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Corbella M, Bravo J, Demkiv AO, Calixto AR, Sompiyachoke K, Bergonzi C, Elias MH, Kamerlin SCL. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592096. [PMID: 38746346 PMCID: PMC11092605 DOI: 10.1101/2024.05.01.592096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.
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Sun T, Wang M, Liang W, Gao P, Liu Q, Yan X. Revealing mechanism of Methazolamide for treatment of ankylosing spondylitis based on network pharmacology and GSEA. Sci Rep 2023; 13:15370. [PMID: 37717047 PMCID: PMC10505193 DOI: 10.1038/s41598-023-42721-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/14/2023] [Indexed: 09/18/2023] Open
Abstract
Methazolamide is a carbonic anhydrase (CA) inhibitor with satisfactory safety. Our previous studies have demonstrated the elevation of CA1 expression and the therapeutic effect of Methazolamide in Ankylosing spondylitis (AS). In this study, we explored the pathogenic role of CA1 and the pharmacological mechanism of Methazolamide in AS through Gene Set Enrichment Analysis (GSEA) and network pharmacology. Seven out of twelve CA1 related gene sets were enriched in AS group. CA1 was core enriched in above seven gene sets involving zinc ion binding, arylesterase activity and one carbon metabolic process. Functional analysis of the candidate target genes obtained from the intersection of AS associated genes and Methazolamide target genes indicated that Methazolamide exerts therapeutic effects on AS mainly through inflammatory pathways which regulate the production of tumor necrosis factor, IL-6 and nitric oxide. PTGS2, ESR1, GSK3β, JAK2, NOS2 and CA1 were selected as therapeutic targets of Methazolamide in AS. Molecular docking and molecular dynamics simulations were performed successfully. In addition, we innovatively obtained the intersection of Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and GSEA results, and found that 18 GO terms and 5 KEGG terms were indicated in the pharmacological mechanism of Methazolamide in AS, involving bone mineralization, angiogenesis, inflammation, and chemokine signaling pathways. Nevertheless, validation for these mechanisms is needed in vivo/vitro experiments.
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Affiliation(s)
- Tao Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China
| | - Manzhi Wang
- Department of Hematology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
| | - Weiqiang Liang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China
| | - Ping Gao
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China
| | - Qiang Liu
- Department of Cardiology, Shandong Medicine and Health Key Laboratory of Cardiac Electrophysiology and Arrhythmia, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Xinfeng Yan
- Department of Orthopedic Surgery, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China.
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3
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NMR Properties of the Cyanide Anion, a Quasisymmetric Two-Faced Hydrogen Bonding Acceptor. Symmetry (Basel) 2021. [DOI: 10.3390/sym13071298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The isotopically enriched cyanide anion, (13C≡15N)−, has a great potential as the NMR probe of non-covalent interactions. However, hydrogen cyanide is highly toxic and can decompose explosively. It is therefore desirable to be able to theoretically estimate any valuable results of certain experiments in advance in order to carry out experimental studies only for the most suitable molecular systems. We report the effect of hydrogen bonding on NMR properties of 15N≡13CH···X and 13C≡15NH···X hydrogen bonding complexes in solution, where X = 19F, 15N, and O=31P, calculated at the ωB97XD/def2tzvp and the polarizable continuum model (PCM) approximations. In many cases, the isotropic 13C and 15N chemical shieldings of the cyanide anion are not the most informative NMR properties of such complexes. Instead, the anisotropy of these chemical shieldings and the values of scalar coupling constants, including those across hydrogen bonds, can be used to characterize the geometry of such complexes in solids and solutions. 1J(15N13C) strongly correlates with the length of the N≡C bond.
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Yang L, Lu Y, Tian W, Feng Y, Bai J, Zhang H. Insights into the functional divergence of the haloacid dehalogenase superfamily from phosphomonoesterase to inorganic pyrophosphatase. Arch Biochem Biophys 2021; 705:108896. [PMID: 33940035 DOI: 10.1016/j.abb.2021.108896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 11/20/2022]
Abstract
The evolution of enzyme catalytic structures and mechanisms has drawn increasing attention. In this study, we investigate the functional divergence from phosphomonoesterase to inorganic pyrophosphatase in the haloacid dehalogenase (HAD) superfamily. In this study, a series of models was constructed, and calculations were performed by using density functional theory with the B3LYP functional. The calculations suggest that in most HAD members, the active-site structure is unstable due to the binding of the substrate inorganic pyrophosphate (PPi), and reactions involving PPi cannot be catalyzed. In BT2127, which is a unique member of the HAD superfamily, the Mg2+-coordinating residues Asn172 and Glu47 play a role in stabilizing the active-site structure to adapt to the substrate PPi by providing much stronger coordination interactions with the Mg2+ ion. The calculation results suggest that Asn172 and Glu47 are crucial in the evolution of the inorganic pyrophosphatase activity in the HAD superfamily. Our study provides definitive chemical insight into the functional divergence of the HAD superfamily, and helps in understanding the evolution of enzyme catalytic structures and mechanisms.
