scholarly journals Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity

2020 ◽  
pp. jbc.RA120.015103
Author(s):  
Pedro Latorre-Muro ◽  
Josue Baeza ◽  
Ramon Hurtado-Guerrero ◽  
Thomas Hicks ◽  
Ignacio Delso ◽  
...  
Keyword(s):  
Active Site ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Direct Evidence ◽  
Protein Crystallization ◽  
Metabolic Stress ◽  
Titration Calorimetry ◽  
Acetyl Coa ◽  
Key Enzyme ◽  
Chemically Reacting

Acetylation is known to regulate the activity of cytosolic phosphoenolpyruvate carboxykinase (PCK1), a key enzyme in gluconeogenesis, by promoting the reverse reaction of the enzyme (converting phosphoenolpyruvate to oxaloacetate). It is also known that the histone acetyltransferase p300 can induce PCK1 acetylation in cells, but whether that is a direct or indirect function was not known. Here we initially set out to determine whether p300 can acetylate directly PCK1 in vitro. We report that p300 weakly acetylates PCK1, but surprisingly, using several techniques including protein crystallization, mass spectrometry, isothermal titration calorimetry (ITC), saturation-transfer difference nuclear magnetic resonance (STD-NMR) and molecular docking, we found that PCK1 is also able to acetylate itself using acetyl-CoA independently of p300. This reaction yielded an acetylated recombinant PCK1 with a 3-fold decrease in kcat without changes in Km for all substrates. Acetylation stoichiometry was determined for 14 residues, including residues lining the active site. Structural and kinetic analyses determined that site-directed acetylation of K244, located inside the active site, altered this site and rendered the enzyme inactive. Additionally, we found that acetyl-CoA binding to the active site is specific and metal dependent. Our findings provide direct evidence for acetyl-CoA binding and chemically reacting with the active site of PCK1 and suggest a newly discovered regulatory mechanism of PCK1 during metabolic stress.

Sirtuin-dependent reversible lysine acetylation controls the activity of acetyl-Coenzyme A synthetase in Campylobacter jejuni

2021 ◽  
Author(s):  
Victoria L. Jeter ◽  
Jorge C. Escalante-Semerena
Keyword(s):  
Campylobacter Jejuni ◽  
Posttranslational Modifications ◽  
Active Site ◽  
Protein Function ◽  
Metabolic Enzyme ◽  
Lysine Acetylation ◽  
Class Iii ◽  
Acetyl Coa

Posttranslational modifications are mechanisms for rapid control of protein function used by cells from all domains of life. Acetylation of the epsilon amino group ( N ε ) of an active-site lysine of the AMP-forming acetyl-CoA synthetase (Acs) enzyme is the paradigm for the posttranslational control of the activity of metabolic enzymes. In bacteria, the alluded active-site lysine of Acs enzymes can be modified by a number of different GCN5-type N -acetyltransferases (GNATs). Acs activity is lost as a result of acetylation, and restored by deacetylation. Using a heterologous host, we show that Campylobacter jejuni NCTC11168 synthesizes enzymes that control Acs function by reversible lysine acetylation (RLA). This work validates the function of gene products encoded by the cj1537c , cj1715, and cj1050c loci, namely the AMP-forming acetate:CoA ligase ( Cj Acs), a type IV GCN5-type lysine acetyltransferase (GNAT, hereafter Cj LatA), and a NAD + -dependent (class III) sirtuin deacylase ( Cj CobB), respectively. To our knowledge, these are the first in vivo and in vitro data on C. jejuni enzymes that control the activity of Cj Acs. IMPORTANCE This work is important because it provides the experimental evidence needed to support the assignment of function to three key enzymes, two of which control the reversible posttranslational modification of an active-site lysyl residue of the central metabolic enzyme acetyl-CoA synthetase ( Cj Acs). We can now generate Campylobacter jejuni mutant strains defective in these functions, so we can establish the conditions in which this mode of regulation of Cj Acs is triggered in this bacterium. Such knowledge may provide new therapeutic strategies for the control of this pathogen.

scholarly journals Overcoming Chemoresistance to Vemurafenib in Melanoma via Targeted Inhibition of PCK1 Using 3-mercaptopropionic Acid

