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Laseke AJ, Boram TJ, Schneider NO, Lohman JR, Maurice MS. Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase. Biochemistry 2023; 62:2632-2644. [PMID: 37603581 PMCID: PMC10693930 DOI: 10.1021/acs.biochem.3c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Allosteric regulation of the essential anaplerotic enzyme, pyruvate carboxylase (PC), is vital for metabolic homeostasis. PC catalyzes the bicarbonate- and ATP-dependent carboxylation of pyruvate to form oxaloacetate. Dysregulation of PC activity can impact glucose and redox metabolism, which contributes to the pathogenicity of many diseases. To maintain homeostasis, PC is allosterically activated by acetyl-CoA and allosterically inhibited by l-aspartate. In this study, we further characterize the molecular basis of allosteric regulation in Staphylococcus aureus PC (SaPC) using slowly/nonhydrolyzable dethia analogues of acetyl-CoA and site-directed mutagenesis of residues at the biotin carboxylase homodimer interface. The dethia analogues fully activate SaPC but demonstrate significantly reduced binding affinities relative to acetyl-CoA. Residues Arg21, Lys46, and Glu418 of SaPC are located at the biotin carboxylase dimer interface and play a critical role in both allosteric activation and inhibition. A structure of R21A SaPC in complex with acetyl-CoA reveals an intact molecule of acetyl-CoA bound at the allosteric site, offering new molecular insights into the acetyl-CoA binding site. This study demonstrates that the biotin carboxylase domain dimer interface is a critical allosteric site in PC, serving as a convergence point for allosteric activation by acetyl-CoA and inhibition by l-aspartate.
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Affiliation(s)
- Amanda J. Laseke
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
| | - Trevor J. Boram
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
| | - Nicholas O. Schneider
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
| | - Jeremy R. Lohman
- Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, United States
- Current Address: Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824
| | - Martin St. Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201-1881, USA
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2
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Rattanapornsompong K, Sirithanakorn C, Jitrapakdee S, Attwood PV. The role of the phosphate groups of trinitrophenyl adenosine 5'-triphosphate (TNP-ATP) in allosteric activation of pyruvate carboxylase and the inhibition of acetyl CoA-dependent activation. Arch Biochem Biophys 2021; 711:109017. [PMID: 34411580 DOI: 10.1016/j.abb.2021.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/26/2021] [Accepted: 08/14/2021] [Indexed: 10/20/2022]
Abstract
A previous study showed that 2'-3'-O-(2,4,6-trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP) was a weak allosteric activator of Rhizobium etli pyruvate carboxylase (RePC) in the absence of acetyl-CoA. On the other hand, TNP-ATP inhibited the allosteric activation of RePC by acetyl-CoA. Here, we aimed to study the role of triphosphate group of TNP-ATP on its allosteric activation of the enzyme and inhibition of acetyl-CoA-dependent activation of RePC using TNP-ATP and its derivatives, including TNP-ADP, TNP-AMP and TNP-adenosine. The pyruvate carboxylation activity was assayed to determine the effect of reducing the number of phosphate groups in TNP-ATP derivatives on allosteric activation and inhibition of acetyl-CoA activation of RePC and chicken liver pyruvate carboxylase (CLPC). Reducing the number of phosphate groups in TNP-ATP derivatives decreased the activation efficacy for both RePC and CLPC compared to TNP-ATP. The apparent binding affinity and inhibition of activation of the enzymes by acetyl-CoA were also diminished when the number of phosphate groups in the TNP-ATP derivatives was reduced. Whilst TNP-AMP activated RePC, it did not activate CLPC, but it did inhibit acetyl-CoA activation of both RePC and CLPC. Similarly, TNP-adenosine did not activate RePC; however, it did inhibit acetyl-CoA activation using a different mechanism compared to phosphorylated TNP-derivatives. These findings indicate that mechanisms of PC activation and inhibition of acetyl-CoA activation by TNP-ATP and its derivatives are different. This study provides the basis for possible drug development for treatment of metabolic diseases and cancers with aberrant expression of PC.