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Affiliation(s)
- Ling Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, Institute of Theoretical and Simulation Chemistry, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, PR China
| | - Yajie Lu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, Institute of Theoretical and Simulation Chemistry, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, PR China
| | - Weiquan Tian
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Chongqing University, Huxi Campus, Chongqing 401331, PR China
| | - Yulan Feng
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, PR China
| | - Jialin Bai
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, PR China
| | - Hao Zhang
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, PR China.
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5
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Wang L, Yang L, Feng YL, Zhang H. Evolutionary insights into the active-site structures of the metallo-β-lactamase superfamily from a classification study with support vector machine. J Biol Inorg Chem 2020; 25:1023-1034. [PMID: 32945939 DOI: 10.1007/s00775-020-01822-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/05/2020] [Indexed: 12/01/2022]
Abstract
The metallo-β-lactamase (MβL) superfamily, which is intriguing due to its enzyme promiscuity, is a good model enzyme superfamily for studies of catalytic function evolution. Our previous study traced the evolution of the phosphotriesterase activity of the MβL superfamily and found that MβLs go through three typical active-site structures in the development of phosphotriesterase activity. In the present study, taking the three typical active-site structures as class labels, the classification and prediction models, which were established by support vector machine and amino acid composition, classified the MβL members into three classes. The indispensable amino acid compositions showed a surprising performance that was remarkably better than the performance of the dispensable amino acid compositions and even equal to the performance of the 20 native amino acids. We further traced the origin of the classification error and found that there was one subclass adopting a type of active-site structure that was the evolutionary transition between these classes. After that, our classification and prediction models were successfully used to predict several MβL active-site structures that lost the dinuclear structures during crystallization. In summary, our studies established a classification and prediction system for active-site structures that well compensated for experimental methods that recognize protein structure details and suggest that the indispensable amino acids contain much more protein structure information than the dispensable amino acids.
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Affiliation(s)
- Lili Wang
- College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou, 730070, People's Republic of China
| | - Ling Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, Institute of Theoretical and Simulation Chemistry, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150080, People's Republic of China
| | - Yu-Lan Feng
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, People's Republic of China
| | - Hao Zhang
- Biomedical Research Center, College of Life Science and Engineering, Northwest Minzu University, Lanzhou, 730030, People's Republic of China.
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6
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Shenderovich IG, Denisov GS. Solvent effects on acid-base complexes. What is more important: A macroscopic reaction field or solute-solvent interactions? J Chem Phys 2019; 150:204505. [PMID: 31153188 DOI: 10.1063/1.5096946] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Can the geometry of an acid-base complex in solution be reproduced in calculations using an implicit accounting for the solvent effect in the form of a macroscopic reaction field? The answer is, "Yes, it can." Is this field equal to the real electric field experienced by the complex in solution? The answer is, "No, it is not." How can the geometry be correct under wrong conditions? This question is answered using density functional theory modeling of geometric and NMR parameters of pyridine⋯HF⋯(HCF3)n adducts in the absence and presence of an external electric field. This adduct under field approach shows that the N⋯H distance is a function of the H-F distance whatever method is used to change the geometry of the latter. An explicit account for solute-solvent interactions is required to get a realistic value of the solvent reaction field. Besides that, this approach reveals how certain NMR parameters depend on the solvent reaction field, the solute-solvent interactions, and the geometry of the N⋯H-F hydrogen bond. For some of them, the obtained dependences are far from self-evident.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
| | - Gleb S Denisov
- Department of Physics, St.Petersburg State University, Saint Petersburg, Russia
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7
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP. Molecules 2018; 23:molecules23071660. [PMID: 29986514 PMCID: PMC6100192 DOI: 10.3390/molecules23071660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022] Open
Abstract
The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca2+ ion indirectly connecting the buried structural Ca2+ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective.
