Allosteric regulation of the biotin-dependent enzyme pyruvate carboxylase by acetyl-CoA

2012 ◽  
Vol 40 (3) ◽  
pp. 567-572 ◽  
Author(s):  
Abdussalam Adina-Zada ◽  
Tonya N. Zeczycki ◽  
Martin St. Maurice ◽  
Sarawut Jitrapakdee ◽  
W. Wallace Cleland ◽  
...  
Keyword(s):  
Active Site ◽  
Pyruvate Carboxylase ◽  
Structural Effects ◽  
Reaction Conditions ◽  
Acetyl Coa ◽  
X Ray ◽  
Allosteric Interactions ◽  
Crystallographic Structures ◽  
And Staphylococcus Aureus ◽  
Allosteric Activator

The activity of the biotin-dependent enzyme pyruvate carboxylase from many organisms is highly regulated by the allosteric activator acetyl-CoA. A number of X-ray crystallographic structures of the native pyruvate carboxylase tetramer are now available for the enzyme from Rhizobium etli and Staphylococcus aureus. Although all of these structures show that intersubunit catalysis occurs, in the case of the R. etli enzyme, only two of the four subunits have the allosteric activator bound to them and are optimally configured for catalysis of the overall reaction. However, it is apparent that acetyl-CoA binding does not induce the observed asymmetrical tetramer conformation and it is likely that, under normal reaction conditions, all of the subunits have acetyl-CoA bound to them. Thus the activation of the enzyme by acetyl-CoA involves more subtle structural effects, one of which may be to facilitate the correct positioning of Arg353 and biotin in the biotin carboxylase domain active site, thereby promoting biotin carboxylation and, at the same time, preventing abortive decarboxylation of carboxybiotin. It is also apparent from the crystal structures that there are allosteric interactions induced by acetyl-CoA binding in the pair of subunits not optimally configured for catalysis of the overall reaction.

scholarly journals Factors that influence the translocation of the N-carboxybiotin moiety between the two sub-sites of pyruvate carboxylase

1981 ◽  
Vol 199 (3) ◽  
pp. 603-609 ◽  
Author(s):  
G J Goodall ◽  
G S Baldwin ◽  
J C Wallace ◽  
D B Keech
Keyword(s):  
Dissociation Constant ◽  
Carboxy Group ◽  
Active Site ◽  
Pyruvate Carboxylase ◽  
Alternative Substrate ◽  
Acetyl Coa ◽  
Low Concentrations ◽  
Acid Substrate ◽  
Allosteric Activator ◽  
Rate Of Movement

The active site of pyruvate carboxylase, like those of all biotin-dependent carboxylases, is believed to consist of two spatially distinct sub-sites with biotin acting as a mobile carboxy-group carrier oscillating between the two sub-sites. Some of the factors that influence the location and rate of movement of the N-carboxybiotin were studied. The rate of carboxylation of the alternative substrate, 2-oxobutyrate, was measured at 0 degrees C in an assay system where the isolated enzyme--[14C]carboxybiotin was the carboxy-group donor. The results are consistent with the hypothesis that the location of the carboxybiotin in the active site is determined by the presence of Mg2+, acetyl-CoA and the oxo acid substrate. The presence of Mg2+ favours the holding of the complex at the first sub-site, whereas alpha-oxo acids induce the complex to move to the second sub-site. At low concentrations pyruvate induces this movement but does not efficiently act as a carboxy-group acceptor; hydroxypyruvate, glyoxylate and oxamate, though not carboxylated, still induce the movement. The allosteric activator acetyl-CoA exerts only a slight stimulation on the rate of translocation to the second sub-site, and this stimulation arises from an increase in the dissociation constant for Mg2+.

scholarly journals Mechanism of IPPase shown by high resolution Neutron and X-ray crystallography

2014 ◽  
Vol 70 (a1) ◽  
pp. C1211-C1211
Author(s):  
Joseph Ng ◽  
Ronny Hughes ◽  
Michelle Morris ◽  
Leighton Coates ◽  
Matthew Blakeley ◽  
...  
Keyword(s):  
High Resolution ◽  
Active Site ◽  
Inorganic Pyrophosphatase ◽  
Inorganic Pyrophosphate ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Crystallographic Structures ◽  
Hydrolysis Of ◽  
Low Energy Conformations

Soluble inorganic pyrophosphatase (IPPase) catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to form orthophosphate (Pi). The action of this enzyme shifts the overall equilibrium in favor of synthesis during a number of ATP-dependent cellular processes such as in the polymerization of nucleic acids, production of coenzymes and proteins and sulfate assimilation pathways. Two Neutron crystallographic (2.10-2.50Å) and five high-resolution X-ray (0.99Å-1.92Å) structures of the archaeal IPPase from Thermococcus thioreducens have been determined under both cryo and room temperatures. The structures determined include the recombinant IPPase bound to Mg+2, Ca+2, Br-, SO2-2 or PO4-2 involving those with non-hydrolyzed and hydrolyzed pyrophosphate complexes. All the crystallographic structures provide snapshots of the active site corresponding to different stages of the hydrolysis of inorganic pyrophosphate. As a result, a structure-based model of IPPase catalysis is devised showing the enzyme's low-energy conformations, hydration states, movements and nucleophile generation within the active site.

