1
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Sato S, Fan PH, Yeh YC, Liu HW. Complete In Vitro Reconstitution of the Apramycin Biosynthetic Pathway Demonstrates the Unusual Incorporation of a β-d-Sugar Nucleotide in the Final Glycosylation Step. J Am Chem Soc 2024; 146:10103-10114. [PMID: 38546392 DOI: 10.1021/jacs.4c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Apramycin is a widely used aminoglycoside antibiotic with applications in veterinary medicine. It is composed of a 4-amino-4-deoxy-d-glucose moiety and the pseudodisaccharide aprosamine, which is an adduct of 2-deoxystreptamine and an unusual eight-carbon bicyclic dialdose. Despite its extensive study and relevance to medical practice, the biosynthetic pathway of this complex aminoglycoside nevertheless remains incomplete. Herein, the remaining unknown steps of apramycin biosynthesis are reconstituted in vitro, thereby leading to a comprehensive picture of its biological assembly. In particular, phosphomutase AprJ and nucleotide transferase AprK are found to catalyze the conversion of glucose 6-phosphate to NDP-β-d-glucose as a critical biosynthetic intermediate. Moreover, the dehydrogenase AprD5 and transaminase AprL are identified as modifying this intermediate via introduction of an amino group at the 4″ position without requiring prior 6″-deoxygenation as is typically encountered in aminosugar biosynthesis. Finally, the glycoside hydrolase family 65 protein AprO is shown to utilize NDP-β-d-glucose or NDP-4"-amino-4"-deoxy-β-d-glucose to form the 8',1″-O-glycosidic linkage of saccharocin or apramycin, respectively. As the activated sugar nucleotides in all known natural glycosylation reactions involve either NDP-α-d-hexoses or NDP-β-l-hexoses, the reported chemistry expands the scope of known biological glycosylation reactions to NDP-β-d-hexoses, with important implications for the understanding and repurposing of aminoglycoside biosynthesis.
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2
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Singh L, Karthikeyan S, Thakur KG. Biochemical and structural characterization reveals Rv3400 codes for β-phosphoglucomutase in Mycobacterium tuberculosis. Protein Sci 2024; 33:e4943. [PMID: 38501428 PMCID: PMC10949319 DOI: 10.1002/pro.4943] [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: 08/25/2023] [Revised: 01/22/2024] [Accepted: 02/11/2024] [Indexed: 03/20/2024]
Abstract
Mycobacterium tuberculosis (Mtb) adapt to various host environments and utilize a variety of sugars and lipids as carbon sources. Among these sugars, maltose and trehalose, also play crucial role in bacterial physiology and virulence. However, some key enzymes involved in trehalose and maltose metabolism in Mtb are not yet known. Here we structurally and functionally characterized a conserved hypothetical gene Rv3400. We determined the crystal structure of Rv3400 at 1.7 Å resolution. The crystal structure revealed that Rv3400 adopts Rossmann fold and shares high structural similarity with haloacid dehalogenase family of proteins. Our comparative structural analysis suggested that Rv3400 could perform either phosphatase or pyrophosphatase or β-phosphoglucomutase (β-PGM) activity. Using biochemical studies, we further confirmed that Rv3400 performs β-PGM activity and hence, Rv3400 encodes for β-PGM in Mtb. Our data also confirm that Mtb β-PGM is a metal dependent enzyme having broad specificity for divalent metal ions. β-PGM converts β-D-glucose-1-phosphate to β-D-glucose-6-phosphate which is required for the generation of ATP and NADPH through glycolysis and pentose phosphate pathway, respectively. Using site directed mutagenesis followed by biochemical studies, we show that two Asp residues in the highly conserved DxD motif, D29 and D31, are crucial for enzyme activity. While D29A, D31A, D29E, D31E and D29N mutants lost complete activity, D31N mutant retained about 30% activity. This study further helps in understanding the role of β-PGM in the physiology of Mtb.
