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Eida AA, Samadi A, Tsunoda T, Mahmud T. Modifications of Acyl Carrier Protein-Bound Glycosylated Polyketides in Pactamycin Biosynthesis. Chemistry 2023; 29:e202301056. [PMID: 37015882 PMCID: PMC10330135 DOI: 10.1002/chem.202301056] [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: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/06/2023]
Abstract
The potent antitumor antibiotic pactamycin is an aminocyclopentitol-containing natural product produced by the soil bacterium Streptomyces pactum. Recent studies showed that the aminocyclopentitol unit is derived from N-acetyl-D-glucosamine, which is attached to an acyl carrier protein (ACP)-bound polyketide by a glycosyltransferase enzyme, PtmJ. Here, we report a series of post-glycosylation modifications of the sugar moiety of the glycosylated polyketide while it is still attached to the carrier protein. In vitro reconstitution of PtmS (an AMP-ligase), PtmI (an ACP), PtmJ, PtmN (an oxidoreductase), PtmA (an aminotransferase), and PtmB (a putative carbamoyltransferase) showed that the N-acetyl-D-glucosamine moiety of the glycosylated polyketide is first oxidized by PtmN and then transaminated by PtmA to give ACP-bound 3-amino-3-deoxy-N-acetyl-D-glucosaminyl polyketide. The amino group is then coupled with carbamoyl phosphate by PtmB to give a urea functionality. We also show that PtmG is a deacetylase that hydrolyses the C-2 N-acetyl group to give a free amine.
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Affiliation(s)
- Auday A Eida
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331-3507, USA
| | - Arash Samadi
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331-3507, USA
| | - Takeshi Tsunoda
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331-3507, USA
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences, Oregon State University, 203 Pharmacy Building, Corvallis, Oregon, 97331-3507, USA
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2
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Dhar YV, Asif MH. Genome and transcriptome-wide study of carbamoyltransferase genes in major fleshy fruits: A multi-omics study of evolution and functional significance. FRONTIERS IN PLANT SCIENCE 2022; 13:994159. [PMID: 36407603 PMCID: PMC9669488 DOI: 10.3389/fpls.2022.994159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
The carbamoyltransferase or aspartate carbamoyltransferase (ATCase)/ornithine carbamoyltransferase (OTCase) is an evolutionary conserved protein family, which contains two genes, ATCase and OTCase. The ATCase catalyzes the committed step in the synthesis of UMP from which all pyrimidine molecules are synthesized. The second member, OTCase, catalytically regulates the conversion of ornithine to citrulline. This study traces the evolution of the carbomoyltransferase genes in the plant kingdom and their role during fruit ripening in fleshy fruits. These genes are highly conserved throughout the plant kingdom and, except for melon and watermelon, do not show gene expansion in major fleshy fruits. In this study, 393 carbamoyltransferase genes were identified in the plant kingdom, including 30 fleshy fruit representatives. Their detailed phylogeny, evolutionary patterns with their expression during the process of fruit ripening, was analyzed. The ATcase and OTcase genes were conserved throughout the plant kingdom and exhibited lineage-specific signatures. The expression analysis of the ATcase and OTcase genes during fruit development and ripening in climacteric and non-climacteric fruits showed their involvement in fruit ripening irrespective of the type of fruits. No direct role in relation to ethylene-dependent or -independent ripening was identified; however, the co-expression network suggests their involvement in the various ripening processes.
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Affiliation(s)
- Yogeshwar V. Dhar
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research to Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mehar H. Asif
- CSIR-National Botanical Research Institute (CSIR-NBRI), Lucknow, India
- Academy of Scientific and Innovative Research to Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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Lu X, Wang L, Chen Q, Wang Y, Cao Z, Zhou G, Li L. A biosensor based on multifunctional allostery for dynamic analysis of circulating tumor DNA. Chem Commun (Camb) 2020; 56:4184-4187. [DOI: 10.1039/d0cc01560a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multifunctional allosterically regulated DNA molecule beacon assay was applied to engineer a single-step, amplified and dynamic biosensor for controllable analyses of ctDNA.