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Affiliation(s)
| | - Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand; Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand.
| | - Paul V Attwood
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
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3
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Ohuchi S, Koyama H, Shigehisa H. Catalytic Synthesis of Cyclic Guanidines via Hydrogen Atom Transfer and Radical-Polar Crossover. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shunya Ohuchi
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Koyama
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Hiroki Shigehisa
- Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
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4
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Rattanapornsompong K, Jitrapakdee S, Attwood PV. Characterization of intra- and inter-species hybrid tetramers of pyruvate carboxylase: Biotin and the BCCP domain play a crucial role in determination of the kinetics and thermodynamics of catalysis. Arch Biochem Biophys 2020; 695:108630. [DOI: 10.1016/j.abb.2020.108630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/17/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022]
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5
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Characterization of the kinetics and activation thermodynamics of intra- and inter-organism hybrid tetramers of pyruvate carboxylase. Arch Biochem Biophys 2019; 665:87-95. [DOI: 10.1016/j.abb.2019.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/26/2019] [Indexed: 11/18/2022]
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Westerhold LE, Bridges LC, Shaikh SR, Zeczycki TN. Kinetic and Thermodynamic Analysis of Acetyl-CoA Activation of Staphylococcus aureus Pyruvate Carboxylase. Biochemistry 2017; 56:3492-3506. [PMID: 28617592 DOI: 10.1021/acs.biochem.7b00383] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Allosteric regulation of pyruvate carboxylase (PC) activity is pivotal to maintaining metabolic homeostasis. In contrast, dysregulated PC activity contributes to the pathogenesis of numerous diseases, rendering PC a possible target for allosteric therapeutic development. Recent research efforts have focused on demarcating the role of acetyl-CoA, one of the most potent activators of PC, in coordinating catalytic events within the multifunctional enzyme. Herein, we report a kinetic and thermodynamic analysis of acetyl-CoA activation of the Staphylococcus aureus PC (SaPC)-catalyzed carboxylation of pyruvate to identify novel means by which acetyl-CoA synchronizes catalytic events within the PC tetramer. Kinetic and linked-function analysis, or thermodynamic linkage analysis, indicates that the substrates of the biotin carboxylase and carboxyl transferase domain are energetically coupled in the presence of acetyl-CoA. In contrast, both kinetic and energetic coupling between the two domains is lost in the absence of acetyl-CoA, suggesting a functional role for acetyl-CoA in facilitating the long-range transmission of substrate-induced conformational changes within the PC tetramer. Interestingly, thermodynamic activation parameters for the SaPC-catalyzed carboxylation of pyruvate are largely independent of acetyl-CoA. Our results also reveal the possibility that global conformational changes give rise to observed species-specific thermodynamic activation parameters. Taken together, our kinetic and thermodynamic results provide a possible allosteric mechanism by which acetyl-CoA coordinates catalysis within the PC tetramer.
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Affiliation(s)
- Lauren E Westerhold
- Department of Biochemistry and Molecular Biology and East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Lance C Bridges
- Department of Biochemistry, Molecular and Cell Sciences, Arkansas College of Osteopathic Medicine, Arkansas Colleges of Health Education , Ft. Smith, Arkansas 72916, United States
| | - Saame Raza Shaikh
- Department of Biochemistry and Molecular Biology and East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology and East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
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Abstract
Pyruvate carboxylase is a metabolic enzyme that fuels the tricarboxylic acid cycle with one of its intermediates and also participates in the first step of gluconeogenesis. This large enzyme is multifunctional, and each subunit contains two active sites that catalyze two consecutive reactions that lead to the carboxylation of pyruvate into oxaloacetate, and a binding site for acetyl-CoA, an allosteric regulator of the enzyme. Pyruvate carboxylase oligomers arrange in tetramers and covalently attached biotins mediate the transfer of carboxyl groups between distant active sites. In this chapter, some of the recent findings on pyruvate carboxylase functioning are presented, with special focus on the structural studies of the full length enzyme. The emerging picture reveals large movements of domains that even change the overall quaternary organization of pyruvate carboxylase tetramers during catalysis.
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Affiliation(s)
- Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160, Derio, Spain.
