1
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Abhishek S, Deeksha W, Nethravathi KR, Davari MD, Rajakumara E. Allosteric crosstalk in modular proteins: Function fine-tuning and drug design. Comput Struct Biotechnol J 2023; 21:5003-5015. [PMID: 37867971 PMCID: PMC10589753 DOI: 10.1016/j.csbj.2023.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
Modular proteins are regulatory proteins that carry out more than one function. These proteins upregulate or downregulate a biochemical cascade to establish homeostasis in cells. To switch the function or alter the efficiency (based on cellular needs), these proteins require different facilitators that bind to a site different from the catalytic (active/orthosteric) site, aka 'allosteric site', and fine-tune their function. These facilitators (or effectors) are allosteric modulators. In this Review, we have discussed the allostery, characterized them based on their mechanisms, and discussed how allostery plays an important role in the activity modulation and function fine-tuning of proteins. Recently there is an emergence in the discovery of allosteric drugs. We have also emphasized the role, significance, and future of allostery in therapeutic applications.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | - Waghela Deeksha
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
| | | | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle 06120, Germany
| | - Eerappa Rajakumara
- Macromolecular Structural Biology lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana 502284, India
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2
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Burnim AA, Xu D, Spence MA, Jackson CJ, Ando N. Analysis of insertions and extensions in the functional evolution of the ribonucleotide reductase family. Protein Sci 2022; 31:e4483. [PMID: 36307939 PMCID: PMC9669993 DOI: 10.1002/pro.4483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/22/2022] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. In this work, we expand on our recent phylogenetic inference of the entire RNR family and describe the evolutionarily relatedness of insertions and extensions around the structurally homologous catalytic barrel. Using evo-velocity and sequence similarity network (SSN) analyses, we show that the N-terminal regulatory motif known as the ATP-cone domain was likely inherited from an ancestral RNR. By combining SSN analysis with AlphaFold2 predictions, we also show that the C-terminal extensions of class II RNRs can contain folded domains that share homology with an Fe-S cluster assembly protein. Finally, using sequence analysis and AlphaFold2, we show that the sequence motif of a catalytically essential insertion known as the finger loop is tightly coupled to the catalytic mechanism. Based on these results, we propose an evolutionary model for the diversification of the RNR family.
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Affiliation(s)
- Audrey A. Burnim
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
| | - Da Xu
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
| | - Matthew A. Spence
- Research School of ChemistryAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Colin J. Jackson
- Research School of ChemistryAustralian National UniversityCanberraAustralian Capital TerritoryAustralia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceAustralian National UniversityCanberraAustralian Capital TerritoryAustralia,Australian Research Council Centre of Excellence in Synthetic BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Nozomi Ando
- Department of Chemistry and Chemical BiologyCornell UniversityIthacaNew YorkUSA
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3
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Levitz TS, Drennan CL. Starting a new chapter on class Ia ribonucleotide reductases. Curr Opin Struct Biol 2022; 77:102489. [PMID: 36272229 DOI: 10.1016/j.sbi.2022.102489] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 01/21/2023]
Abstract
Ribonucleotide reductases (RNRs) use radical-based chemistry to convert ribonucleotides into deoxyribonucleotides, an essential step in DNA biosynthesis and repair. There are multiple RNR classes, the best studied of which is the class Ia RNR that is found in Escherichia coli, eukaryotes including humans, and many pathogenic and nonpathogenic prokaryotes. This review covers recent advances in our understanding of class Ia RNRs, including a recent reporting of a structure of the active state of the E. coli enzyme and the impacts that the structure has had on spurring research into the mechanism of long-range radical transfer. Additionally, the review considers other recent structural and biochemical research on class Ia RNRs and the potential of that work for the development of anticancer and antibiotic therapeutics.
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Affiliation(s)
- Talya S Levitz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. https://twitter.com/@TalyaLevitz
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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4
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Burnim AA, Spence MA, Xu D, Jackson CJ, Ando N. Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade. eLife 2022; 11:79790. [PMID: 36047668 PMCID: PMC9531940 DOI: 10.7554/elife.79790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/31/2022] [Indexed: 11/30/2022] Open
Abstract
Ribonucleotide reductases (RNRs) are used by all free-living organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study. Billions of years ago, the Earth’s atmosphere had very little oxygen. It was only after some bacteria and early plants evolved to harness energy from sunlight that oxygen began to fill the Earth’s environment. Oxygen is highly reactive and can interfere with enzymes and other molecules that are essential to life. Organisms living at this point in history therefore had to adapt to survive in this new oxygen-rich world. An ancient family of enzymes known as ribonucleotide reductases are used by all free-living organisms and many viruses to repair and replicate their DNA. Because of their essential role in managing DNA, these enzymes have been around on Earth for billions of years. Understanding how they evolved could therefore shed light on how nature adapted to increasing oxygen levels and other environmental changes at the molecular level. One approach to study how proteins evolved is to use computational analysis to construct a phylogenetic tree. This reveals how existing members of a family are related to one another based on the chain of molecules (known as amino acids) that make up each protein. Despite having similar structures and all having the same function, ribonucleotide reductases have remarkably diverse sequences of amino acids. This makes it computationally very demanding to build a phylogenetic tree. To overcome this, Burnim, Spence, Xu et al. created a phylogenetic tree using structural information from a part of the enzyme that is relatively similar in many modern-day ribonucleotide reductases. The final result took seven continuous months on a supercomputer to generate, and includes over 6,000 members of the enzyme family. The phylogenetic tree revealed a new distinct group of ribonucleotide reductases that may explain how one adaptation to increasing levels of oxygen emerged in some family members, while another adaptation emerged in others. The approach used in this work also opens up a new way to study how other highly diverse enzymes and other protein families evolved, potentially revealing new insights about our planet’s past.
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Affiliation(s)
- Audrey A Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Da Xu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States
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5
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Huff SE, Winter JM, Dealwis CG. Inhibitors of the Cancer Target Ribonucleotide Reductase, Past and Present. Biomolecules 2022; 12:biom12060815. [PMID: 35740940 PMCID: PMC9221315 DOI: 10.3390/biom12060815] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/02/2023] Open
Abstract
Ribonucleotide reductase (RR) is an essential multi-subunit enzyme found in all living organisms; it catalyzes the rate-limiting step in dNTP synthesis, namely, the conversion of ribonucleoside diphosphates to deoxyribonucleoside diphosphates. As expression levels of human RR (hRR) are high during cell replication, hRR has long been considered an attractive drug target for a range of proliferative diseases, including cancer. While there are many excellent reviews regarding the structure, function, and clinical importance of hRR, recent years have seen an increase in novel approaches to inhibiting hRR that merit an updated discussion of the existing inhibitors and strategies to target this enzyme. In this review, we discuss the mechanisms and clinical applications of classic nucleoside analog inhibitors of hRRM1 (large catalytic subunit), including gemcitabine and clofarabine, as well as inhibitors of the hRRM2 (free radical housing small subunit), including triapine and hydroxyurea. Additionally, we discuss novel approaches to targeting RR and the discovery of new classes of hRR inhibitors.
