72-89-9Relevant articles and documents
Interchain acetyl transfer in the E2 component of bacterial pyruvate dehydrogenase suggests a model with different roles for each chain in a trimer of the homooligomeric component
Song, Jaeyoung,Jordan, Frank
, p. 2795 - 2803 (2012)
The bacterial pyruvate dehydrogenase complex carries out conversion of pyruvate to acetyl-coenzyme A with the assistance of thiamin diphosphate (ThDP), several other cofactors, and three principal protein components, E1-E3, each present in multiple copies. The E2 component forms the core of the complexes, each copy consisting of variable numbers of lipoyl domains (LDs, lipoic acid covalently amidated at a lysine residue), peripheral subunit binding domains (PSBDs), and catalytic (or core) domains (CDs). The reaction starts with a ThDP-dependent decarboxylation on E1 to an enamine/C2α carbanion, followed by oxidation and acetyl transfer to form S-acetyldihydrolipoamide E2, and then transfer of this acetyl group from the LD to coenzyme A on the CD. The dihydrolipoamide E2 is finally reoxidized by the E3 component. This report investigates whether the acetyl group is passed from the LD to the CD in an intra- or interchain reaction. Using an Escherichia coli E2 component having a single LD, two types of constructs were prepared: one with a Lys to Ala substitution in the LD at the Lys carrying the lipoic acid, making E2 incompetent toward post-translational ligation of lipoic acid and, hence, toward reductive acetylation, and the other in which the His believed to catalyze the transthiolacetylation in the CD is substituted with A or C, the absence of His rendering it incompetent toward acetyl-CoA formation. Both kinetic evidence and mass spectrometric evidence support interchain transfer of the acetyl groups, providing a novel model for the presence of multiples of three chains in all E2 components, and their assembly in bacterial enzymes.
Kinetic mechanism of acetyl-CoA synthase: Steady-state synthesis at variable CO/CO2 pressures
Maynard,Sewell,Lindahl
, p. 4697 - 4703 (2001)
Steady-state initial rates of acetyl-CoA synthesis (v/[Etot]) catalyzed by acetyl-CoA synthase from Clostridium thermoaceticum (ACS) were determined at various partial pressures of CO and CO2. When [CO] was varied from 0 to 100 μM in a balance of Ar, rates increased sharply from 0.3 to 100 min-1. At [CO] > 100 μM, rates declined sharply and eventually stabilized at 10 min-1 at 980 μM CO. Equivalent experiments carried out in CO2 revealed similar inhibitory behavior and residual activity under saturating [CO] Plots of v/[Etot] vs [CO2] at different fixed inhibitory [CO] revealed that Vmax/[Etot] (kcat) decreased with increasing [CO]. Plots of v/[Etot] vs [CO2] at different fixed noninhibitory [CO] showed that Vmax/[Etot] was insensitive to changes in [CO]. Of eleven candidate mechanisms, the simplest one that fit the data best had the following key features: (a) either CO or CO2 (at a designated reductant level and pH) activate the enzyme (E′ + CO ? E, E′ + CO2/2e-/2H+ ? E); (b) CO and CO2 are both substrates that compete for the same enzyme form (E + CO ? ECO, E + CO2/2e-/2H+ ? ECO, and ECO → E + P); (c) between 3 and 5 molecules of CO bind cooperatively to an enzyme form different from that to which CO2 and substrate CO bind (nCO + ECO ? (CO)nECO), and this inhibits catalysis; and (d) the residual activity arises from either the (CO)nECO state or a heterogeneous form of the enzyme. Implications of these results, focusing on the roles of CO and CO2 in catalysis, are discussed.
Kinetics of CO insertion and acetyl group transfer steps, and a model of the acetyl-CoA synthase catalytic mechanism
Tan, Xiangshi,Surovtsev, Ivan V.,Lindahl, Paul A.
, p. 12331 - 12338 (2006)
Acetyl-CoA synthase/carbon monoxide dehydrogenase is a Ni-Fe-S-containing enzyme that catalyzes the synthesis of acetyl-CoA from CO, CoA, and a methyl group. The methyl group is transferred onto the enzyme from a corrinoid-iron-sulfur protein (CoFeSP). The kinetics of two steps within the catalytic mechanism were studied using the stopped-flow method, including the insertion of CO into a putative Ni2+-CH3 bond and the transfer of the resulting acetyl group to CoA. Neither step had been studied previously. Reactions were monitored indirectly, starting with the methylated intermediate form of the enzyme. Resulting traces were analyzed by constructing a simple kinetic model describing the catalytic mechanism under reducing conditions. Besides methyl group transfer, CO insertion, and acetyl group transfer, fitting to experimental traces required the inclusion of an inhibitory step in which CO reversibly bound to the form of the enzyme obtained immediately after product release. Global simulation of the reported datasets afforded a consistent set of kinetic parameters. The equilibrium constant for the overall synthesis of acetyl-CoA was estimated and compared to the product of the individual equilibrium constants. Simulations obtained with the model duplicated the essential behavior of the enzyme, in terms of the variation of activity with [CO], and the time-dependent decay of the NiFeC EPR signal upon reaction with CoFeSP. Under standard assay conditions, the model suggests that the vast majority of active enzyme molecules in a population should be in the methylated form, suggesting that the subsequent catalytic step, namely CO insertion, is rate limiting. This conclusion is further supported by a sensitivity analysis showing that the rate is most sensitively affected by a change in the rate coefficient associated with the CO insertion step.