2021 ◽  
Author(s):  
Ming Ren ◽  
Lu Wang ◽  
Xin-Yi Deng ◽  
Zi-Xu Gao ◽  
Qiang Wang ◽  
...  
Keyword(s):  
Phosphoenolpyruvate Carboxykinase ◽  
Acquired Resistance ◽  
Xenograft Model ◽  
Metabolic Reprogramming ◽  
Mercaptopropionic Acid ◽  
Subcutaneous Xenograft ◽  
Key Enzyme ◽  
Targeted Inhibition ◽  
Sphere Formation

Abstract Background:BRAF inhibitors are the mainstay treatment for melanoma with the V600E mutation, but its resistance to BRAFi remains a clinical challenge. Therefore, it is necessary to explore the mechanism of BRAFi resistance and develop new therapeutic targets. Methods:We established an A2058 melanoma cell line with acquired resistance to vemurafenib in vitro. RNA sequencing was used to identify the target gene and signaling pathway which were related to the resistance.A series of in vitro assays were applied to confirm the function of PCK1, including test of scratch,transwell,cell viability,flow cytometry,sphere formation,western blot and ROS detection.Western blot was taken to identify the activation of PI3K/Akt pathway.We constructed the subcutaneous xenograft model of melanoma,and the mice were randomly injected with DMSO,vemurafenib,and combination of vemurafenib and 3-mercaptopropionic acid.Finally, tumor size,ROS in tissue,and immunohistochemistry were analyzed to validate the findings.Results:We identified that the activation of PI3K/Akt pathway led to the overexpression of phosphoenolpyruvate carboxykinase 1, a key enzyme of gluconeogenesis. An elevated PCK1 level induced intracellular metabolic reprogramming, thereby lowering oxidative stress contributed to the chemoresistance to vemurafenib. 3-mercaptopropionic acid , an antihyperglycemic agent, could inhibit the viability of PCK1 then bring oxidative damage to drug-resistant cells. As a result, 3-mercaptopropionic acid sensitized the cells to the killing effect of vemurafenib, exerting a synergistic anti-tumor effect in combination with vemurafenib. Conclusions:Our study demonstrates that the PI3K/Akt-PCK1-ROS axis plays an important role in BRAFi-resistant melanoma and that using the antihyperglycemic agent 3-MPA is a feasible strategy to restore its therapeutic sensitivity.

scholarly journals Design and Characterisation of Inhibitory Peptides against Bleg1_2478, an Evolutionary Divergent B3 Metallo-β-lactamase

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5797
Author(s):  
Gayathri Selvaraju ◽  
Thean Chor Leow ◽  
Abu Bakar Salleh ◽  
Yahaya M. Normi
Keyword(s):  
Active Site ◽  
Protein Complexes ◽  
Hypothetical Protein ◽  
Titration Calorimetry ◽  
Binding Properties ◽  
Vitro Assay ◽  
In Silico Docking ◽  
Inhibitory Peptides ◽  
Catalytic Function

Previously, a hypothetical protein (HP) termed Bleg1_2437 (currently named Bleg1_2478) from Bacillus lehensis G1 was discovered to be an evolutionary divergent B3 subclass metallo-β-lactamase (MBL). Due to the scarcity of clinical inhibitors for B3 MBLs and the divergent nature of Bleg1_2478, this study aimed to design and characterise peptides as inhibitors against Bleg1_2478. Through in silico docking, RSWPWH and SSWWDR peptides with comparable binding energy to ampicillin were obtained. In vitro assay results showed RSWPWH and SSWWDR inhibited the activity of Bleg1_2478 by 50% at concentrations as low as 0.90 µM and 0.50 µM, respectively. At 10 µM of RSWPWH and 20 µM of SSWWDR, the activity of Bleg1_2478 was almost completely inhibited. Isothermal titration calorimetry (ITC) analyses showed slightly improved binding properties of the peptides compared to ampicillin. Docked peptide–protein complexes revealed that RSWPWH bound near the vicinity of the Bleg1_2478 active site while SSWWDR bound at the center of the active site itself. We postulate that the peptides caused the inhibition of Bleg1_2478 by reducing or blocking the accessibility of its active site from ampicillin, thus hampering its catalytic function.

scholarly journals The Yeast GID Complex, a Novel Ubiquitin Ligase (E3) Involved in the Regulation of Carbohydrate Metabolism