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Affiliation(s)
- Sarah E. Huff
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
| | - Jordan M. Winter
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Akron, OH 44106, USA;
| | - Chris G. Dealwis
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
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6
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Levitz TS, Andree GA, Jonnalagadda R, Dawson CD, Bjork RE, Drennan CL. A rapid and sensitive assay for quantifying the activity of both aerobic and anaerobic ribonucleotide reductases acting upon any or all substrates. PLoS One 2022; 17:e0269572. [PMID: 35675376 PMCID: PMC9176816 DOI: 10.1371/journal.pone.0269572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/23/2022] [Indexed: 01/21/2023] Open
Abstract
Ribonucleotide reductases (RNRs) use radical-based chemistry to catalyze the conversion of all four ribonucleotides to deoxyribonucleotides. The ubiquitous nature of RNRs necessitates multiple RNR classes that differ from each other in terms of the phosphorylation state of the ribonucleotide substrates, oxygen tolerance, and the nature of both the metallocofactor employed and the reducing systems. Although these differences allow RNRs to produce deoxyribonucleotides needed for DNA biosynthesis under a wide range of environmental conditions, they also present a challenge for establishment of a universal activity assay. Additionally, many current RNR assays are limited in that they only follow the conversion of one ribonucleotide substrate at a time, but in the cell, all four ribonucleotides are actively being converted into deoxyribonucleotide products as dictated by the cellular concentrations of allosteric specificity effectors. Here, we present a liquid chromatography with tandem mass spectrometry (LC-MS/MS)-based assay that can determine the activity of both aerobic and anaerobic RNRs on any combination of substrates using any combination of allosteric effectors. We demonstrate that this assay generates activity data similar to past published results with the canonical Escherichia coli aerobic class Ia RNR. We also show that this assay can be used for an anaerobic class III RNR that employs formate as the reductant, i.e. Streptococcus thermophilus RNR. We further show that this class III RNR is allosterically regulated by dATP and ATP. Lastly, we present activity data for the simultaneous reduction of all four ribonucleotide substrates by the E. coli class Ia RNR under various combinations of allosteric specificity effectors. This validated LC-MS/MS assay is higher throughput and more versatile than the historically established radioactive activity and coupled RNR activity assays as well as a number of the published HPLC-based assays. The presented assay will allow for the study of a wide range of RNR enzymes under a wide range of conditions, facilitating the study of previously uncharacterized RNRs.
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Affiliation(s)
- Talya S. Levitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Gisele A. Andree
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Rohan Jonnalagadda
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Christopher D. Dawson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Rebekah E. Bjork
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Catherine L. Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States of America,* E-mail:
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7
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Meyer A, Kehl A, Cui C, Reichardt FAK, Hecker F, Funk LM, Pan KT, Urlaub H, Tittmann K, Stubbe J, Bennati M. 19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active Tyrosines across the α/β Interface of E. coli Ribonucleotide Reductase. J Am Chem Soc 2022; 144:11270-11282. [PMID: 35652913 PMCID: PMC9248007 DOI: 10.1021/jacs.2c02906] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Ribonucleotide reductases
(RNRs) catalyze the reduction of ribonucleotides
to deoxyribonucleotides, thereby playing a key role in DNA replication
and repair. Escherichia coli class
Ia RNR is an α2β2 enzyme complex
that uses a reversible multistep radical transfer (RT) over 32 Å
across its two subunits, α and β, to initiate, using its
metallo-cofactor in β2, nucleotide reduction in α2. Each step is proposed to involve a distinct proton-coupled
electron-transfer (PCET) process. An unresolved step is the RT involving
Y356(β) and Y731(α) across the α/β
interface. Using 2,3,5-F3Y122-β2 with 3,5-F2Y731-α2, GDP (substrate) and TTP (allosteric effector), a Y356• intermediate was trapped and its identity was
verified by 263 GHz electron paramagnetic resonance (EPR) and 34 GHz
pulse electron–electron double resonance spectroscopies. 94
GHz 19F electron-nuclear double resonance spectroscopy
allowed measuring the interspin distances between Y356• and the 19F nuclei of 3,5-F2Y731 in this RNR mutant. Similar experiments with the
double mutant E52Q/F3Y122-β2 were carried out for comparison to the recently published
cryo-EM structure of a holo RNR complex. For both mutant combinations,
the distance measurements reveal two conformations of 3,5-F2Y731. Remarkably, one conformation is consistent with
3,5-F2Y731 within the H-bond distance to Y356•, whereas the second one is consistent
with the conformation observed in the cryo-EM structure. The observations
unexpectedly suggest the possibility of a colinear PCET, in which
electron and proton are transferred from the same donor to the same
acceptor between Y356 and Y731. The results
highlight the important role of state-of-the-art EPR spectroscopy
to decipher this mechanism.
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Affiliation(s)
- Andreas Meyer
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Annemarie Kehl
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Fehmke A K Reichardt
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Henning Urlaub
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Kai Tittmann
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - JoAnne Stubbe
- Department of Chemistry and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Marina Bennati
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Chemistry, Georg-August University, 37077 Göttingen, Germany
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8
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Narasimhan J, Letinski S, Jung SP, Gerasyuto A, Wang J, Arnold M, Chen G, Hedrick J, Dumble M, Ravichandran K, Levitz T, Cui C, Drennan CL, Stubbe J, Karp G, Branstrom A. Ribonucleotide reductase, a novel drug target for gonorrhea. eLife 2022; 11:e67447. [PMID: 35137690 PMCID: PMC8865847 DOI: 10.7554/elife.67447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic-resistant Neisseria gonorrhoeae (Ng) are an emerging public health threat due to increasing numbers of multidrug resistant (MDR) organisms. We identified two novel orally active inhibitors, PTC-847 and PTC-672, that exhibit a narrow spectrum of activity against Ng including MDR isolates. By selecting organisms resistant to the novel inhibitors and sequencing their genomes, we identified a new therapeutic target, the class Ia ribonucleotide reductase (RNR). Resistance mutations in Ng map to the N-terminal cone domain of the α subunit, which we show here is involved in forming an inhibited α4β4 state in the presence of the β subunit and allosteric effector dATP. Enzyme assays confirm that PTC-847 and PTC-672 inhibit Ng RNR and reveal that allosteric effector dATP potentiates the inhibitory effect. Oral administration of PTC-672 reduces Ng infection in a mouse model and may have therapeutic potential for treatment of Ng that is resistant to current drugs.
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Affiliation(s)
| | | | | | | | - Jiashi Wang
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | | | - Jean Hedrick
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | - Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Talya Levitz
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Gary Karp
- PTC Therapeutics, IncSouth PlainfieldUnited States
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9
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Roberts DE, Benton AM, Fabian-Bayola C, Spuches AM, Offenbacher AR. Thermodynamic and biophysical study of fatty acid effector binding to soybean lipoxygenase: implications for allostery driven by helix α2 dynamics. FEBS Lett 2022; 596:350-359. [PMID: 34997975 DOI: 10.1002/1873-3468.14275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022]
Abstract
Previous comparative kinetic isotope effects have inferred an allosteric site for fatty acids and their derivatives that modulates substrate selectivity in 15-lipoxygenases. Hydrogen-deuterium exchange also previously revealed regionally defined enhanced protein flexibility, centred at helix α2 - a gate to the substrate entrance. Direct evidence for allosteric binding and a complete understanding of its mechanism remains elusive. In this study, we examine the binding thermodynamics of the fatty acid mimic, oleyl sulfate (OS), with the monomeric model plant 15-LOX, soybean lipoxygenase (SLO), using isothermal titration calorimetry. Dynamic light scattering and differential scanning calorimetry rule out OS-induced oligomerization or structural changes. These data provide evidence that the fatty acid allosteric regulation of SLO is controlled by the dynamics of helix α2.