The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine
Bremer, Erhard,Czech, Laura,Dickschat, Jeroen S.,Erb, Tobias J.,Hoeppner, Astrid,Kobus, Stefanie,Lauterbach, Lukas,Richter, Alexandra A.,Smits, Sander H. J.,Zarzycki, Jan
, p. 2822 - 2838 (2020)
Ectoine is a solute compatible with the physiologies of both prokaryotic and eukaryotic cells and is widely synthesized by bacteria as an osmotic stress protectant. Because it preserves functional attributes of proteins and macromolecular complexes, it is considered a chemical chaperone and has found numerous practical applications. However, the mechanism of its biosynthesis is incompletely understood. The second step in ectoine biosynthesis is catalyzed by L-2,4-diaminobutyrate acetyltransferase (EctA; EC 2.3.1.178), which transfers the acetyl group from acetyl-CoA to EctB-formed L-2,4-diaminobutyrate (DAB), yielding N-γ-acetyl-L-2,4-diaminobutyrate (N-γ- ADABA), the substrate of ectoine synthase (EctC). Here, we report the biochemical and structural characterization of the EctA enzyme from the thermotolerant bacterium Paenibacillus lautus (Pl). We found that (Pl)EctA forms a homodimer whose enzyme activity is highly regiospecific by producing N-γ- ADABA but not the ectoine catabolic intermediate N-α-acetyl- L-2,4-diaminobutyric acid. High-resolution crystal structures of (Pl)EctA (at 1.2-2.2?resolution) (i) for its apo-form, (ii) in complex with CoA, (iii) in complex with DAB, (iv) in complex with both CoA and DAB, and (v) in the presence of the product N-γ- ADABA were obtained. To pinpoint residues involved in DAB binding, we probed the structure-function relationship of (Pl)EctA by site-directed mutagenesis. Phylogenomics shows that EctA-type proteins from both Bacteria and Archaea are evolutionarily highly conserved, including catalytically important residues. Collectively, our biochemical and structural findings yielded detailed insights into the catalytic core of the EctA enzyme that laid the foundation for unraveling its reaction mechanism.
Identification of an α-Oxoamine Synthase and a One-Pot Two-Step Enzymatic Synthesis of α-Amino Ketones
Zhou, Ting,Gao, Du,Li, Jia-Xin,Xu, Min-Juan,Xu, Jun
supporting information, p. 37 - 41 (2020/12/21)
Alb29, an α-oxoamine synthase involved in albogrisin biosynthesis in Streptomyces albogriseolus MGR072, was characterized and responsible for the incorporation of l-glutamate to acyl-coenzyme A substrates. Combined with Alb29 and Mgr36 (an acyl-coenzyme A ligase), a one-pot enzymatic system was established to synthesize seven α-amino ketones. When these α-amino ketones were fed into the alb29 knockout strain Δalb29, respectively, the albogrisin analogs with different side chains were observed.
Repurposing the 3-Isocyanobutanoic Acid Adenylation Enzyme SfaB for Versatile Amidation and Thioesterification
Zhu, Mengyi,Wang, Lijuan,He, Jing
supporting information, p. 2030 - 2035 (2020/11/30)
Genome mining of microbial natural products enables chemists not only to discover the bioactive molecules with novel skeletons, but also to identify the enzymes that catalyze diverse chemical reactions. Exploring the substrate promiscuity and catalytic mechanism of those biosynthetic enzymes facilitates the development of potential biocatalysts. SfaB is an acyl adenylate-forming enzyme that adenylates a unique building block, 3-isocyanobutanoic acid, in the biosynthetic pathway of the diisonitrile natural product SF2768 produced by Streptomyces thioluteus, and this AMP-ligase was demonstrated to accept a broad range of short-chain fatty acids (SCFAs). Herein, we repurpose SfaB to catalyze amidation or thioesterification between those SCFAs and various amine or thiol nucleophiles, thereby providing an alternative enzymatic approach to prepare the corresponding amides and thioesters in vitro.
