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Minnow YVT, Suthagar K, Clinch K, Ducati RG, Ghosh A, Buckler JN, Harijan RK, Cahill SM, Tyler PC, Schramm VL. Inhibition and Mechanism of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase. ACS Chem Biol 2022; 17:3407-3419. [PMID: 36413975 PMCID: PMC9772100 DOI: 10.1021/acschembio.2c00546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPRT) is essential for purine salvage of hypoxanthine into parasite purine nucleotides. Transition state analogue inhibitors of PfHGXPRT are characterized by kinetic analysis, thermodynamic parameters, and X-ray crystal structures. Compound 1, 9-deazaguanine linked to an acyclic ribocation phosphonate mimic, shows a kinetic Ki of 0.5 nM. Isothermal titration calorimetry (ITC) experiments of 1 binding to PfHGXPRT reveal enthalpically driven binding with negative cooperativity for the binding of two inhibitor molecules in the tetrameric enzyme. Crystal structures of 1 bound to PfHGXPRT define the hydrogen bond and ionic contacts to complement binding thermodynamics. Dynamics of ribosyl transfer from 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) to hypoxanthine were examined by 18O isotope exchange at the bridging phosphoryl oxygen of PRPP pyrophosphate. Rotational constraints or short transition state lifetimes prevent torsional rotation and positional isotope exchange of bridging to nonbridging oxygen in the α-pyrophosphoryl group. Thermodynamic analysis of the transition state analogue and magnesium pyrophosphate binding reveal random and cooperative binding to PfHGXPRT, unlike the obligatory ordered reaction kinetics reported earlier for substrate kinetics.
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Affiliation(s)
- Yacoba V. T. Minnow
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Kajitha Suthagar
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5010, New Zealand
| | - Keith Clinch
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5010, New Zealand
| | - Rodrigo G. Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Joshua N. Buckler
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5010, New Zealand
| | - Rajesh K. Harijan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Sean M. Cahill
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Peter C. Tyler
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt 5010, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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Vithani N, Ankush Jagtap PK, Verma SK, Tripathi R, Awasthi S, Nair NN, Prakash B. Mechanism of Mg 2+-Accompanied Product Release in Sugar Nucleotidyltransferases. Structure 2019. [PMID: 29514078 DOI: 10.1016/j.str.2018.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg2+ ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the "slow" conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg2+, and propose a general mechanism of product release during the nucleotidyl transfer by SNTs.
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Affiliation(s)
- Neha Vithani
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Pravin Kumar Ankush Jagtap
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Sunil Kumar Verma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Shalini Awasthi
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India.
| | - Balaji Prakash
- Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore 570020, India.
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Pu Z, Zhao M, Zhang Y, Sun W, Bao Y. Dynamic Description of the Catalytic Cycle of Malate Enzyme: Stereoselective Recognition of Substrate, Chemical Reaction, and Ligand Release. J Phys Chem B 2018; 122:12241-12250. [PMID: 30500201 DOI: 10.1021/acs.jpcb.8b05135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In protein engineering, investigations of catalytic cycle facilitate rational design of enzymes. In the present work, deeper analysis on the catalytic cycle of malate enzyme (EC 1.1.1.40), an enzyme involved in cancer metabolic and fatty acid synthesis, was performed. In substrate binding, stereoselective recognition of a substrate originates from distance and angle difference between two chiral substrates and Mn2+ as well as monodentate or coplanar ion reaction with Arg165. In catalytic transformation, the activation barrier for the hydride transfer of d-malate is 20.28 kcal/mol higher than that for l-malate. The activation barrier for β-decarboxylation of oxaloacetate is about 4.59 kcal/mol higher than the activation barrier for the hydride transfer of l-malate. The effective activation barrier is 16.44 kcal/mol, which is in close agreement with the value derived from the application of transition-state theory and the Eyring equation to kcat. In ligand release, l/d-malate needs to overcome a higher barrier than pyruvate to break all bonds in parallel and then to escape from the binding pocket. Leu167 and Asn421 comprise a swinging gate to control the product release. The more open gate is possibly required in the direction of pyruvate to l-malate. Our studies are focused on extending structural knowledge regarding the malate enzyme and provided a powerful strategy for future experimental investigations.
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Affiliation(s)
- Zhongji Pu
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Mengdi Zhao
- Department of Nanoenergy Engineering , Pusan National University , Busan 46241 , Republic of Korea
| | - Yue Zhang
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Wenhui Sun
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Yongming Bao
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China.,School of Food and Environment Science and Engineering , Dalian University of Technology , Panjin 124221 , China
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Karmakar T, Balasubramanian S. Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO 2 Release from AMDase and Its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter. J Phys Chem B 2016; 120:11644-11653. [PMID: 27775347 DOI: 10.1021/acs.jpcb.6b07034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules phenylacetate (PAC) and carbon dioxide (CO2), from the wild-type (WT) and its G74C/C188S mutant enzymes. Both of the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior. A higher free energy barrier for the release of PAC from G74C/C188S compared to that in the WT is consistent with the experimentally observed compromised efficiency of the mutant. The release of CO2 precedes that of PAC; free energy barriers for CO2 and PAC release in the WT enzyme are calculated to be ∼1-2 and ∼23 kcal/mol, respectively. Postdecarboxylation, CO2 moves toward a hydrophobic pocket formed by Pro 14, Leu 38, Leu 40, Leu 77, and the side chain of Tyr 48 which serves as its temporary "reservoir". CO2 releases following a channel mainly decorated by apolar residues, unlike in the case of oxalate decarboxylase where polar residues mediate its transport.
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Affiliation(s)
- Tarak Karmakar
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
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