2008 ◽  
Vol 19 (8) ◽  
pp. 3323-3333 ◽  
Author(s):  
Olivier Santt ◽  
Thorsten Pfirrmann ◽  
Bernhard Braun ◽  
Jeannette Juretschke ◽  
Philipp Kimmig ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Ubiquitin Ligase ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Ring Finger ◽  
Vitro Assay ◽  
Fructose 1,6 Bisphosphatase ◽  
Key Enzyme ◽  
Ubiquitin Ligase E3

Glucose-dependent regulation of carbon metabolism is a subject of intensive studies. We have previously shown that the switch from gluconeogenesis to glycolysis is associated with ubiquitin-proteasome linked elimination of the key enzyme fructose-1,6-bisphosphatase. Seven glucose induced degradation deficient (Gid)-proteins found previously in a genomic screen were shown to form a complex that binds FBPase. One of the subunits, Gid2/Rmd5, contains a degenerated RING finger domain. In an in vitro assay, heterologous expression of GST-Gid2 leads to polyubiquitination of proteins. In addition, we show that a mutation in the degenerated RING domain of Gid2/Rmd5 abolishes fructose-1,6-bisphosphatase polyubiquitination and elimination in vivo. Six Gid proteins are present in gluconeogenic cells. A seventh protein, Gid4/Vid24, occurs upon glucose addition to gluconeogenic cells and is afterwards eliminated. Forcing abnormal expression of Gid4/Vid24 in gluconeogenic cells leads to fructose-1,6-bisphosphatase degradation. This suggests that Gid4/Vid24 initiates fructose-1,6-bisphosphatase polyubiquitination by the Gid complex and its subsequent elimination by the proteasome. We also show that an additional gluconeogenic enzyme, phosphoenolpyruvate carboxykinase, is subject to Gid complex-dependent degradation. Our study uncovers a new type of ubiquitin ligase complex composed of novel subunits involved in carbohydrate metabolism and identifies Gid4/Vid24 as a major regulator of this E3.

Active site characterization and activity of the human aspartyl (asparaginyl) β-hydroxylase

Metallomics ◽  
2021 ◽  
Vol 13 (10) ◽  
Author(s):  
Jenna M Greve ◽  
Andrew M Pinkham ◽  
Zechariah Thompson ◽  
J A Cowan
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Catalytic Domain ◽  
Negative Impact ◽  
Enzyme Stability ◽  
Titration Calorimetry ◽  
Cellular Biochemistry ◽  
Biophysical Approach

Abstract Human aspartyl/asparaginyl beta-hydroxylase (HAAH) is a member of the superfamily of nonheme Fe2+/α-ketoglutarate (αKG) dependent oxygenase enzymes with a noncanonical active site. HAAH hydroxylates epidermal growth factor (EGF) like domains to form the β-hydroxylated product from substrate asparagine or aspartic acid and has been suggested to have a negative impact in a variety of cancers. In addition to iron, HAAH also binds divalent calcium, although the role of the latter is not understood. Herein, the metal binding chemistry and influence on enzyme stability and activity have been evaluated by a combined biochemical and biophysical approach. Metal binding parameters for the HAAH active site were determined by use of isothermal titration calorimetry, demonstrating a high-affinity regulatory binding site for Ca2+ in the catalytic domain in addition to the catalytic Fe2+ cofactor. We have analyzed various active site derivatives, utilizing LC-MS and a new HPLC technique to determine the role of metal binding and the second coordination sphere in enzyme activity, discovering a previously unreported residue as vital for HAAH turnover. This analysis of the in vitro biochemical function of HAAH furthers the understanding of its importance to cellular biochemistry and metabolic pathways.

scholarly journals The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleotide selectivity of PNPs

2018 ◽  
Author(s):  
Juliana Roberta Torini ◽  
Larissa Romanello ◽  
Fernanda Aparecida Heleno Batista ◽  
Vitor Hugo Balasco Serrão ◽  
Muhammad Faheem ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Schistosoma Mansoni ◽  
Binding Site ◽  
Kinetic Parameters ◽  
Isothermal Titration Calorimetry ◽  
Active Site ◽  
Binding Mode ◽  
Titration Calorimetry ◽  
Purine Salvage ◽  
Key Enzyme