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8
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Sirithanakorn C, Jitrapakdee S, Attwood PV. Investigation of the Roles of Allosteric Domain Arginine, Aspartate, and Glutamate Residues of Rhizobium etli Pyruvate Carboxylase in Relation to Its Activation by Acetyl CoA. Biochemistry 2016; 55:4220-8. [PMID: 27379711 DOI: 10.1021/acs.biochem.6b00548] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of allosteric activation of pyruvate carboxylase by acetyl CoA is not fully understood. Here we have examined the roles of residues near the acetyl CoA binding site in the allosteric activation of Rhizobium etli pyruvate carboxylase using site-directed mutagenesis. Arg429 was found to be especially important for acetyl CoA binding as substitution with serine resulted in a 100-fold increase in the Ka of acetyl CoA activation and a large decrease in the cooperativity of this activation. Asp420 and Arg424, which do not make direct contact with bound acetyl CoA, were nonetheless found to affect acetyl CoA binding when mutated, probably through changed interactions with another acetyl CoA binding residue, Arg427. Thermodynamic activation parameters for the pyruvate carboxylation reaction were determined from modified Arrhenius plots and showed that acetyl CoA acts to decrease the activation free energy of the reaction by both increasing the activation entropy and decreasing the activation enthalpy. Most importantly, mutations of Asp420, Arg424, and Arg429 enhanced the activity of the enzyme in the absence of acetyl CoA. A main focus of this work was the detailed investigation of how this increase in activity occurred in the R424S mutant. This mutation decreased the activation enthalpy of the pyruvate carboxylation reaction by an amount consistent with removal of a single hydrogen bond. It is postulated that Arg424 forms a hydrogen bonding interaction with another residue that stabilizes the asymmetrical conformation of the R. etli pyruvate carboxylase tetramer, constraining its interconversion to the symmetrical conformer that is required for catalysis.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Department of Biochemistry, Faculty of Science, Mahidol University , Bangkok 10400, Thailand
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University , Bangkok 10400, Thailand
| | - Paul V Attwood
- School of Chemistry and Biochemistry, The University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia
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9
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Westerhold LE, Adams SL, Bergman HL, Zeczycki TN. Pyruvate Occupancy in the Carboxyl Transferase Domain of Pyruvate Carboxylase Facilitates Product Release from the Biotin Carboxylase Domain through an Intermolecular Mechanism. Biochemistry 2016; 55:3447-60. [PMID: 27254467 DOI: 10.1021/acs.biochem.6b00372] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein structure, ligand binding, and catalytic turnover contributes to the governance of catalytic events occurring at spatially distinct domains in multifunctional enzymes. Coordination of these catalytic events partially rests on the ability of spatially discrete active sites to communicate with other allosteric and active sites on the same polypeptide chain (intramolecular) or on different polypeptide chains (intermolecular) within the holoenzyme. Often, communication results in long-range effects on substrate binding or product release. For example, pyruvate binding to the carboxyl transferase (CT) domain of pyruvate carboxylase (PC) increases the rate of product release in the biotin carboxylase (BC) domain. In order to address how CT domain ligand occupancy is "sensed" by other domains, we generated functional, mixed hybrid tetramers using the E218A (inactive BC domain) and T882S (low pyruvate binding, low activity) mutant forms of PC. The apparent Ka pyruvate for the pyruvate-stimulated release of Pi catalyzed by the T882S:E218A[1:1] hybrid tetramer was comparable to the wild-type enzyme and nearly 10-fold lower than that for the T882S homotetramer. In addition, the ratio of the rates of oxaloacetate formation to Pi release for the WT:T882S[1:1] and E218A:T882S[1:1] hybrid tetramer-catalyzed reactions was 0.5 and 0.6, respectively, while the T882S homotetramer exhibited a near 1:1 coupling of the two domains, suggesting that the mechanisms coordinating catalytic events is more complicated that we initially assumed. The results presented here are consistent with an intermolecular communication mechanism, where pyruvate binding to the CT domain is "sensed" by domains on a different polypeptide chain within the tetramer.
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Affiliation(s)
- Lauren E Westerhold
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Stephanie L Adams
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Hanna L Bergman
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology and the ‡East Carolina Diabetes and Obesity Institute, Brody School of Medicine at East Carolina University , Greenville, North Carolina 27834, United States
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10
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Choosangtong K, Sirithanakorn C, Adina-Zada A, Wallace JC, Jitrapakdee S, Attwood PV. Residues in the acetyl CoA binding site of pyruvate carboxylase involved in allosteric regulation. FEBS Lett 2015; 589:2073-9. [PMID: 26149215 DOI: 10.1016/j.febslet.2015.06.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
We have examined the roles of Asp1018, Glu1027, Arg469 and Asp471 in the allosteric domain of Rhizobium etli pyruvate carboxylase. Arg469 and Asp471 interact directly with the allosteric activator acetyl coenzyme A (acetyl CoA) and the R469S and R469K mutants showed increased enzymic activity in the presence and absence of acetyl CoA, whilst the D471A mutant exhibited no acetyl CoA-activation. E1027A, E1027R and D1018A mutants had increased activity in the absence of acetyl CoA, but not in its presence. These results suggest that most of these residues impose restrictions on the structure and/or dynamics of the enzyme to affect activity.