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Affiliation(s)
| | - Amy M Benton
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | | | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC, USA
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10
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Long MJC, Ly P, Aye Y. Still no Rest for the Reductases: Ribonucleotide Reductase (RNR) Structure and Function: An Update. Subcell Biochem 2022; 99:155-197. [PMID: 36151376 DOI: 10.1007/978-3-031-00793-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herein we present a multidisciplinary discussion of ribonucleotide reductase (RNR), the essential enzyme uniquely responsible for conversion of ribonucleotides to deoxyribonucleotides. This chapter primarily presents an overview of this multifaceted and complex enzyme, covering RNR's role in enzymology, biochemistry, medicinal chemistry, and cell biology. It further focuses on RNR from mammals, whose interesting and often conflicting roles in health and disease are coming more into focus. We present pitfalls that we think have not always been dealt with by researchers in each area and further seek to unite some of the field-specific observations surrounding this enzyme. Our work is thus not intended to cover any one topic in extreme detail, but rather give what we consider to be the necessary broad grounding to understand this critical enzyme holistically. Although this is an approach we have advocated in many different areas of scientific research, there is arguably no other single enzyme that embodies the need for such broad study than RNR. Thus, we submit that RNR itself is a paradigm of interdisciplinary research that is of interest from the perspective of the generalist and the specialist alike. We hope that the discussions herein will thus be helpful to not only those wanting to tackle RNR-specific problems, but also those working on similar interdisciplinary projects centering around other enzymes.
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Affiliation(s)
- Marcus J C Long
- University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Biochemistry, UNIL, Epalinges, Switzerland
| | - Phillippe Ly
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- EPFL SB ISIC LEAGO, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- EPFL SB ISIC LEAGO, Lausanne, Switzerland.
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11
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Rehling D, Scaletti ER, Rozman Grinberg I, Lundin D, Sahlin M, Hofer A, Sjöberg BM, Stenmark P. Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus. Biochemistry 2021; 61:92-106. [PMID: 34941255 PMCID: PMC8772380 DOI: 10.1021/acs.biochem.1c00503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme with a complex mechanism of allosteric regulation found in nearly all living organisms. Class I RNRs are composed of two proteins, a large α-subunit (R1) and a smaller β-subunit (R2) that exist as homodimers, that combine to form an active heterotetramer. Aquifex aeolicus is a hyperthermophilic bacterium with an unusual RNR encoding a 346-residue intein in the DNA sequence encoding its R2 subunit. We present the first structures of the A. aeolicus R1 and R2 (AaR1 and AaR2, respectively) proteins as well as the biophysical and biochemical characterization of active and inactive A. aeolicus RNR. While the active oligomeric state and activity regulation of A. aeolicus RNR are similar to those of other characterized RNRs, the X-ray crystal structures also reveal distinct features and adaptations. Specifically, AaR1 contains a β-hairpin hook structure at the dimer interface, which has an interesting π-stacking interaction absent in other members of the NrdAh subclass, and its ATP cone houses two ATP molecules. We determined structures of two AaR2 proteins: one purified from a construct lacking the intein (AaR2) and a second purified from a construct including the intein sequence (AaR2_genomic). These structures in the context of metal content analysis and activity data indicate that AaR2_genomic displays much higher iron occupancy and activity compared to AaR2, suggesting that the intein is important for facilitating complete iron incorporation, particularly in the Fe2 site of the mature R2 protein, which may be important for the survival of A. aeolicus in low-oxygen environments.
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Affiliation(s)
- Daniel Rehling
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Emma Rose Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Inna Rozman Grinberg
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Anders Hofer
- Department of Biochemistry and Biophysics, Umeå University, SE-907 36 Umeå, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
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12
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Levitz TS, Brignole EJ, Fong I, Darrow MC, Drennan CL. Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex. J Struct Biol 2021; 214:107825. [PMID: 34906669 PMCID: PMC8994553 DOI: 10.1016/j.jsb.2021.107825] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides and is a promising antibiotic target, but few RNRs have been structurally characterized. We present the use of the chameleon, a commercially-available piezoelectric cryogenic electron microscopy plunger, to address complex denaturation in the Neisseria gonorrhoeae class Ia RNR. Here, we characterize the extent of denaturation of the ring-shaped complex following grid preparation using a traditional plunger and using a chameleon with varying dispense-to-plunge times. We also characterize how dispense-to-plunge time influences the amount of protein sample required for grid preparation and preferred orientation of the sample. We demonstrate that the fastest dispense-to-plunge time of 54 ms is sufficient for generation of a data set that produces a high quality structure, and that a traditional plunging technique or slow chameleon dispense-to-plunge times generate data sets limited in resolution by complex denaturation. The 4.3 Å resolution structure of Neisseria gonorrhoeae class Ia RNR in the inactive α4β4 oligomeric state solved using the chameleon with a fast dispense-to-plunge time yields molecular information regarding similarities and differences to the well studied Escherichia coli class Ia RNR α4β4 ring.
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Affiliation(s)
- Talya S Levitz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA; MIT.nano, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Ivan Fong
- SPT Labtech Melbourn Science Park, Cambridge Rd, Melbourn SG8 6HB, United Kingdom
| | - Michele C Darrow
- SPT Labtech Melbourn Science Park, Cambridge Rd, Melbourn SG8 6HB, United Kingdom.
| | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Smethurst DGJ, Shcherbik N. Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules. J Biol Chem 2021; 297:101374. [PMID: 34732319 PMCID: PMC8633580 DOI: 10.1016/j.jbc.2021.101374] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023] Open
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Affiliation(s)
- Daniel G J Smethurst
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
| | - Natalia Shcherbik
- Department for Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, New Jersey, USA.
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14
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Abstract
Radicals in biology, once thought to all be bad actors, are now known to play a central role in many enzymatic reactions. Of the known radical-based enzymes, ribonucleotide reductases (RNRs) are pre-eminent as they are essential in the biology of all organisms by providing the building blocks and controlling the fidelity of DNA replication and repair. Intense examination of RNRs has led to the development of new tools and a guiding framework for the study of radicals in biology, pointing the way to future frontiers in radical enzymology.
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Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
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15
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Elserafy M, El-Shiekh I, Fleifel D, Atteya R, AlOkda A, Abdrabbou MM, Nasr M, El-Khamisy SF. A role for Rad5 in ribonucleoside monophosphate (rNMP) tolerance. Life Sci Alliance 2021; 4:4/10/e202000966. [PMID: 34407997 PMCID: PMC8380674 DOI: 10.26508/lsa.202000966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 07/24/2021] [Accepted: 07/03/2021] [Indexed: 11/29/2022] Open
Abstract
Ribonucleoside incorporation in genomic DNA poses a significant threat to genomic integrity. Here, we describe how cells tolerate this threat and discuss implications for cancer therapeutics. Ribonucleoside monophosphate (rNMP) incorporation in genomic DNA poses a significant threat to genomic integrity. In addition to repair, DNA damage tolerance mechanisms ensure replication progression upon encountering unrepaired lesions. One player in the tolerance mechanism is Rad5, which is an E3 ubiquitin ligase and helicase. Here, we report a new role for yeast Rad5 in tolerating rNMP incorporation, in the absence of the bona fide ribonucleotide excision repair pathway via RNase H2. This role of Rad5 is further highlighted after replication stress induced by hydroxyurea or by increasing rNMP genomic burden using a mutant DNA polymerase (Pol ε - Pol2-M644G). We further demonstrate the importance of the ATPase and ubiquitin ligase domains of Rad5 in rNMP tolerance. These findings suggest a similar role for the human Rad5 homologues helicase-like transcription factor (HLTF) and SNF2 Histone Linker PHD RING Helicase (SHPRH) in rNMP tolerance, which may impact the response of cancer cells to replication stress-inducing therapeutics.