Characterization of acetyl-CoA synthetase kinetics and ATP-binding
Gallego-Jara, Julia,Terol, Gema Lozano,écija Conesa, Ana,Zambelli, Barbara,Cánovas Díaz, Manuel,de Diego Puente, Teresa
, p. 1040 - 1049 (2019/04/04)
Background: The superfamily of adenylating enzymes is a large family of enzymes broadly distributed from bacteria to humans. Acetyl-CoA synthetase (Acs), member of this family, is a metabolic enzyme with an essential role in Escherichia coli (E. coli) acetate metabolism, whose catalytic activity is regulated by acetylation/deacetylation in vivo. Methods: In this study, the kinetics and thermodynamic parameters of deacetylated and acetylated E. coli Acs were studied for the adenylating step. Moreover, the role of the T264, K270, D500 and K609 residues in catalysis and ATP-binding was also determined by Isothermal titration calorimetry. Results: The results showed that native Acs enzyme binds ATP in an endothermic way. The dissociation constant has been determined and ATP-binding showed no significant differences between acetylated and deacetylated enzyme, although kcat was much higher for the deacetylated enzyme. However, K609 lysine mutation resulted in an increase in ATP-Acs-affinity and in a total loss of enzymatic activity, while T264 and D500 mutant proteins showed a total loss of ATP-binding ability and a decrease in catalytic activity. K609 site-specified acetylation induced a change in Acs conformation which resulted in an exothermic and more energetic ATP-binding. Conclusions: The differences in ATP-binding could explain the broadly conserved inactivation of Acs when K609 is acetylated. General Significance: The results presented in this study demonstrate the importance of the selected residues in Acs ATP-binding and represent an advance in our understanding of the adenylation step of the superfamily of adenylating enzymes and of their acetylation/deacetylation regulation.
Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion
Nguyen, Vinh H.,Singh, Noreen,Medina, Ana,Usón, Isabel,Fraser, Marie E.
, p. 1840 - 1849 (2019/08/30)
ATP-citrate lyase (ACLY) catalyzes production of acetyl-CoA and oxaloacetate from CoA and citrate using ATP. In humans, this cytoplasmic enzyme connects energy metabolism from carbohydrates to the production of lipids. In certain bacteria, ACLY is used to fix carbon in the reductive tricarboxylic acid cycle. The carboxy(C)-terminal portion of ACLY shows sequence similarity to citrate synthase of the tricarboxylic acid cycle. To investigate the roles of residues of ACLY equivalent to active site residues of citrate synthase, these residues in ACLY from Chlorobium limicola were mutated, and the proteins were investigated using kinetics assays and biophysical techniques. To obtain the crystal structure of the C-terminal portion of ACLY, full-length C. limicola ACLY was cleaved, first non-specifically with chymotrypsin and subsequently with Tobacco Etch Virus protease. Crystals of the C-terminal portion diffracted to high resolution, providing structures that show the positions of active site residues and how ACLY tetramerizes.
Functional chararacterization of the enzymes TabB and TabD involved in tabtoxin biosynthesis by Pseudomonas syringae
Manning, Margot E.,Danson, Eli J.,Calderone, Christopher T.
, (2018/01/12)
Pseudomonas syringae pv. tabaci ATCC 11528 produces tabtoxin, a β-lactam-containing dipeptide phytotoxin. Tabtoxinine-β-lactam (TβL), one of tabtoxin's constituent amino acids, structurally mimics lysine, and many of the proteins encoded by the tabtoxin biosynthetic gene cluster are homologs of lysine biosynthetic enzymes, suggesting that the tabtoxin and lysine biosynthetic routes parallel one another. We cloned and expressed TabB and TabD, predicted homologs of tetrahydrodipicolinate (THDPA)-N-acyltransferase and N-acyl-THDPA aminotransferase, respectively, to determine their activities in vitro. We confirmed that TabB succinylates THDPA and that TabD is a PLP-dependent aminotransferase that utilizes glutamate as an amine donor. Surprisingly, we also found that though TabD could utilize the TabB product N-succinyl-THDPA as a substrate, THDPA itself was also recognized. These observations reveal that TabB functionally duplicates DapD, the THDPA-N-succinyltransferase involved in lysine biosynthesis, and reinforce the close relationship between the metabolic logics underpinning the respective biosynthetic pathways.
A Flexible Polyphosphate-Driven Regeneration System for Coenzyme A Dependent Catalysis
Mordhorst, Silja,Maurer, Alice,Popadi?, Désirée,Brech, Johanna,Andexer, Jennifer N.
, p. 4164 - 4168 (2017/10/23)
Coenzyme A (CoA) is a common cofactor in biochemical reactions, and CoA-dependent enzymes catalyze essential steps in anabolism and catabolism. This complex molecule also plays an important role in the synthesis of many high-value products, such as synthetic antibiotics, vitamins, pheromones, and biopolymers. Nevertheless, the synthetic potential for biocatalytic processes cannot be fully exploited owing to the lack of an efficient regeneration system. Here, we report an acyl-CoA regeneration system with integrated adenosine triphosphate (ATP) regeneration that is based on inexpensive polyphosphate as the single energy source. In the four-enzyme cascade, two cofactors, acyl-CoA and ATP, are each regenerated up to 2000 times. The applicability for different acyl donors and acceptors is shown by HPLC analysis. Owing to its flexibility toward virtually all relevant substrates, the system has the potential to make CoA-dependent reactions more accessible for chemical synthesis in vitro.