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Affiliation(s)
- Latika Singh
- Division of Protein Science and EngineeringCouncil of Scientific and Industrial Research—Institute of Microbial Technology (CSIR‐IMTECH)ChandigarhIndia
| | - Subramanian Karthikeyan
- Division of Protein Science and EngineeringCouncil of Scientific and Industrial Research—Institute of Microbial Technology (CSIR‐IMTECH)ChandigarhIndia
| | - Krishan Gopal Thakur
- Division of Protein Science and EngineeringCouncil of Scientific and Industrial Research—Institute of Microbial Technology (CSIR‐IMTECH)ChandigarhIndia
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3
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Baumann P, Jin Y. Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3- complexes. Commun Chem 2024; 7:19. [PMID: 38297137 PMCID: PMC10830474 DOI: 10.1038/s42004-024-01105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Tyrosine phosphorylation on Ras by Src kinase is known to uncouple Ras from upstream regulation and downstream communication. However, the mechanisms by which phosphorylation modulates these interactions have not been detailed. Here, the major mono-phosphorylation level on tyrosine64 is quantified by 31P NMR and mutagenesis. Crystal structures of unphosphorylated and tyrosine64-phosphorylated Ras in complex with a BeF3- ground state analogue reveal "closed" Ras conformations very different from those of the "open" conformations previously observed for non-hydrolysable GTP analogue structures of Ras. They deliver new mechanistic and conformational insights into intrinsic GTP hydrolysis. Phosphorylation of tyrosine64 delivers conformational changes distant from the active site, showing why phosphorylated Ras has reduced affinity to its downstream effector Raf. 19F NMR provides evidence for changes in the intrinsic GTPase and nucleotide exchange rate and identifies the concurrent presence of a major "closed" conformation alongside a minor yet functionally important "open" conformation at the ground state of Ras. This study expands the application of metal fluoride complexes in revealing major and minor conformational changes of dynamic and modified Ras proteins.
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Affiliation(s)
- Patrick Baumann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yi Jin
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, University of Manchester, M13 9PL, Manchester, UK.
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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4
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Santos MC, Botelho FD, Gonçalves AS, Kitagawa DAS, Borges CVN, Carvalho-Silva T, Bernardo LB, Ferreira CN, Rodrigues RB, Ferreira Neto DC, Nepovimova E, Kuča K, LaPlante SR, Lima ALS, França TCC, Cavalcante SFA. Are the current commercially available oximes capable of reactivating acetylcholinesterase inhibited by the nerve agents of the A-series? Arch Toxicol 2022; 96:2559-2572. [PMID: 35666269 DOI: 10.1007/s00204-022-03316-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022]
Abstract
The misuse of novichok agents in assassination attempts has been reported in the international media since 2018. These relatively new class of neurotoxic agents is claimed to be more toxic than the agents of the G and V series and so far, there is no report yet in literature about potential antidotes against them. To shed some light into this issue, we report here the design and synthesis of NTMGMP, a surrogate of A-242 and also the first surrogate of a novichok agent useful for experimental evaluation of antidotes. Furthermore, the efficiency of the current commercial oximes to reactivate NTMGMP-inhibited acetylcholinesterase (AChE) was evaluated. The Ellman test was used to confirm the complete inhibition of AChE, and to compare the subsequent rates of reactivation in vitro as well as to evaluate aging. In parallel, molecular docking, molecular dynamics and MM-PBSA studies were performed on a computational model of the human AChE (HssAChE)/NTMGMP complex to assess the reactivation performances of the commercial oximes in silico. Experimental and theoretical studies matched the exact hierarchy of efficiency and pointed to trimedoxime as the most promising commercial oxime for reactivation of AChE inhibited by A-242.
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Affiliation(s)
- Marcelo C Santos
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Fernanda D Botelho
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Arlan S Gonçalves
- Federal Institute of Education, Science and Technology of Espírito Santo - Units Vila Velha and Vitória, Vitória, ES, Brazil.,Federal University of Espírito Santo, Unit Goiabeiras, Vitória, ES, Brazil
| | - Daniel A S Kitagawa
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Caio V N Borges
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Taynara Carvalho-Silva
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Leandro B Bernardo
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil.,Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Cíntia N Ferreira
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Rafael B Rodrigues
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil
| | - Denise C Ferreira Neto
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Eugenie Nepovimova
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Kamil Kuča
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada
| | - Antonio L S Lima
- Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Tanos C C França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil. .,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic. .,Université de Québec, INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, H7V 1B7, Canada.
| | - Samir F A Cavalcante
- Institute of Chemical, Biological, Radiological and Nuclear Defense (IDQBRN), Brazilian Army Technological Center (CTEx), Rio de Janeiro, Brazil. .,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.
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5
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Theoretical assessment of the performances of commercial oximes on the reactivation of acetylcholinesterase inhibited by the nerve agent A-242 (novichok). Food Chem Toxicol 2022; 165:113084. [PMID: 35489467 DOI: 10.1016/j.fct.2022.113084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/24/2022] [Indexed: 01/19/2023]
Abstract
The nerve agents of the A-series are relatively recent chemical weapons with no antidote available yet. Once inside the human body, those chemicals act similarly to the classic nerve agents, by binding to the catalytic residue Serine 203 (Ser203) of human acetylcholinesterase (HssAChE) and thus preventing the proper function of this enzyme. However, there is no experimental evidence yet if the current antidotes for intoxication by nerve agents are also capable of restoring AChE inhibited by the nerve agents of the A-series. In order to launch some light on this issue, we used computational techniques (molecular docking, molecular dynamics and MM-PBSA interaction energy calculations) to assess the performances of the four currently available commercial oximes (2-PAM, HI-6, obidoxime and trimedoxime) when in contact with HssAChE inhibited by the agent A-242. Based on the near-attack conformation (NAC) criterion, our results suggest that the commercial oximes would have limited efficacy to reactivate the enzyme since they are not able to properly approach the adduct Ser203-A-242. Among those oximes, trimedoxime seems to be the most promising, since it showed lower values of energy in the MM-PBSA calculations, a higher stability inside the catalytic anionic center (CAS) of HssAChE, and was able to adopt a position closer to the NAC that could enable the reactivation mechanism.