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Affiliation(s)
- Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Dalia Fleifel
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Abdelrahman AlOkda
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed M Abdrabbou
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mostafa Nasr
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Sherif F El-Khamisy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt .,The Healthy Lifespan Institute and Institute of Neuroscience, School of Bioscience, University of Sheffield, South Yorkshire, UK.,The Institute of Cancer Therapeutics, University of Bradford, West Yorkshire, UK.,Center for Genomics, Zewail City of Science and Technology, Giza, Egypt
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16
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Watson RA, Offenbacher AR, Barry BA. Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy. J Phys Chem B 2021; 125:8362-8372. [PMID: 34289692 DOI: 10.1021/acs.jpcb.1c03038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α2 and β2, which form an active but unstable heterodimer of dimers, α2β2. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α2β2 complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.
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Affiliation(s)
- Ryan Atlee Watson
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Adam R Offenbacher
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States.,Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Bridgette A Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
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17
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Wozniak KJ, Simmons LA. Hydroxyurea Induces a Stress Response That Alters DNA Replication and Nucleotide Metabolism in Bacillus subtilis. J Bacteriol 2021; 203:e0017121. [PMID: 34031038 PMCID: PMC8407345 DOI: 10.1128/jb.00171-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022] Open
Abstract
Hydroxyurea (HU) is classified as a ribonucleotide reductase (RNR) inhibitor and has been widely used to stall DNA replication by depleting deoxyribonucleoside triphosphate (dNTP) pools. Recent evidence in Escherichia coli shows that HU readily forms breakdown products that damage DNA directly, indicating that toxicity is a result of secondary effects. Because HU is so widely used in the laboratory and as a clinical therapeutic, it is important to understand its biological effects. To determine how Bacillus subtilis responds to HU-induced stress, we performed saturating transposon insertion mutagenesis followed by deep sequencing (Tn-seq), transcriptome sequencing (RNA-seq) analysis, and measurement of replication fork progression. Our data show that B. subtilis cells elongate, and replication fork progression is slowed, following HU challenge. The transcriptomic data show that B. subtilis cells initially mount a metabolic response likely caused by dNTP pool depletion before inducing the DNA damage response (SOS) after prolonged exposure. To compensate for reduced nucleotide pools, B. subtilis upregulates the purine and pyrimidine biosynthetic machinery and downregulates the enzymes producing ribose 5-phosphate. We show that overexpression of the RNR genes nrdEF suppresses the growth interference caused by HU, suggesting that RNR is an important target of HU in B. subtilis. Although genes involved in nucleotide and carbon metabolism showed considerable differential expression, we also find that genes of unknown function (y-genes) represent the largest class of differentially expressed genes. Deletion of individual y-genes caused moderate growth interference in the presence of HU, suggesting that cells have several ways of coping with HU-induced metabolic stress. IMPORTANCE Hydroxyurea (HU) has been widely used as a clinical therapeutic and an inhibitor of DNA replication. Some evidence suggests that HU inhibits ribonucleotide reductase, depleting dNTP pools, while other evidence shows that toxic HU breakdown products are responsible for growth inhibition and genotoxic stress. Here, we use multiple, complementary approaches to characterize the response of Bacillus subtilis to HU. B. subtilis responds by upregulating the expression of purine and pyrimidine biosynthesis. We show that HU challenge reduced DNA replication and that overexpression of the ribonucleotide reductase operon suppressed growth interference by HU. Our results demonstrate that HU targets RNR and several other metabolic enzymes contributing to toxicity in bacteria.
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Affiliation(s)
- Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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18
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Lim JPL, Braza MKE, Nellas RB. The effect of ligand affinity to the contact dynamics of the ligand binding domain of thyroid hormone receptor - retinoid X receptor. J Mol Graph Model 2021; 104:107829. [PMID: 33450664 DOI: 10.1016/j.jmgm.2020.107829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/19/2020] [Accepted: 12/21/2020] [Indexed: 11/19/2022]
Abstract
Ligand-based allostery has been gaining attention for its importance in protein regulation and implication in drug design. One of the interesting cases of protein allostery is the thyroid hormone receptor - retinoid x receptor (TR:RXR), which regulates the gene expression of important physiological processes, such as development and metabolism. It is regulated by the TR native ligand triiodothyronine (T3), which displays anticooperative behavior to the RXR ligand 9-cis retinoic acid (9C). In contrast to this anticooperative behavior, 9C has been shown to increase the activity of TR:RXR. Here we probed the influence of the affinity and the interactions of the TR ligand to the allostery of the TR:RXR through contact dynamics and residue networks. The TR ligand analogs were designed to have higher (G2) and lower (N1) binding energies than T3 when docked to the TR:RXR(9C) complex. The aqueous TR(N1/T3/G2):RXR(9C) complexes were subjected to 30 ns all-atom simulations using theNAMD. The program CAMERRA was used to capture the subtle perturbations of TR:RXR by mapping the residue contact dynamics. Various parts of the TR ligands; including the hydrophilic head, the iodine substituents, and the ligand tail; have been probed for their significance in ligand affinity. The results on the T3 and G2 complexes suggest that ligand affinity can be utilized as a predictor for anticooperative systems on which ligand is more likely to dissociate or remain bound. All 3 complexes also display distinct contact networks for cross-dimer signalling and ligand communication. Understanding ligand-based allostery could potentially unveil secrets of ligand-regulated protein dynamics, a foundation for the design of better and more efficient allosteric drugs.
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Affiliation(s)
- James Peter L Lim
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Mac Kevin E Braza
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines Diliman, Quezon City, Philippines.
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19
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Tinzl M, Hilvert D. Trapping Transient Protein Species by Genetic Code Expansion. Chembiochem 2020; 22:92-99. [PMID: 32810341 DOI: 10.1002/cbic.202000523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Nature employs a limited number of genetically encoded amino acids for the construction of functional proteins. By engineering components of the cellular translation machinery, however, it is now possible to genetically encode noncanonical building blocks with tailored electronic and structural properties. The ability to incorporate unique chemical functionality into proteins provides a powerful tool to probe mechanism and create novel function. In this minireview, we highlight several recent studies that illustrate how noncanonical amino acids have been used to capture and characterize reactive intermediates, fine-tune the catalytic properties of enzymes, and stabilize short-lived protein-protein complexes.
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Affiliation(s)
- Matthias Tinzl
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
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20
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Martínez-Carranza M, Jonna VR, Lundin D, Sahlin M, Carlson LA, Jemal N, Högbom M, Sjöberg BM, Stenmark P, Hofer A. A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site. J Biol Chem 2020; 295:15576-15587. [PMID: 32883811 DOI: 10.1074/jbc.ra120.014895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.