scholarly journals Pyruvate carboxylase catalysis of phosphate transfer between carbamoyl phosphate and ADP

1991 ◽  
Vol 273 (2) ◽  
pp. 443-448 ◽  
Author(s):  
P V Attwood ◽  
B D L A Graneri
Keyword(s):  
Active Site ◽  
Pyruvate Carboxylase ◽  
Reverse Reaction ◽  
Carbamoyl Phosphate ◽  
Acetyl Coa ◽  
Essential Requirement ◽  
Pyruvate Carboxylation ◽  
Ionizable Residues ◽  
Ph Profiles

In a reaction that is analogous to the phosphorylation of ADP from carboxyphosphate, pyruvate carboxylase catalyses the formation of ATP from carbamoyl phosphate and ADP at a rate that is about 0.3% of the pyruvate-carboxylation reaction and about 3% of the full reverse reaction. Acetyl-CoA stimulates the phosphorylation of ADP from carbamoyl phosphate but is not an essential requirement of the reaction. Mg2+ also stimulates the reaction, and in the range of Mg2+ concentrations considered the effect of V is much larger in the absence of acetyl-CoA than in its presence. Acetyl-CoA and Mg2+ may be acting in a co-operative way to stimulate the phosphorylation of ADP in a similar way to their effects on the pyruvate-carboxylation reaction. The phosphorylation of ADP by carbamoyl phosphate is also stimulated by the presence of biotin in the part of the active site where this reaction occurs, but again it is not absolutely required for the reaction to proceed. The pH profiles of the phosphorylation of ADP by carbamoyl phosphate indicate that there are at least two ionizable residues involved in the reaction, one of which probably has a role in the release of carbamate from the active site.

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 Structure, mechanism and regulation of pyruvate carboxylase

2008 ◽  
Vol 413 (3) ◽  
pp. 369-387 ◽  
Author(s):  
Sarawut Jitrapakdee ◽  
Martin St Maurice ◽  
Ivan Rayment ◽  
W. Wallace Cleland ◽  
John C. Wallace ◽  
...  
Keyword(s):  
Active Site ◽  
Pyruvate Carboxylase ◽  
Polypeptide Chain ◽  
Tricarboxylic Acid Cycle ◽  
Biotin Carboxylase ◽  
Acetyl Coa ◽  
Specific Expression ◽  
Allosteric Effector ◽  
Bona Fide ◽  
And Function

PC (pyruvate carboxylase) is a biotin-containing enzyme that catalyses the HCO3−- and MgATP-dependent carboxylation of pyruvate to form oxaloacetate. This is a very important anaplerotic reaction, replenishing oxaloacetate withdrawn from the tricarboxylic acid cycle for various pivotal biochemical pathways. PC is therefore considered as an enzyme that is crucial for intermediary metabolism, controlling fuel partitioning toward gluconeogenesis or lipogenesis and in insulin secretion. The enzyme was discovered in 1959 and over the last decade there has been much progress in understanding its structure and function. PC from most organisms is a tetrameric protein that is allosterically regulated by acetyl-CoA and aspartate. High-resolution crystal structures of the holoenzyme with various ligands bound have recently been determined, and have revealed details of the binding sites and the relative positions of the biotin carboxylase, carboxyltransferase and biotin carboxyl carrier domains, and also a unique allosteric effector domain. In the presence of the allosteric effector, acetyl-CoA, the biotin moiety transfers the carboxy group between the biotin carboxylase domain active site on one polypeptide chain and the carboxyltransferase active site on the adjacent antiparallel polypeptide chain. In addition, the bona fide role of PC in the non-gluconeogenic tissues has been studied using a combination of classical biochemistry and genetic approaches. The first cloning of the promoter of the PC gene in mammals and subsequent transcriptional studies reveal some key cognate transcription factors regulating tissue-specific expression. The present review summarizes these advances and also offers some prospects in terms of future directions for the study of this important enzyme.

scholarly journals Tyrosine 121 moves revealing a druggable pocket that couples catalysis to ATP-binding in serine racemase

2021 ◽  
Author(s):  
Chloe R. Koulouris ◽  
Sian E. Gardiner ◽  
Tessa K. Harris ◽  
Karen T. Elvers ◽  
S. Mark Roe ◽  
...  
Keyword(s):  
Synaptic Plasticity ◽  
Active Site ◽  
Serine Racemase ◽  
Hydroxyl Group ◽  
Catalytic Residue ◽  
Dimer Interface ◽  
X Ray ◽  
The Core ◽  
Small Domain ◽  
Allosteric Activator