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Affiliation(s)
- Kamonman Choosangtong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Chaiyos Sirithanakorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Abdul Adina-Zada
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - John C Wallace
- School of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Sarawut Jitrapakdee
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
| | - Paul V Attwood
- School of Chemistry and Biochemistry, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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Sirithanakorn C, Adina-Zada A, Wallace JC, Jitrapakdee S, Attwood PV. Mechanisms of inhibition of Rhizobium etli pyruvate carboxylase by L-aspartate. Biochemistry 2014; 53:7100-6. [PMID: 25330457 PMCID: PMC4238798 DOI: 10.1021/bi501113u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
L-aspartate is a regulatory feedback inhibitor of the biotin-dependent enzyme pyruvate carboxylase in response to increased levels of tricarboxylic acid cycle intermediates. Detailed studies of L-aspartate inhibition of pyruvate carboxylase have been mainly confined to eukaryotic microbial enzymes, and aspects of its mode of action remain unclear. Here we examine its inhibition of the bacterial enzyme Rhizobium etli pyruvate carboxylase. Kinetic studies demonstrated that L-aspartate binds to the enzyme cooperatively and inhibits the enzyme competitively with respect to acetyl-CoA. L-aspartate also inhibits activation of the enzyme by MgTNP-ATP. The action of L-aspartate was not confined to inhibition of acetyl-CoA binding, because the acetyl-CoA-independent activity of the enzyme was also inhibited by increasing concentrations of L-aspartate. This inhibition of acetyl-CoA-independent activity was demonstrated to be focused in the biotin carboxylation domain of the enzyme, and it had no effect on the oxamate-induced oxaloacetate decarboxylation reaction that occurs in the carboxyl transferase domain. L-aspartate was shown to competitively inhibit bicarbonate-dependent MgATP cleavage with respect to MgATP but also probably inhibits carboxybiotin formation and/or translocation of the carboxybiotin to the site of pyruvate carboxylation. Unlike acetyl-CoA, L-aspartate has no effect on the coupling between MgATP cleavage and oxaloacetate formation. The results suggest that the three allosteric effector sites (acetyl-CoA, MgTNP-ATP, and L-aspartate) are spatially distinct but connected by a network of allosteric interactions.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Department of Biochemistry, Faculty of Science, Mahidol University , Bangkok 10400, Thailand
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12
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Lietzan AD, St Maurice M. A substrate-induced biotin binding pocket in the carboxyltransferase domain of pyruvate carboxylase. J Biol Chem 2013; 288:19915-25. [PMID: 23698000 DOI: 10.1074/jbc.m113.477828] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Biotin-dependent enzymes catalyze carboxyl transfer reactions by efficiently coordinating multiple reactions between spatially distinct active sites. Pyruvate carboxylase (PC), a multifunctional biotin-dependent enzyme, catalyzes the bicarbonate- and MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To complete the overall reaction, the tethered biotin prosthetic group must first gain access to the biotin carboxylase domain and become carboxylated and then translocate to the carboxyltransferase domain, where the carboxyl group is transferred from biotin to pyruvate. Here, we report structural and kinetic evidence for the formation of a substrate-induced biotin binding pocket in the carboxyltransferase domain of PC from Rhizobium etli. Structures of the carboxyltransferase domain reveal that R. etli PC occupies a symmetrical conformation in the absence of the biotin carboxylase domain and that the carboxyltransferase domain active site is conformationally rearranged upon pyruvate binding. This conformational change is stabilized by the interaction of the conserved residues Asp(590) and Tyr(628) and results in the formation of the biotin binding pocket. Site-directed mutations at these residues reduce the rate of biotin-dependent reactions but have no effect on the rate of biotin-independent oxaloacetate decarboxylation. Given the conservation with carboxyltransferase domains in oxaloacetate decarboxylase and transcarboxylase, the structure-based mechanism described for PC may be applicable to the larger family of biotin-dependent enzymes.
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Affiliation(s)
- Adam D Lietzan
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
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