AbstractPurine nucleoside phosphorylases (PNPs) play an important role in the blood fluke parasite Schistosoma mansoni as a key enzyme of the purine salvage pathway. Here we present the structural and kinetic characterization of a new PNP isoform from S. mansoni, named as SmPNP2. Screening of different ligands using a thermofluorescence approach indicated cytidine and cytosine as potential ligands. The binding of cytosine was confirmed by isothermal titration calorimetry, with a KD of 27 μM, and kinetic parameters for cytidine catalysis were obtained by ITC resulting in a KM of 76.3 μM. SmPNP2 also displays catalytic activity against inosine and adenosine, making it the first described PNP with robust catalytic activity towards both pyrimidines and purines. Crystallographic structures of SmPNP2 with different ligands were obtained and comparison of these structures with the previously described S. mansoni PNP (SmPNP1) provided clues for the unique capability of SmPNP2 to bind pyrimidines. When compared with the structure of SmPNP1, substitutions in the vicinity of SmPNP2 active site alter the architecture of the nucleoside base binding site allowing an alternative binding mode for nucleosides, with a 180° rotation from the canonical binding mode. The remarkable plasticity of this binding site deepens the understanding of the correlation between structure and nucleotide selectivity, offering new ways to analyses PNP activity.Author SummarySchistosoma mansoni is a human parasite dependent on purine salvage for purine bases supply. Purine nucleoside phosphorylase (PNP) is a key enzyme in this pathway. It carries two PNP isoforms, one previously characterized (SmPNP1) and one unknown (SmPNP2). Here we present the crystallographic structure of SmPNP2 and its complex with cytosine, cytidine, ribose-l-phosphate, adenine, hypoxanthine, and tubercidin. Cytidine and cytosine were identified as ligands of SmPNP2 using a thermofluorescence approach. Binding of cytosine was proven by Isothermal Titration Calorimetry (ITC) and cytidine, inosine, and adenosine kinetic parameters were also obtained. Purine bases showed different binding in the active site, rotated 180° from the canonical binding mode. It’s the first report showing a Low Molecular Mass PNP capable of catalyzing both types of nucleotide bases. The SmPNP2 odd behavior sheds a new light on the Schistosoma mansoni’s life cycle metabolic adaptation.

Phosphorylation-activity relationships of AMPK and acetyl-CoA carboxylase in muscle

2002 ◽  
Vol 92 (6) ◽  
pp. 2475-2482 ◽  
Author(s):  
S. H. Park ◽  
S. R. Gammon ◽  
J. D. Knippers ◽  
S. R. Paulsen ◽  
D. S. Rubink ◽  
...  
Keyword(s):  
Gastrocnemius Muscle ◽  
Direct Evidence ◽  
Acid Oxidation ◽  
Direct Link ◽  
Acetyl Coa Carboxylase ◽  
Acetyl Coa ◽  
Antibody Preparation ◽  
Amp Activated Protein Kinase ◽  
Linear Correlations

AMP-activated protein kinase (AMPK) is activated during muscle contraction in response to the increase in AMP and decrease in phosphocreatine (PCr). Once activated, AMPK has been proposed to phosphorylate a number of targets, resulting in increases in glucose transport, fatty acid oxidation, and gene transcription. Although it has been possible to directly observe phosphorylation of one of these targets, acetyl-CoA carboxylase (ACC) in vitro, it has been more difficult to obtain direct evidence of ACC phosphorylation in contracting skeletal muscle. In these experiments using a phosphoserine antibody to ACC and a phosphothreonine antibody to AMPK, evidence was obtained for phosphorylation and activation of ACC in vitro, in gastrocnemius muscle electrically stimulated at different frequencies, and in muscle from rats running on the treadmill. Significant negative linear correlations between phospho-ACC and ACC activity were observed in all models ( P < 0.01). The decline in ACC activity was related to the decrease in PCr and the rise in AMP. A relationship between phospho-AMPK (threonine 172) and activity of AMPK immunoprecipitated with anti-α2 subunit antibody preparation was also observed. These data provide the first evidence of a direct link between extent of phosphorylation of these proteins at sites recognized by the antibodies and activity of the enzymes in electrically stimulated muscle and in muscle of rats running on the treadmill.