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Affiliation(s)
| | | | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Newal Jemal
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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21
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Cell-cycle-dependent phosphorylation of RRM1 ensures efficient DNA replication and regulates cancer vulnerability to ATR inhibition. Oncogene 2020; 39:5721-5733. [PMID: 32712628 DOI: 10.1038/s41388-020-01403-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 11/08/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate-limiting step of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs) building blocks for DNA synthesis, and is a well-recognized target for cancer therapy. RNR is a heterotetramer consisting of two large RRM1 subunits and two small RRM2 subunits. RNR activity is greatly stimulated by transcriptional activation of RRM2 during S/G2 phase to ensure adequate dNTP supply for DNA replication. However, little is known about the cell-cycle-dependent regulation of RNR activity through RRM1. Here, we report that RRM1 is phosphorylated at Ser 559 by CDK2/cyclin A during S/G2 phase. And this S559 phosphorylation of RRM1enhances RNR enzymatic activity and is required for maintaining sufficient dNTPs during normal DNA replication. Defective RRM1 S559 phosphorylation causes DNA replication stress, double-strand break, and genomic instability. Moreover, combined targeting of RRM1 S559 phosphorylation and ATR triggers lethal replication stress and profound antitumor effects. Thus, this posttranslational phosphorylation of RRM1 provides an alternative mechanism to finely regulating RNR and therapeutic opportunities for cancer treatment.
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22
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Greene BL, Kang G, Cui C, Bennati M, Nocera DG, Drennan CL, Stubbe J. Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets. Annu Rev Biochem 2020; 89:45-75. [PMID: 32569524 PMCID: PMC7316142 DOI: 10.1146/annurev-biochem-013118-111843] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Chang Cui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department of Chemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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23
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Kang G, Taguchi AT, Stubbe J, Drennan CL. Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Science 2020; 368:424-427. [PMID: 32217749 DOI: 10.1126/science.aba6794] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/16/2020] [Indexed: 12/27/2022]
Abstract
Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide reduction reaction in all RNRs requires the generation of a transient active site thiyl radical, and in class I RNRs, this process involves a long-range radical transfer between two subunits, α and β. Because of the transient subunit association, an atomic resolution structure of an active α2β2 RNR complex has been elusive. We used a doubly substituted β2, E52Q/(2,3,5)-trifluorotyrosine122-β2, to trap wild-type α2 in a long-lived α2β2 complex. We report the structure of this complex by means of cryo-electron microscopy to 3.6-angstrom resolution, allowing for structural visualization of a 32-angstrom-long radical transfer pathway that affords RNR activity.
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Affiliation(s)
- Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Alexander T Taguchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA. .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge MA, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge MA, USA
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24
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Liu B, Großhans J. The role of dNTP metabolites in control of the embryonic cell cycle. Cell Cycle 2019; 18:2817-2827. [PMID: 31544596 PMCID: PMC6791698 DOI: 10.1080/15384101.2019.1665948] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 01/06/2023] Open
Abstract
Deoxyribonucleotide metabolites (dNTPs) are the substrates for DNA synthesis. It has been proposed that their availability influences the progression of the cell cycle during development and pathological situations such as tumor growth. The mechanism has remained unclear for the link between cell cycle and dNTP levels beyond their role as substrates. Here, we review recent studies concerned with the dynamics of dNTP levels in early embryos and the role of DNA replication checkpoint as a sensor of dNTP levels.
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Affiliation(s)
- Boyang Liu
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
| | - Jörg Großhans
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
- Entwicklungsgenetik, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
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25
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Thomas WC, Brooks FP, Burnim AA, Bacik JP, Stubbe J, Kaelber JT, Chen JZ, Ando N. Convergent allostery in ribonucleotide reductase. Nat Commun 2019; 10:2653. [PMID: 31201319 PMCID: PMC6572854 DOI: 10.1038/s41467-019-10568-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/20/2019] [Indexed: 02/04/2023] Open
Abstract
Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery. Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides, which is an essential step in DNA synthesis. Here the authors use small-angle X-ray scattering, X-ray crystallography, and cryo-electron microscopy to capture active and inactive forms of the Bacillus subtilis RNR and provide mechanistic insights into a convergent form of allosteric regulation.
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Affiliation(s)
- William C Thomas
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - F Phil Brooks
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Audrey A Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - John-Paul Bacik
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - James Z Chen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA. .,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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26
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Rose HR, Maggiolo AO, McBride MJ, Palowitch GM, Pandelia ME, Davis KM, Yennawar NH, Boal AK. Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. Biochemistry 2019; 58:1845-1860. [PMID: 30855138 PMCID: PMC6456427 DOI: 10.1021/acs.biochem.8b01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class I ribonucleotide reductases (RNRs) share a common mechanism of nucleotide reduction in a catalytic α subunit. All RNRs initiate catalysis with a thiyl radical, generated in class I enzymes by a metallocofactor in a separate β subunit. Class Id RNRs use a simple mechanism of cofactor activation involving oxidation of a MnII2 cluster by free superoxide to yield a metal-based MnIIIMnIV oxidant. This simple cofactor assembly pathway suggests that class Id RNRs may be representative of the evolutionary precursors to more complex class Ia-c enzymes. X-ray crystal structures of two class Id α proteins from Flavobacterium johnsoniae ( Fj) and Actinobacillus ureae ( Au) reveal that this subunit is distinctly small. The enzyme completely lacks common N-terminal ATP-cone allosteric motifs that regulate overall activity, a process that normally occurs by dATP-induced formation of inhibitory quaternary structures to prevent productive β subunit association. Class Id RNR activity is insensitive to dATP in the Fj and Au enzymes evaluated here, as expected. However, the class Id α protein from Fj adopts higher-order structures, detected crystallographically and in solution. The Au enzyme does not exhibit these quaternary forms. Our study reveals structural similarity between bacterial class Id and eukaryotic class Ia α subunits in conservation of an internal auxiliary domain. Our findings with the Fj enzyme illustrate that nucleotide-independent higher-order quaternary structures can form in simple RNRs with truncated or missing allosteric motifs.
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Affiliation(s)
- Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Ailiena O. Maggiolo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Gavin M. Palowitch
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Katherine M. Davis
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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27
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Pham B, Lindsay RJ, Shen T. Effector-Binding-Directed Dimerization and Dynamic Communication between Allosteric Sites of Ribonucleotide Reductase. Biochemistry 2019; 58:697-705. [PMID: 30571104 DOI: 10.1021/acs.biochem.8b01131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Proteins forming dimers or larger complexes can be strongly influenced by their effector-binding status. We investigated how the effector-binding event is coupled with interface formation via computer simulations, and we quantified the correlation of two types of contact interactions: between the effector and its binding pocket and between protein monomers. This was achieved by connecting the protein dynamics at the monomeric level with the oligomer interface information. We applied this method to ribonucleotide reductase (RNR), an essential enzyme for de novo DNA synthesis. RNR contains two important allosteric sites, the s-site (specificity site) and the a-site (activity site), which bind different effectors. We studied these different binding states with atomistic simulation and used their coarse-grained contact information to analyze the protein dynamics. The results reveal that the effector-protein dynamics at the s-site and dimer interface formation are positively coupled. We further quantify the resonance level between these two events, which can be applied to other similar systems. At the a-site, different effector-binding states (ATP vs dATP) drastically alter the protein dynamics and affect the activity of the enzyme. On the basis of these results, we propose a new mechanism of how the a-site regulates enzyme activation.