ABSTRACTHuman serine racemase (hSR) catalyses racemisation of L-serine to D-serine, the latter of which is a co-agonist of the NMDA subtype of glutamate receptors that are important in synaptic plasticity, learning and memory. In a ‘closed’ hSR structure containing the allosteric activator ATP, the inhibitor malonate is enclosed between the large and small domains while ATP is distal to the active site, residing at the dimer interface with the Tyr121 hydroxyl group contacting the ATP a-phosphate. In contrast, in ‘open’ hSR structures, Tyr121 sits in the core of the small domain with its hydroxyl contacting the key catalytic residue Ser84. The ability to regulate SR activity by flipping Tyr121 from the core of the small domain to the dimer interface appears to have evolved in animals with a CNS. Multiple X-ray crystallographic enzymefragment structures show that Tyr121 is flipped out of its pocket, suggesting that this pocket is druggable.

Surfactant involved in Copper Sulfide Nanocrystallites Synthesis

2009 ◽  
Vol 59 (12) ◽  
Author(s):  
Claudia Maria Simonescu ◽  
Valentin Serban Teodorescu ◽  
Camelia Capatina
Keyword(s):  
Copper Sulfide ◽  
X Ray Diffraction ◽  
Reaction Parameters ◽  
Reaction Conditions ◽  
X Ray ◽  
Selected Area Electron Diffraction ◽  
Transmission Electron ◽  
Shape Of Nanoparticles ◽  
Tem Transmission Electron Microscopy ◽  
Shape And Size

This paper presents the obtaining of copper sulfide CuS (covelite) from Cu(CH3COO)2.H2O and thioacetamide (TAA) system. The reaction was conducted in presence or absence of sodium-bis(2-ethylhexyl) sulfosuccinate (Na-AOT). The effects of various reaction parameters on the size and on the shape of nanoparticles have been examined. CuS obtained was characterized by X ray diffraction, IR spectroscopy, TEM � transmission electron microscopy and SAED selected area electron diffraction. The influence of surfactant to the shape and size of CuS (covellite) nanocrystals was established. The size of the nanocrystals varied from 10-60 nm depending on the reaction conditions such as quantity of surfactant.

One-pot Synthesis of Pyrazolone Sulfones by Iodine-catalyzed Sulfenylation of Pyrazolones with Aryl Sulfonyl Hydrazides Followed by Oxidation in Water

2018 ◽  
Vol 15 (3) ◽  
pp. 380-387
Author(s):  
Xia Zhao ◽  
Xiaoyu Lu ◽  
Lipeng Zhang ◽  
Tianjiao Li ◽  
Kui Lu
Keyword(s):  
Double Bond ◽  
Efficient Method ◽  
Room Temperature ◽  
Sulfonyl Chloride ◽  
Antibacterial Activities ◽  
Oxidation Reactions ◽  
Reaction Conditions ◽  
One Pot ◽  
X Ray ◽  
Amide Form

Aim and Objective: Pyrazolone sulfones have been reported to exhibit herbicidal and antibacterial activities. In spite of their good bioactivities, only a few methods have been developed to prepare pyrazolone sulfones. However, the substrate scope of these methods is limited. Moreover, the direct sulfonylation of pyrazolone by aryl sulfonyl chloride failed to give pyrazolone sulfones. Thus, developing a more efficient method to synthesize pyrazolone sulfones is very important. Materials and Method: Pyrazolone, aryl sulphonyl hydrazide, iodine, p-toluenesulphonic acid and water were mixed in a sealed tube, which was heated to 100°C for 12 hours. The mixture was cooled to 0°C and m-CPBA was added in batches. The mixture was allowed to stir for 30 min at room temperature. The crude product was purified by silica gel column chromatography to afford sulfuryl pyrazolone. Results: In all cases, the sulfenylation products were formed smoothly under the optimized reaction conditions, and were then oxidized to the corresponding sulfones in good yields by 3-chloroperoxybenzoic acid (m-CPBA) in water. Single crystal X-ray analysis of pyrazolone sulfone 4aa showed that the major tautomer of pyrazolone sulfones was the amide form instead of the enol form observed for pyrazolone thioethers. Moreover, the C=N double bond isomerized to form an α,β-unsaturated C=C double bond. Conclusion: An efficient method to synthesize pyrazolone thioethers by iodine-catalyzed sulfenylation of pyrazolones with aryl sulfonyl hydrazides in water was developed. Moreover, this method was employed to synthesize pyrazolone sulfones in one-pot by subsequent sulfenylation and oxidation reactions.

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