxalase III

2017 ◽  
Vol 37 (6) ◽  
Author(s):  
Hyo Jung Kim ◽  
Ki-Young Lee ◽  
Ae-Ran Kwon ◽  
Bong-Jin Lee
Keyword(s):  
Staphylococcus Aureus ◽  
Reaction Mechanism ◽  
Quaternary Structure ◽  
Hypothetical Protein ◽  
Catalytic Triad ◽  
Common Theme ◽  
Functional Studies ◽  
The Common ◽  
Cellular Stresses ◽  
Glyoxalase Iii

The DJ-1/ThiJ/PfpI superfamily of proteins is highly conserved across all biological kingdoms showing divergent multifunctions, such as chaperone, catalase, protease, and kinase. The common theme of these functions is responding to and managing various cellular stresses. DJ-1/ThiJ/PfpI superfamily members are classified into three subfamilies according to their quaternary structure (DJ-1-, YhbO-, and Hsp-types). The Hsp-type subfamily includes Hsp31, a chaperone and glyoxalase III. SAV0551, an Hsp-type subfamily member from Staphylococcus aureus, is a hypothetical protein that is predicted as Hsp31. Thus, to reveal the function and reaction mechanism of SAV0551, the crystal structure of SAV0551 was determined. The overall folds in SAV0551 are similar to other members of the Hsp-type subfamily. We have shown that SAV0551 functions as a chaperone and that the surface structure is crucial for holding unfolded substrates. As many DJ-1/ThiJ/PfpI superfamily proteins have been characterized as glyoxalase III, our study also demonstrates SAV0551 as a glyoxalase III that is independent of any cofactors. The reaction mechanism was evaluated via a glyoxylate-bound structure that mimics the hemithioacetal reaction intermediate. We have confirmed that the components required for reaction are present in the structure, including a catalytic triad for a catalytic action, His78 as a base, and a water molecule for hydrolysis. Our functional studies based on the crystal structures of native and glyoxylate-bound SAV0551 will provide a better understanding of the reaction mechanism of a chaperone and glyoxalase III.

scholarly journals Bicarbonate-dependent ATP cleavage catalysed by pyruvate carboxylase in the absence of pyruvate

1992 ◽  
Vol 287 (3) ◽  
pp. 1011-1017 ◽  
Author(s):  
P V Attwood ◽  
B D L A Graneri
Keyword(s):  
Reaction Mechanism ◽  
Atpase Activity ◽  
Active Site ◽  
Pyruvate Carboxylase ◽  
Substrate Inhibition ◽  
Cleavage Reaction ◽  
Acetyl Coa ◽  
Enzyme Preparations ◽  
Pyruvate Carboxylation ◽  
Rate Of Movement

Preparations of pyruvate carboxylase catalyse the cleavage of MgATP in the absence of pyruvate and acetyl-CoA. The rate of this cleavage is higher in the presence of HCO3- than in its absence. Incubation of the enzyme preparations with an excess of the pyruvate carboxylase inhibitor, avidin, completely abolishes the pyruvate carboxylating activity of the enzyme preparations but only abolishes the HCO3(-)-dependent MgATP cleaving activity, with no effect on the HCO3(-)-independent ATPase activity. The HCO3(-)-dependent MgATP cleavage is also sensitive to inhibition by a pyruvate carboxylase inhibitor, oxamate, and the dependence of the reaction on the free Mg2+ concentration is similar to that of the pyruvate-carboxylation reaction, whereas the HCO3(-)-independent MgATP cleavage is not dependent on the concentration of free Mg2+ in the range tested. This indicates that MgATP cleavage by pyruvate carboxylase is entirely dependent on the presence of HCO3- and that there may be a low level of ATPase contamination in the enzyme preparations. In addition, inhibition of the HCO3(-)-dependent MgATP cleavage by both avidin and oxamate indicate that although biotin does not directly participate in the reaction, its presence is required in that part of the active site of the enzyme. The rate of HCO3(-)-dependent MgATP cleavage is about 0.07% of that of the full pyruvate carboxylation reaction under similar conditions with saturating substrates. The reaction mechanism is sequential with respect to MgATP and HCO3- addition and Mg2+ adds at equilibrium before MgATP. Acetyl-CoA stimulates the HCO3(-)-dependent MgATP cleavage at low MgATP concentrations, with the stimulation being greater at low Mg2+ concentrations. At high levels of MgATP in the presence of acetyl-CoA, substrate inhibition is evident and is more pronounced at increasing concentrations of Mg2+. This inhibition appears to be, at least in part, caused by inhibition of decarboxylation of the enzyme-carboxybiotin complex by the binding to this complex of Mg2+ and MgATP, which probably act to reduce the rate of movement of carboxybiotin from the site of the MgATP cleavage reaction to that of the pyruvate carboxylation reaction where it is unstable and decarboxylates.