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Affiliation(s)
- Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Richard J Lindsay
- UT-ORNL Graduate School of Genome Science and Technology , Knoxville , Tennessee 37996 , United States
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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28
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Greene BL, Stubbe J, Nocera DG. Photochemical Rescue of a Conformationally Inactivated Ribonucleotide Reductase. J Am Chem Soc 2018; 140:15744-15752. [PMID: 30347141 DOI: 10.1021/jacs.8b07902] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class Ia ribonucleotide reductase (RNR) of Escherichia coli contains an unusually stable tyrosyl radical cofactor in the β2 subunit (Y122•) necessary for nucleotide reductase activity. Upon binding the cognate α2 subunit, loaded with nucleoside diphosphate substrate and an allosteric/activity effector, a rate determining conformational change(s) enables rapid radical transfer (RT) within the active α2β2 complex from the Y122• site in β2 to the substrate activating cysteine residue (C439) in α2 via a pathway of redox active amino acids (Y122[β] ↔ W48[β]? ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]) spanning >35 Å. Ionizable residues at the α2β2 interface are essential in mediating RT, and therefore control activity. One of these mutations, E350X (where X = A, D, Q) in β2, obviates all RT, though the mechanism of control by which E350 mediates RT remains unclear. Herein, we utilize an E350Q-photoβ2 construct to photochemically rescue RNR activity from an otherwise inactive construct, wherein the initial RT event (Y122• → Y356) is replaced by direct photochemical radical generation of Y356•. These data present compelling evidence that E350 conveys allosteric information between the α2 and β2 subunits facilitating conformational gating of RT that specifically targets Y122• reduction, while the fidelity of the remainder of the RT pathway is retained.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | | | - Daniel G Nocera
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
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29
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Gillet N, Elstner M, Kubař T. Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer. J Chem Phys 2018; 149:072328. [PMID: 30134697 DOI: 10.1063/1.5027100] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new concept of free energy calculations of chemical reactions by means of extended sampling molecular dynamics simulations. Biasing potentials are applied on partial atomic charges, which may be combined with atomic coordinates either in a single collective variable or in multi-dimensional biasing simulations. The necessary additional gradients are obtained by solving coupled-perturbed equations within the approximative density-functional tight-binding method. The new computational scheme was implemented in a combination of Gromacs and Plumed. As a prospective application, proton-coupled electron transfer in a model molecular system is studied. Two collective variables are introduced naturally, one for the proton transfer and the other for the electron transfer. The results are in qualitative agreement with the extended free simulations performed for reference. Free energy minima as well as the mechanism of the process are identified correctly, while the topology of the transition region and the height of the energy barrier are only reproduced qualitatively. The application also illustrates possible difficulties with the new methodology. These may be inefficient sampling of spatial coordinates when atomic charges are biased exclusively and a decreased stability of the simulations. Still, the new approach represents a viable alternative for free energy calculations of a certain class of chemical reactions, for instance a proton-coupled electron transfer in proteins.
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Affiliation(s)
- Natacha Gillet
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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30
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Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D. Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein. J Am Chem Soc 2018; 140:9827-9843. [DOI: 10.1021/jacs.8b01596] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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31
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Parker MJ, Maggiolo AO, Thomas WC, Kim A, Meisburger SP, Ando N, Boal AK, Stubbe J. An endogenous dAMP ligand in Bacillus subtilis class Ib RNR promotes assembly of a noncanonical dimer for regulation by dATP. Proc Natl Acad Sci U S A 2018; 115:E4594-E4603. [PMID: 29712847 PMCID: PMC5960316 DOI: 10.1073/pnas.1800356115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high fidelity of DNA replication and repair is attributable, in part, to the allosteric regulation of ribonucleotide reductases (RNRs) that maintains proper deoxynucleotide pool sizes and ratios in vivo. In class Ia RNRs, ATP (stimulatory) and dATP (inhibitory) regulate activity by binding to the ATP-cone domain at the N terminus of the large α subunit and altering the enzyme's quaternary structure. Class Ib RNRs, in contrast, have a partial cone domain and have generally been found to be insensitive to dATP inhibition. An exception is the Bacillus subtilis Ib RNR, which we recently reported to be inhibited by physiological concentrations of dATP. Here, we demonstrate that the α subunit of this RNR contains tightly bound deoxyadenosine 5'-monophosphate (dAMP) in its N-terminal domain and that dATP inhibition of CDP reduction is enhanced by its presence. X-ray crystallography reveals a previously unobserved (noncanonical) α2 dimer with its entire interface composed of the partial N-terminal cone domains, each binding a dAMP molecule. Using small-angle X-ray scattering (SAXS), we show that this noncanonical α2 dimer is the predominant form of the dAMP-bound α in solution and further show that addition of dATP leads to the formation of larger oligomers. Based on this information, we propose a model to describe the mechanism by which the noncanonical α2 inhibits the activity of the B. subtilis Ib RNR in a dATP- and dAMP-dependent manner.
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Affiliation(s)
- Mackenzie J Parker
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ailiena O Maggiolo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - William C Thomas
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Albert Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ 08544;
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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32
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Chen PYT, Funk MA, Brignole EJ, Drennan CL. Disruption of an oligomeric interface prevents allosteric inhibition of Escherichia coli class Ia ribonucleotide reductase. J Biol Chem 2018; 293:10404-10412. [PMID: 29700111 DOI: 10.1074/jbc.ra118.002569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/17/2018] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) convert ribonucleotides to deoxynucleotides, a process essential for DNA biosynthesis and repair. Class Ia RNRs require two dimeric subunits for activity: an α2 subunit that houses the active site and allosteric regulatory sites and a β2 subunit that houses the diferric tyrosyl radical cofactor. Ribonucleotide reduction requires that both subunits form a compact α2β2 state allowing for radical transfer from β2 to α2 RNR activity is regulated allosterically by dATP, which inhibits RNR, and by ATP, which restores activity. For the well-studied Escherichia coli class Ia RNR, dATP binding to an allosteric site on α promotes formation of an α4β4 ring-like state. Here, we investigate whether the α4β4 formation causes or results from RNR inhibition. We demonstrate that substitutions at the α-β interface (S37D/S39A-α2, S39R-α2, S39F-α2, E42K-α2, or L43Q-α2) that disrupt the α4β4 oligomer abrogate dATP-mediated inhibition, consistent with the idea that α4β4 formation is required for dATP's allosteric inhibition of RNR. Our results further reveal that the α-β interface in the inhibited state is highly sensitive to manipulation, with a single substitution interfering with complex formation. We also discover that residues at the α-β interface whose substitution has previously been shown to cause a mutator phenotype in Escherichia coli (i.e. S39F-α2 or E42K-α2) are impaired only in their activity regulation, thus linking this phenotype with the inability to allosterically down-regulate RNR. Whereas the cytotoxicity of RNR inhibition is well-established, these data emphasize the importance of down-regulation of RNR activity.