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6
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Pfeiffer M, Crean RM, Moreira C, Parracino A, Oberdorfer G, Brecker L, Hammerschmidt F, Kamerlin SCL, Nidetzky B. Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase. ACS Catal 2022; 12:3357-3370. [PMID: 35356705 PMCID: PMC8938923 DOI: 10.1021/acscatal.1c05656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/31/2022] [Indexed: 01/15/2023]
Abstract
![]()
The cooperative interplay
between the functional devices of a preorganized
active site is fundamental to enzyme catalysis. An in-depth understanding
of this phenomenon is central to elucidating the remarkable efficiency
of natural enzymes and provides an essential benchmark for enzyme
design and engineering. Here, we study the functional interconnectedness
of the catalytic nucleophile (His18) in an acid phosphatase by analyzing
the consequences of its replacement with aspartate. We present crystallographic,
biochemical, and computational evidence for a conserved mechanistic
pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy
relationships for phosphoryl transfer from phosphomonoester substrates
to His18/Asp18 provide evidence for the cooperative interplay between
the nucleophilic and general-acid catalytic groups in the wild-type
enzyme, and its substantial loss in the H18D variant. As an isolated
factor of phosphatase efficiency, the advantage of a histidine compared
to an aspartate nucleophile is ∼104-fold. Cooperativity
with the catalytic acid adds ≥102-fold to that advantage.
Empirical valence bond simulations of phosphoryl transfer from glucose
1-phosphate to His and Asp in the enzyme explain the loss of activity
of the Asp18 enzyme through a combination of impaired substrate positioning
in the Michaelis complex, as well as a shift from early to late protonation
of the leaving group in the H18D variant. The evidence presented furthermore
suggests that the cooperative nature of catalysis distinguishes the
enzymatic reaction from the corresponding reaction in solution and
is enabled by the electrostatic preorganization of the active site.
Our results reveal sophisticated discrimination in multifunctional
catalysis of a highly proficient phosphatase active site.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Rory M Crean
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Catia Moreira
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Antonietta Parracino
- Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Petersgasse 12/II, 8010 Graz, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Department of Organic Chemistry, University of Vienna, Währingerstraße 38, 1090 Vienna, Austria
| | | | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12/I, 8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
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7
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Robertson AJ, Cruz-Navarrete FA, Wood HP, Vekaria N, Hounslow AM, Bisson C, Cliff MJ, Baxter NJ, Waltho JP. An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition. ACS Catal 2022; 12:3149-3164. [PMID: 35692864 PMCID: PMC9171722 DOI: 10.1021/acscatal.1c05524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/10/2022] [Indexed: 02/05/2023]
Abstract
Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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Affiliation(s)
- Angus J. Robertson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Henry P. Wood
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Nikita Vekaria
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrea M. Hounslow
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Claudine Bisson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
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8
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Robertson AJ, Wilson AL, Burn MJ, Cliff MJ, Popelier PLA, Waltho JP. The Relationship between Enzyme Conformational Change, Proton Transfer, and Phosphoryl Transfer in β-Phosphoglucomutase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angus J. Robertson
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Alex L. Wilson
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Matthew J. Burn
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Matthew J. Cliff
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Paul L. A. Popelier
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
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9
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Allomorphy as a mechanism of post-translational control of enzyme activity. Nat Commun 2020; 11:5538. [PMID: 33139716 PMCID: PMC7608592 DOI: 10.1038/s41467-020-19215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 11/08/2022] Open
Abstract
Enzyme regulation is vital for metabolic adaptability in living systems. Fine control of enzyme activity is often delivered through post-translational mechanisms, such as allostery or allokairy. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for complete catabolism of trehalose and maltose, through the isomerisation of β-glucose 1-phosphate to glucose 6-phosphate via β-glucose 1,6-bisphosphate. Surprisingly for a gatekeeper of glycolysis, no fine control mechanism of βPGM has yet been reported. Herein, we describe allomorphy, a post-translational control mechanism of enzyme activity. In βPGM, isomerisation of the K145-P146 peptide bond results in the population of two conformers that have different activities owing to repositioning of the K145 sidechain. In vivo phosphorylating agents, such as fructose 1,6-bisphosphate, generate phosphorylated forms of both conformers, leading to a lag phase in activity until the more active phosphorylated conformer dominates. In contrast, the reaction intermediate β-glucose 1,6-bisphosphate, whose concentration depends on the β-glucose 1-phosphate concentration, couples the conformational switch and the phosphorylation step, resulting in the rapid generation of the more active phosphorylated conformer. In enabling different behaviours for different allomorphic activators, allomorphy allows an organism to maximise its responsiveness to environmental changes while minimising the diversion of valuable metabolites. β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for catabolism of trehalose and maltose. Coupled analyses of multiple βPGM structures and enzymatic activity lead to the proposal of allomorphy — a post-translational mechanism controlling enzyme activity.