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Affiliation(s)
- Xing Lu
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Liqian Wang
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Fudan University
- Shanghai 200433
- P. R. China
| | - Qingxue Chen
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Yulan Wang
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Zhenxiong Cao
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Guobao Zhou
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
| | - Lei Li
- College of Biological
- Chemical Sciences and Engineering
- Jiaxing University
- Jiaxing 314001
- China
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4
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Pisco JP, de Chiara C, Pacholarz KJ, Garza-Garcia A, Ogrodowicz RW, Walker PA, Barran PE, Smerdon SJ, de Carvalho LPS. Uncoupling conformational states from activity in an allosteric enzyme. Nat Commun 2017; 8:203. [PMID: 28781362 PMCID: PMC5545217 DOI: 10.1038/s41467-017-00224-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 06/13/2017] [Indexed: 02/07/2023] Open
Abstract
ATP-phosphoribosyltransferase (ATP-PRT) is a hexameric enzyme in conformational equilibrium between an open and seemingly active state and a closed and presumably inhibited form. The structure-function relationship of allosteric regulation in this system is still not fully understood. Here, we develop a screening strategy for modulators of ATP-PRT and identify 3-(2-thienyl)-l-alanine (TIH) as an allosteric activator of this enzyme. Kinetic analysis reveals co-occupancy of the allosteric sites by TIH and l-histidine. Crystallographic and native ion-mobility mass spectrometry data show that the TIH-bound activated form of the enzyme closely resembles the inhibited l-histidine-bound closed conformation, revealing the uncoupling between ATP-PRT open and closed conformations and its functional state. These findings suggest that dynamic processes are responsible for ATP-PRT allosteric regulation and that similar mechanisms might also be found in other enzymes bearing a ferredoxin-like allosteric domain. Active and inactive state ATP-phosphoribosyltransferases (ATP-PRTs) are believed to have different conformations. Here the authors show that in both states, ATP-PRT has a similar structural arrangement, suggesting that dynamic alterations are involved in ATP-PRT regulation by allosteric modulators.
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Affiliation(s)
- João P Pisco
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Cesira de Chiara
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kamila J Pacholarz
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology & School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Acely Garza-Garcia
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Philip A Walker
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology & School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Stephen J Smerdon
- Structural Biology of DNA-damage Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Luiz Pedro S de Carvalho
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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5
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Gorecki J, Gorecka JN, Nowakowski B, Ueno H, Yoshikawa K. How many enzyme molecules are needed for discrimination oriented applications? Phys Chem Chem Phys 2016; 18:20518-27. [PMID: 27405538 DOI: 10.1039/c6cp03860c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical reactions establish a molecular mechanism for information processing in living organisms. Here we consider a simple enzymatic reaction model that can be used to discriminate parameters characterizing periodic reagent inflow. Numerical simulations based on the kinetic equations show that there exist a range of inflow frequencies and amplitudes in which the time evolution of the system is very sensitive to small changes in the values of these parameters. However, the kinetic equations are derived for the thermodynamic limit, whereas in a real biological medium, like a cell, the number of enzyme molecules is an integer and finite. We use stochastic simulations to estimate discriminator reliability as a function of the number of enzyme molecules involved. For systems with 10 000 molecules the functionality predicted by kinetic equations is confirmed. If the number of molecules is decreased to 100, discrimination becomes unreliable.
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Affiliation(s)
- Jerzy Gorecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Joanna N Gorecka
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Bogdan Nowakowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and SGGW, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Hiroshi Ueno
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
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Fu LL, Wang R, Wang Y, Lin J. Proteomic identification of responsive proteins of Vibrio parahaemolyticus under high hydrostatic pressure. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:2630-2638. [PMID: 24473993 DOI: 10.1002/jsfa.6595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/21/2014] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND High hydrostatic pressure (HHP) processing is currently being used as a treatment for certain foods to inhibit spoilage organisms and control the presence of foodborne pathogens. In this study proteome profiles were performed by two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF identification to determine the effects of HHP (50, 100, 150 and 200 MPa, each for 10 min) on Vibrio parahaemolyticus ATCC 17802 (∼8 log CFU mL⁻¹) in order to understand how it responds to mechanical stress injury. RESULTS Multiple comparisons of 2-DE revealed that the majority of changes in protein abundance occurred in a pressure-dependent fashion. A total of 18 differentially expressed protein spots were successfully identified by MALDI-TOF/TOF analysis. Moreover, quantitative RT-PCR and immunoblotting also substantiated the changes of transcriptional and translational levels of representative proteins. CONCLUSIONS Our results suggested that V. parahaemolyticus may respond to HHP treatment through suppression of membrane stability and functionality (PfaC, Alr2, MltA, PLA2 and PatH), depression of biosynthesis and cellular processes (NadB, PyrB and ArgB), decreased levels of transcription (RpoD) and translation (RpsA, RplJ and PheS), and effective activation of protein folding and stress-related elements (GroES, DnaK and GroEL). This study may provide insight into the nature of the cellular targets of high pressure and in high-pressure resistance mechanisms in V. parahaemolyticus.