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Affiliation(s)
| | | | - Edward J Brignole
- From the Departments of Chemistry and.,Biology and.,the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Catherine L Drennan
- From the Departments of Chemistry and .,Biology and.,the Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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33
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Brignole EJ, Tsai KL, Chittuluru J, Li H, Aye Y, Penczek PA, Stubbe J, Drennan CL, Asturias F. 3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound. eLife 2018; 7:31502. [PMID: 29460780 PMCID: PMC5819950 DOI: 10.7554/elife.31502] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
Ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides, a reaction essential for DNA replication and repair. Human RNR requires two subunits for activity, the α subunit contains the active site, and the β subunit houses the radical cofactor. Here, we present a 3.3-Å resolution structure by cryo-electron microscopy (EM) of a dATP-inhibited state of human RNR. This structure, which was determined in the presence of substrate CDP and allosteric regulators ATP and dATP, has three α2 units arranged in an α6 ring. At near-atomic resolution, these data provide insight into the molecular basis for CDP recognition by allosteric specificity effectors dATP/ATP. Additionally, we present lower-resolution EM structures of human α6 in the presence of both the anticancer drug clofarabine triphosphate and β2. Together, these structures support a model for RNR inhibition in which β2 is excluded from binding in a radical transfer competent position when α exists as a stable hexamer. Cells often need to make more DNA, for example when they are about to divide or need to repair their genetic information. The building blocks of DNA – also called deoxyribonucleotides – are created through a series of biochemical reactions. Among the enzymes that accomplish these reactions, ribonucleotide reductases (or RNRs, for short) perform a key irreversible step. One prominent class of RNR contains two basic units, named alpha and beta. The active form of these RNRs is made up of a pair of alpha units (α2), which associates with a pair of beta units (β2) to create an α2β2 structure. α2 captures molecules called ribonucleotides and, with the help of β2, converts them to deoxyribonucleotides that after futher processing will be used to create DNA. As RNR produces deoxyribonucleotides, levels of DNA building blocks in the cell rise. To avoid overstocking the cell, RNR contains an ‘off switch’ that is triggered when levels of one of the DNA building blocks, dATP, is high enough to occupy a particular site on the alpha unit. Binding of dATP to this site results in three pairs of alpha units getting together to form a stable ring of six units (called α6). How the formation of this stable α6 ring actually turns off RNR was an open question. Here, Brignole, Tsai et al. use a microscopy method called cryo-EM to reveal the three-dimensional structure of the inactive human RNR almost down to the level of individual atoms. When the alpha pairs form an α6 ring, the hole in the center of this circle is smaller than β2, keeping β2 away from α2. This inaccessibility leads to RNR being switched off. If RNR is inactive, DNA synthesis is impaired and cells cannot divide. In turn, controlling whether or not cells proliferate is key to fighting diseases like cancer (where ‘rogue’ cells keep replicating) or bacterial infections. Certain cancer treatments already target RNR, and create the inactive α6 ring structure. In addition, in bacteria, the inactive form of RNR is different from the human one and forms an α4β4 ring,rather than an α6 ring. Understanding the structure of the human inactive RNR could help scientists to find both new anticancer and antibacterial drugs.
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Affiliation(s)
- Edward J Brignole
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Kuang-Lei Tsai
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
| | - Johnathan Chittuluru
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
| | - Haoran Li
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Yimon Aye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, Houston, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Francisco Asturias
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
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34
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Huff SE, Mohammed FA, Yang M, Agrawal P, Pink J, Harris ME, Dealwis CG, Viswanathan R. Structure-Guided Synthesis and Mechanistic Studies Reveal Sweetspots on Naphthyl Salicyl Hydrazone Scaffold as Non-Nucleosidic Competitive, Reversible Inhibitors of Human Ribonucleotide Reductase. J Med Chem 2018; 61:666-680. [PMID: 29253340 PMCID: PMC5808567 DOI: 10.1021/acs.jmedchem.7b00530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductase (RR), an established cancer target, is usually inhibited by antimetabolites, which display multiple cross-reactive effects. Recently, we discovered a naphthyl salicyl acyl hydrazone-based inhibitor (NSAH or E-3a) of human RR (hRR) binding at the catalytic site (C-site) and inhibiting hRR reversibly. We herein report the synthesis and biochemical characterization of 25 distinct analogs. We designed each analog through docking to the C-site of hRR based on our 2.7 Å X-ray crystal structure (PDB ID: 5TUS). Broad tolerance to minor structural variations preserving inhibitory potency is observed. E-3f (82% yield) displayed an in vitro IC50 of 5.3 ± 1.8 μM against hRR, making it the most potent in this series. Kinetic assays reveal that E-3a, E-3c, E-3t, and E-3w bind and inhibit hRR through a reversible and competitive mode. Target selectivity toward the R1 subunit of hRR is established, providing a novel way of inhibition of this crucial enzyme.
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Affiliation(s)
- Sarah E. Huff
- Department of Chemistry, Case Western Reserve University, College of Arts and Sciences, Millis Science Center: Rm 216, 2074, Adelbert Road, Cleveland, OH 44106-7078
| | - Faiz Ahmad Mohammed
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Ave, Cleveland, OH 44106
| | - Mu Yang
- Department of Chemistry, Case Western Reserve University, College of Arts and Sciences, Millis Science Center: Rm 216, 2074, Adelbert Road, Cleveland, OH 44106-7078
| | - Prashansa Agrawal
- Department of Chemistry, Case Western Reserve University, College of Arts and Sciences, Millis Science Center: Rm 216, 2074, Adelbert Road, Cleveland, OH 44106-7078
| | - John Pink
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Ave, Cleveland, OH 44106
| | - Michael E. Harris
- Department of Chemistry, University of Florida, PO Box 117200, Gainseville, FL 32611
| | - Chris G. Dealwis
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Ave, Cleveland, OH 44106
- Center for Proteomics and the Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106
| | - Rajesh Viswanathan
- Frank Hovorka Assistant Professor of Chemistry and Scientific Oversight Board Member – Small Molecule Drug Discovery Core, CWRU, 10900 Euclid Ave, Cleveland, OH 44106
- Department of Chemistry, Case Western Reserve University, College of Arts and Sciences, Millis Science Center: Rm 216, 2074, Adelbert Road, Cleveland, OH 44106-7078
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35
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Rozman Grinberg I, Lundin D, Hasan M, Crona M, Jonna VR, Loderer C, Sahlin M, Markova N, Borovok I, Berggren G, Hofer A, Logan DT, Sjöberg BM. Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit. eLife 2018; 7:31529. [PMID: 29388911 PMCID: PMC5794259 DOI: 10.7554/elife.31529] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 12/23/2017] [Indexed: 12/27/2022] Open
Abstract
Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leeuwenhoekiella blandensis radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 Å crystal structure. We also present evidence for an MnIIIMnIV metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex. When a cell copies its DNA, it uses four different building blocks called deoxyribonucleotides (dNTPs). These consist of one of the four ‘bases’ (A, T, C and G), which pair up to link the two strands of DNA in the double helix, bound to a sugar and a phosphate group. If the cell contains too little or too much of one of these building blocks, an incorrect base may be inserted into the DNA. This results in a mutation, which in bacteria can cause death, and in animals may lead to cancer. The enzyme that fabricates and carefully controls the amount of each dNTP building block inside a cell is called ribonucleotide reductase. Once there are enough building blocks in a cell the enzyme is turned off. A part of the enzyme called the ATP-cone acts as an on/off switch to control this activity. The ribonucleotide reductase consists of a large component and a small component. Until now, studies of the ATP-cone have found it only in the large component of the enzyme. However, when looking through a public database of sequence data, Rozman Grinberg et al. noticed that ribonucleotide reductases in some bacteria have their ATP-cone joined to the small component. Does this ATP-cone also control the amounts of dNTP building blocks inside cells and, if so, how? Rozman Grinberg et al. studied one such ATP-cone in a ribonucleotide reductase from a bacterium (named Leeuwenhoekiella blandensis) found in the Mediterranean Sea. This revealed that when the amount of dNTP building blocks reaches a certain limit, the ATP-cone turns off the enzyme. Examining the three-dimensional structure of the enzyme using a technique called X-ray crystallography revealed that when turned off, the enzyme’s small components are glued together in pairs. This prevents them from working. Rozman Grinberg et al. also discovered that this enzyme contains a new type of metal center with two manganese ions suggesting that a new reaction mechanism may operate in this class of ribonucleotide reductase. These findings support a theory that biological on/off switches can evolve rapidly. In addition to its evolutionary and biomedical interest, understanding how the ATP-cone works might help to improve the enzymes used in industrial processes.