scholarly journals Characterizing the Importance of the Biotin Carboxylase Domain Dimer for Staphylococcus aureus Pyruvate Carboxylase Catalysis

Biochemistry ◽  
2013 ◽  
Vol 52 (3) ◽  
pp. 488-496 ◽  
Author(s):  
Linda P. C. Yu ◽  
Chi-Yuan Chou ◽  
Philip H. Choi ◽  
Liang Tong
Keyword(s):  
Staphylococcus Aureus ◽  
Pyruvate Carboxylase ◽  
Biotin Carboxylase

scholarly journals Pig liver pyruvate carboxylase. The reaction pathway for the decarboxylation of oxaloacetate

1974 ◽  
Vol 139 (2) ◽  
pp. 321-329 ◽  
Author(s):  
Graham B. Warren ◽  
Keith F. Tipton
Keyword(s):  
Reaction Mechanism ◽  
Pyruvate Carboxylase ◽  
Reaction Pathway ◽  
Quantitative Description ◽  
Preceding Paper ◽  
Back Reaction ◽  
Acetyl Coa ◽  
Pig Liver ◽  
Non Linear ◽  
Catalytic Cycles

1. The reaction pathway for the decarboxylation of oxaloacetate, catalysed by pig liver pyruvate carboxylase, was studied in the presence of saturating concentrations of K+ and acetyl-CoA. 2. Free Mg2+ binds to the enzyme in an equilibrium fashion and remains bound during all further catalytic cycles. MgADP− and Pi bind randomly, at equilibrium, followed by the binding of oxaloacetate. Pyruvate is released before the ordered steay-state release of HCO3− and MgATP2−. 3. These results are entirely consistent with studies on the carboxylation of pyruvate presented in the preceding paper (Warren & Tipton, 1974b) and together they allow a quantitative description of the reaction mechanism of pig liver pyruvate carboxylase. 4. In the absence of other substrates of the back reaction pig liver pyruvate carboxylase will decarboxylate oxaloacetate in a manner that is not inhibited by avidin. 5. Reciprocal plots involving oxaloacetate are non-linear curves, which suggest a negatively co-operative interaction between this substrate and the enzyme.

Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from staphylococcus aureus

1998 ◽  
Vol 5 (5) ◽  
pp. 357-362 ◽  
Author(s):  
Michael Hennig ◽  
Allan D′Arcy ◽  
Isabella C. Hampele ◽  
Malcolm G.P. Page ◽  
Christian Oefner ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Staphylococcus Aureus ◽  
Reaction Mechanism ◽  
Dihydroneopterin Aldolase

Cytochemical Studies of Cell Wall Biosynthesis in Staphylococcus Aureus

1972 ◽  
Vol 30 ◽  
pp. 328-329
Author(s):  
Masaatsu Koike ◽  
Koichi Nakashima ◽  
Kyoko Iida
Keyword(s):  
Staphylococcus Aureus ◽  
Periodate Oxidation ◽  
Early Time ◽  
The Other ◽  
Penicillin G ◽  
Cell Wall Biosynthesis ◽  
Septal Wall ◽  
Peptidoglycan Biosynthesis ◽  
Gram Positive Bacteria ◽  
Cross Linkage

Penicillin exerts the activity to inhibit the peptide cross linkage between each polysaccharide backbone at the final stage of wall-peptidoglycan biosynthesis of bacteria. Morphologically, alterations of the septal wall and mesosome in gram-positive bacteria, which were occurred in early time after treatment with penicillin, have been observed. In this experiment, these alterations were cytochemically investigated by means of silver-methenamine staining after periodate oxidation, which is applied for detection of localization of wall mucopolysaccharide.Staphylococcus aureus strain 209P treated with 100 u/ml of penicillin G was divided into two aliquotes. One was fixed by Kellenberger-Ryter's OSO4 fixative at 30, 60 and 120 min after addition of the antibiotic, dehydrated through alcohol series, and embedded in Epon 812 (Specimen A). The other was fixed by 21 glutaraldehyde, dehydrated through glycolmethacrylate series and embedded in glycolmethacrylate mixture, according to Bernhard's method (Specimen B).

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