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Affiliation(s)
- Ling-Lin Fu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, P.R. China
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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8
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Enhanced cytidine production by a recombinant Escherichia coli strain using genetic manipulation strategies. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0760-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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9
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Chubukov V, Uhr M, Le Chat L, Kleijn RJ, Jules M, Link H, Aymerich S, Stelling J, Sauer U. Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis. Mol Syst Biol 2013; 9:709. [PMID: 24281055 PMCID: PMC4039378 DOI: 10.1038/msb.2013.66] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/23/2013] [Indexed: 12/18/2022] Open
Abstract
Regulation of enzyme expression is one key mechanism by which cells control their metabolic programs. In this work, a quantitative analysis of metabolism in a model bacterium under different conditions shows that expression alone cannot explain the majority of the observed metabolic changes. ![]()
Most enzymes are indeed highly expressed in conditions where they are more active. Quantitatively, however, the observed changes in expression between conditions do not match the changes in activity for most enzymes. A good quantitative match is only observed for enzymes involved in the TCA cycle. Metabolomics reveals that increased substrate availability explains only a few instances of changes in activity.
One of the key ways in which microbes are thought to regulate their metabolism is by modulating the availability of enzymes through transcriptional regulation. However, the limited success of efforts to manipulate metabolic fluxes by rewiring the transcriptional network has cast doubt on the idea that transcript abundance controls metabolic fluxes. In this study, we investigate control of metabolic flux in the model bacterium Bacillus subtilis by quantifying fluxes, transcripts, and metabolites in eight metabolic states enforced by different environmental conditions. We find that most enzymes whose flux switches between on and off states, such as those involved in substrate uptake, exhibit large corresponding transcriptional changes. However, for the majority of enzymes in central metabolism, enzyme concentrations were insufficient to explain the observed fluxes—only for a number of reactions in the tricarboxylic acid cycle were enzyme changes approximately proportional to flux changes. Surprisingly, substrate changes revealed by metabolomics were also insufficient to explain observed fluxes, leaving a large role for allosteric regulation and enzyme modification in the control of metabolic fluxes.
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Affiliation(s)
- Victor Chubukov
- Institute of Molecular System Biology, ETH Zurich, Zurich, Switzerland
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10
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Privman V, Zavalov O, Halámková L, Moseley F, Halámek J, Katz E. Networked Enzymatic Logic Gates with Filtering: New Theoretical Modeling Expressions and Their Experimental Application. J Phys Chem B 2013; 117:14928-39. [DOI: 10.1021/jp408973g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | - Lenka Halámková
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | | | - Jan Halámek
- Department
of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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11
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Bakshi S, Zavalov O, Halámek J, Privman V, Katz E. Modularity of Biochemical Filtering for Inducing Sigmoid Response in Both Inputs in an Enzymatic AND Gate. J Phys Chem B 2013; 117:9857-65. [DOI: 10.1021/jp4058675] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Saira Bakshi
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Oleksandr Zavalov
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Jan Halámek
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Vladimir Privman
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
| | - Evgeny Katz
- Department
of Chemistry and Biomolecular Science and ‡Department of Physics, Clarkson University, Potsdam, New York
13676, United States
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12
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Privman V, Fratto BE, Zavalov O, Halámek J, Katz E. Enzymatic AND logic gate with sigmoid response induced by photochemically controlled oxidation of the output. J Phys Chem B 2013; 117:7559-68. [PMID: 23731012 DOI: 10.1021/jp404054f] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.
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Affiliation(s)
- Vladimir Privman
- Department of Physics, Clarkson University, Potsdam, New York 13676, USA
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13
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Mendes KR, Martinez JA, Kantrowitz ER. Asymmetric allosteric signaling in aspartate transcarbamoylase. ACS Chem Biol 2010; 5:499-506. [PMID: 20210358 DOI: 10.1021/cb9003207] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we use the fluorescence from a genetically encoded unnatural amino acid, l-(7-hydroxycoumarin-4-yl)ethylglycine (HCE-Gly), replacing an amino acid in the regulatory site of Escherichia coli aspartate transcarbamoylase (ATCase) to decipher the molecular details of regulation of this allosteric enzyme. The fluorescence of HCE-Gly is exquisitely sensitive to the binding of all four nucleotide effectors. Although ATP and CTP are primarily responsible for influencing enzyme activity, the results of our fluorescent binding studies indicate that UTP and GTP bind with similar affinities, suggesting a dissociation between nucleotide binding and control of enzyme activity. Furthermore, while CTP is the strongest regulator of enzyme activity, it binds selectively to only a fraction of regulatory sites, allowing UTP to effectively fill the residual ones. Our results suggest that CTP and UTP are not competing for the same binding sites, but instead reveal an asymmetry between the two allosteric sites on the regulatory subunit of the enzyme. Correlation of binding and activity measurements explain how ATCase uses asymmetric allosteric sites to achieve regulatory sensitivity over a broad range of heterotropic effector concentrations.
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Affiliation(s)
- Kimberly R. Mendes
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Jessica A. Martinez
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
| | - Evan R. Kantrowitz
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467
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