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9
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Zhang H, Yang L, Ding W, Ma Y. Theoretical Studies on the Catalytic Cycle of Histidine Acid Phosphatases Revealing an Acid Proof Mechanism. J Phys Chem B 2018; 122:7530-7538. [DOI: 10.1021/acs.jpcb.8b04808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, P. R. China
| | - Ling Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Wanjian Ding
- College of Chemistry, Beijing Normal University, Beijing 100086, P. R. China
| | - Yingying Ma
- Institute of Mining Technology, Inner Mongolia University of Technology. Hohhot 010051, P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation. Hohhot 010051, P. R. China
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10
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Zhang H, Yang L, Yan LF, Liao RZ, Tian WQ. Evolution of phosphotriesterase activities of the metallo-β-lactamase family: A theoretical study. J Inorg Biochem 2018; 184:8-14. [DOI: 10.1016/j.jinorgbio.2018.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
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11
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Shenderovich IG. Simplified calculation approaches designed to reproduce the geometry of hydrogen bonds in molecular complexes in aprotic solvents. J Chem Phys 2018; 148:124313. [PMID: 29604820 DOI: 10.1063/1.5011163] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The impact of the environment onto the geometry of hydrogen bonds can be critically important for the properties of the questioned molecular system. The paper reports on the design of calculation approaches capable to simulate the effect of aprotic polar solvents on the geometric and NMR parameters of intermolecular hydrogen bonds. A hydrogen fluoride and pyridine complex has been used as the main model system because the experimental estimates of these parameters are available for it. Specifically, F-H, F⋯N, and H-N distances, the values of 15N NMR shift, and spin-spin coupling constants 1J(19F1H), 1hJ(1H15N), and 2hJ(19F15N) have been analyzed. Calculation approaches based on the gas-phase and the Polarizable Continuum Model (PCM) approximations and their combinations with geometric constraints and additional noncovalent interactions have been probed. The main result of this work is that the effect of an aprotic polar solvent on the geometry of a proton-donor⋯H⋯proton-acceptor complex cannot be reproduced under the PCM approximation if no correction for solvent-solute interactions is made. These interactions can be implicitly accounted for using a simple computational protocol.
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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12
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Purg M, Pabis A, Baier F, Tokuriki N, Jackson C, Kamerlin SCL. Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0150. [PMID: 27698033 PMCID: PMC5052733 DOI: 10.1098/rsta.2016.0150] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 05/27/2023]
Abstract
Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal-metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Miha Purg
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
| | - Florian Baier
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, Canada V6T 1Z4
| | - Colin Jackson
- Research School of Chemistry, Building 138, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, Uppsala 75124, Sweden
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13
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Campbell E, Kaltenbach M, Correy GJ, Carr PD, Porebski BT, Livingstone EK, Afriat-Jurnou L, Buckle AM, Weik M, Hollfelder F, Tokuriki N, Jackson CJ. The role of protein dynamics in the evolution of new enzyme function. Nat Chem Biol 2016; 12:944-950. [PMID: 27618189 DOI: 10.1038/nchembio.2175] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022]
Abstract
Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.
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Affiliation(s)
- Eleanor Campbell
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Miriam Kaltenbach
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Galen J Correy
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Paul D Carr
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Benjamin T Porebski
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Emma K Livingstone
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Livnat Afriat-Jurnou
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Ashley M Buckle
- Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Martin Weik
- Institut de Biologie Structurale, University Grenoble Alpes, Commissariat à l'Energie Atomique and Centre National de la Recherche Scientifique, Grenoble, France
| | | | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
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14
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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15
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Pabis A, Kamerlin SCL. Promiscuity and electrostatic flexibility in the alkaline phosphatase superfamily. Curr Opin Struct Biol 2015; 37:14-21. [PMID: 26716576 DOI: 10.1016/j.sbi.2015.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 12/17/2022]
Abstract
Catalytic promiscuity, that is, the ability of single enzymes to facilitate the turnover of multiple, chemically distinct substrates, is a widespread phenomenon that plays an important role in the evolution of enzyme function. Additionally, such pre-existing multifunctionality can be harnessed in artificial enzyme design. The members of the alkaline phosphatase superfamily have served extensively as both experimental and computational model systems for enhancing our understanding of catalytic promiscuity. In this Opinion, we present key recent computational studies into the catalytic activity of these highly promiscuous enzymes, highlighting the valuable insight they have provided into both the molecular basis for catalytic promiscuity in general, and its implications for the evolution of phosphatase activity.
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Affiliation(s)
- Anna Pabis
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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16
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Bordes I, Ruiz-Pernía JJ, Castillo R, Moliner V. A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution. Org Biomol Chem 2015; 13:10179-90. [PMID: 26303076 DOI: 10.1039/c5ob01079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone kinase enzyme. In this paper the reference uncatalyzed reaction in solution has been studied in order to define the foundations of the chemical reaction and to determine the most adequate computational method to describe this electronically complex reaction. In particular, the phosphorylation reaction mechanism between adenosine triphosphate (ATP) and Dha in aqueous solution has been studied by means of quantum mechanics/molecular mechanics (QM/MM) Molecular Dynamics (MD) simulations with the QM subset of atoms described with semi-empirical and DFT methods. The results appear to be strongly dependent on the level of calculation, which will have to be taken into account for future studies of the reaction catalyzed by enzymes. In particular, PM3/MM renders lower free energy barriers and a less endergonic process than AM1d/MM and PM6/MM methods. Nevertheless, the concerted pathway was not located with the former combination of potentials.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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