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10
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Cruz-Navarrete FA, Baxter NJ, Wood HP, Hounslow AM, Waltho JP. 1H, 15N and 13C backbone resonance assignments of the P146A variant of β-phosphoglucomutase from Lactococcus lactis in its substrate-free form. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:349-356. [PMID: 31396843 PMCID: PMC6713671 DOI: 10.1007/s12104-019-09904-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
β-Phosphoglucomutase (βPGM) is a magnesium-dependent phosphoryl transfer enzyme that catalyses the reversible isomerisation of β-glucose 1-phosphate and glucose 6-phosphate, via two phosphoryl transfer steps and a β-glucose 1,6-bisphosphate intermediate. Substrate-free βPGM is an essential component of the catalytic cycle and an understanding of its dynamics would present significant insights into βPGM functionality, and enzyme catalysed phosphoryl transfer in general. Previously, 30 residues around the active site of substrate-free βPGMWT were identified as undergoing extensive millisecond dynamics and were unassignable. Here we report 1H, 15N and 13C backbone resonance assignments of the P146A variant (βPGMP146A) in its substrate-free form, where the K145-A146 peptide bond adopts a trans conformation in contrast to all crystal structures of βPGMWT, where the K145-P146 peptide bond is cis. In βPGMP146A millisecond dynamics are suppressed for all but 17 residues, allowing 92% of backbone resonances to be assigned. Secondary structure predictions using TALOS-N reflect βPGM crystal structures, and a chemical shift comparison between substrate-free βPGMP146A and βPGMWT confirms that the solution conformations are very similar, except for the D137-A147 loop. Hence, the isomerisation state of the 145-146 peptide bond has little effect on structure but the cis conformation triggers millisecond dynamics in the hinge (V12-T16), the nucleophile (D8) and residues that coordinate the transferring phosphate group (D8 and S114-S116), and the D137-A147 loop (V141-A142 and K145). These millisecond dynamics occur in addition to those for residues involved in coordinating the catalytic MgII ion and the L44-L53 loop responsible for substrate discrimination.
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Affiliation(s)
- F Aaron Cruz-Navarrete
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Henry P Wood
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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11
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Pandya MJ, Schiffers S, Hounslow AM, Baxter NJ, Williamson MP. Why the Energy Landscape of Barnase Is Hierarchical. Front Mol Biosci 2018; 5:115. [PMID: 30619881 PMCID: PMC6306431 DOI: 10.3389/fmolb.2018.00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/07/2018] [Indexed: 01/29/2023] Open
Abstract
We have used NMR and computational methods to characterize the dynamics of the ribonuclease barnase over a wide range of timescales in free and inhibitor-bound states. Using temperature- and denaturant-dependent measurements of chemical shift, we show that barnase undergoes frequent and highly populated hinge bending. Using relaxation dispersion, we characterize a slower and less populated motion with a rate of 750 ± 200 s−1, involving residues around the lip of the active site, which occurs in both free and bound states and therefore suggests conformational selection. Normal mode calculations characterize correlated hinge bending motions on a very rapid timescale. These three measurements are combined with previous measurements and molecular dynamics calculations on barnase to characterize its dynamic landscape on timescales from picoseconds to milliseconds and length scales from 0.1 to 2.5 nm. We show that barnase has two different large-scale fluctuations: one on a timescale of 10−9−10−6 s that has no free energy barrier and is a hinge bending that is determined by the architecture of the protein; and one on a timescale of milliseconds (i.e., 750 s−1) that has a significant free energy barrier and starts from a partially hinge-bent conformation. These two motions can be described as hierarchical, in that the more highly populated faster motion provides a platform for the slower (less probable) motion. The implications are discussed. The use of temperature and denaturant is suggested as a simple and general way to characterize motions on the intermediate ns-μs timescale.
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Affiliation(s)
- Maya J Pandya
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Stefanie Schiffers
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
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