Characterization of P. aeruginosa Glucose 6- Phosphate Isomerase: A Functional Insight via In-Vitro Activity Study

2020 ◽  
Vol 20 (29) ◽  
pp. 2651-2661
Author(s):  
Deekshi Angira ◽  
Nalini Natarajan ◽  
Samir R. Dedania ◽  
Darshan H. Patel ◽  
Vijay Thiruvenkatam
Keyword(s):  
Active Site ◽  
Expression System ◽  
Homology Model ◽  
Competitive Inhibitor ◽  
Membered Ring ◽  
Titration Calorimetry ◽  
Motility Factor ◽  
Differential Scanning Fluorimetry ◽  
Ic50 Values

Background: Glucose-6-phosphate isomerase (G6PI) catalyses the second step in glycolysis in the reversible interconversion of an aldohexose glucose 6-phosphate, a six membered ring moiety to a ketohexose, fructose 6-phosphate five membered ring moiety. This enzyme is of utmost importance due to its multifunctional role like neuroleukin, autocrine motility factor, etc. in various species. G6PI from Pseudomonas aeruginosa is less explored for its moonlighting properties. These properties can be predicted by studying the active site conservation of residues and their interaction with the specific ligand. Methods: Here, we study the G6PI in a self-inducible construct in bacterial expression system with its purification using Ni-NTA chromatography. The secondary structure of pure G6PI is estimated using circular dichroism to further predict the proper folding form of the protein. The bioactivity of the purified enzyme is quantified using phosphoglucose isomerase colorimetric kit with a value of 12.5 mU/mL. Differential scanning fluorimetry and isothermal titration calorimetry were employed to monitor the interaction of G6PI with its competitive inhibitor, erythrose 4-phosphate and calculated the Tm, Kd and IC50 values. Further, the homology model for the protein was prepared to study the interaction with the erythrose 4-phosphate. MD simulation of the complex was performed at 100 ns to identify the binding interactions. Results: We identified hydrogen bonds and water bridges dominating the interactions in the active site holding the protein and ligand with strong affinity. Conclusion : G6PI was successfully crystallized and data has been collected at 6Å. We are focused on improving the crystal quality for obtaining higher resolution data.

Ancylostoma caninum Anticoagulant Peptide Blocks Metastasis In Vivo and Inhibits Factor Xa Binding to Melanoma Cells In Vitro

1998 ◽  
Vol 79 (05) ◽  
pp. 1041-1047 ◽  
Author(s):  
Kathleen M. Donnelly ◽  
Michael E. Bromberg ◽  
Aaron Milstone ◽  
Jennifer Madison McNiff ◽  
Gordon Terwilliger ◽  
...  
Keyword(s):  
Active Site ◽  
Thrombin Generation ◽  
Factor Xa ◽  
Coagulation Factor ◽  
Melanoma Cells ◽  
Factor V ◽  
Ancylostoma Caninum ◽  
Metastatic Activity

SummaryWe evaluated the in vivo anti-metastatic activity of recombinant Ancylostoma caninum Anticoagulant Peptide (rAcAP), a potent (Ki = 265 pM) and specific active site inhibitor of human coagulation factor Xa originally isolated from bloodfeeding hookworms. Subcutaneous injection of SCID mice with rAcAP (0.01-0.2 mg/mouse) prior to tail vein injection of LOX human melanoma cells resulted in a dose dependent reduction in pulmonary metastases. In order to elucidate potential mechanisms of rAcAP’s anti-metastatic activity, experiments were carried out to identify specific interactions between factor Xa and LOX. Binding of biotinylated factor Xa to LOX monolayers was both specific and saturable (Kd = 15 nM). Competition experiments using antibodies to previously identified factor Xa binding proteins, including factor V/Va, effector cell protease receptor-1, and tissue factor pathway inhibitor failed to implicate any of these molecules as significant binding sites for Factor Xa. Functional prothrombinase activity was also supported by LOX, with a half maximal rate of thrombin generation detected at a factor Xa concentration of 2.4 nM. Additional competition experiments using an excess of either rAcAP or active site blocked factor Xa (EGR-Xa) revealed that most of the total factor Xa binding to LOX is mediated via interaction with the enzyme’s active site, predicting that the vast majority of cell-associated factor Xa does not participate directly in thrombin generation. In addition to establishing two distinct mechanisms of factor Xa binding to melanoma, these data raise the possibility that rAcAP’s antimetastatic effect in vivo might involve novel non-coagulant pathways, perhaps via inhibition of active-site mediated interactions between factor Xa and tumor cells.

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