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Affiliation(s)
- Inna Rozman Grinberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mahmudul Hasan
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | | | - Christoph Loderer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Ilya Borovok
- Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Gustav Berggren
- Department of Chemistry, Uppsala University, Uppsala, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Derek T Logan
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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36
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Knappenberger AJ, Grandhi S, Sheth R, Ahmad MF, Viswanathan R, Harris ME. Phylogenetic sequence analysis and functional studies reveal compensatory amino acid substitutions in loop 2 of human ribonucleotide reductase. J Biol Chem 2017; 292:16463-16476. [PMID: 28808063 DOI: 10.1074/jbc.m117.798769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/17/2017] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic class I ribonucleotide reductases (RRs) generate deoxyribonucleotides for DNA synthesis. Binding of dNTP effectors is coupled to the formation of active dimers and induces conformational changes in a short loop (loop 2) to regulate RR specificity among its nucleoside diphosphate substrates. Moreover, ATP and dATP bind at an additional allosteric site 40 Å away from loop 2 and thereby drive formation of activated or inactive hexamers, respectively. To better understand how dNTP binding influences specificity, activity, and oligomerization of human RR, we aligned >300 eukaryotic RR sequences to examine natural sequence variation in loop 2. We found that most amino acids in eukaryotic loop 2 were nearly invariant in this sample; however, two positions co-varied as nonconservative substitutions (N291G and P294K; human numbering). We also found that the individual N291G and P294K substitutions in human RR additively affect substrate specificity. The P294K substitution significantly impaired effector-induced oligomerization required for enzyme activity, and oligomerization was rescued in the N291G/P294K enzyme. None of the other mutants exhibited altered ATP-mediated hexamerization; however, certain combinations of loop 2 mutations and dNTP effectors perturbed ATP's role as an allosteric activator. Our results demonstrate that the observed compensatory covariation of amino acids in eukaryotic loop 2 is essential for its role in dNTP-induced dimerization. In contrast, defects in substrate specificity are not rescued in the double mutant, implying that functional sequence variation elsewhere in the protein is necessary. These findings yield insight into loop 2's roles in regulating RR specificity, allostery, and oligomerization.
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Song Y, Marmion RA, Park JO, Biswas D, Rabinowitz JD, Shvartsman SY. Dynamic Control of dNTP Synthesis in Early Embryos. Dev Cell 2017; 42:301-308.e3. [PMID: 28735680 DOI: 10.1016/j.devcel.2017.06.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/13/2017] [Accepted: 06/16/2017] [Indexed: 02/06/2023]
Abstract
Exponential increase of cell numbers in early embryos requires large amounts of DNA precursors (deoxyribonucleoside triphosphates (dNTPs)). Little is understood about how embryos satisfy this demand. We examined dNTP metabolism in the early Drosophila embryo, in which gastrulation is preceded by 13 sequential nuclear cleavages within only 2 hr of fertilization. Surprisingly, despite the breakneck speed at which Drosophila embryos synthesize DNA, maternally deposited dNTPs can generate less than half of the genomes needed to reach gastrulation. The rest of the dNTPs are synthesized "on the go." The rate-limiting enzyme of dNTP synthesis, ribonucleotide reductase, is inhibited by endogenous levels of deoxyATP (dATP) present at fertilization and is activated as dATP is depleted via DNA polymerization. This feedback inhibition renders the concentration of dNTPs at gastrulation robust, with respect to large variations in maternal supplies, and is essential for normal progression of embryogenesis.
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Affiliation(s)
- Yonghyun Song
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Robert A Marmion
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Junyoung O Park
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Debopriyo Biswas
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA.
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Potent competitive inhibition of human ribonucleotide reductase by a nonnucleoside small molecule. Proc Natl Acad Sci U S A 2017; 114:8241-8246. [PMID: 28716944 DOI: 10.1073/pnas.1620220114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human ribonucleotide reductase (hRR) is crucial for DNA replication and maintenance of a balanced dNTP pool, and is an established cancer target. Nucleoside analogs such as gemcitabine diphosphate and clofarabine nucleotides target the large subunit (hRRM1) of hRR. These drugs have a poor therapeutic index due to toxicity caused by additional effects, including DNA chain termination. The discovery of nonnucleoside, reversible, small-molecule inhibitors with greater specificity against hRRM1 is a key step in the development of more effective treatments for cancer. Here, we report the identification and characterization of a unique nonnucleoside small-molecule hRR inhibitor, naphthyl salicylic acyl hydrazone (NSAH), using virtual screening, binding affinity, inhibition, and cell toxicity assays. NSAH binds to hRRM1 with an apparent dissociation constant of 37 µM, and steady-state kinetics reveal a competitive mode of inhibition. A 2.66-Å resolution crystal structure of NSAH in complex with hRRM1 demonstrates that NSAH functions by binding at the catalytic site (C-site) where it makes both common and unique contacts with the enzyme compared with NDP substrates. Importantly, the IC50 for NSAH is within twofold of gemcitabine for growth inhibition of multiple cancer cell lines, while demonstrating little cytotoxicity against normal mobilized peripheral blood progenitor cells. NSAH depresses dGTP and dATP levels in the dNTP pool causing S-phase arrest, providing evidence for RR inhibition in cells. This report of a nonnucleoside reversible inhibitor binding at the catalytic site of hRRM1 provides a starting point for the design of a unique class of hRR inhibitors.
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Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase. Essays Biochem 2017; 61:281-292. [PMID: 28487404 DOI: 10.1042/ebc20160072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/17/2022]
Abstract
Escherichia coli class Ia ribonucleotide reductase (RNR) catalyzes the conversion of nucleotides to 2'-deoxynucleotides using a radical mechanism. Each turnover requires radical transfer from an assembled diferric tyrosyl radical (Y•) cofactor to the enzyme active site over 35 Å away. This unprecedented reaction occurs via an amino acid radical hopping pathway spanning two protein subunits. To study the mechanism of radical transport in RNR, a suite of biochemical approaches have been developed, such as site-directed incorporation of unnatural amino acids with altered electronic properties and photochemical generation of radical intermediates. The resulting variant RNRs have been investigated using a variety of time-resolved physical techniques, including transient absorption and stopped-flow UV-Vis spectroscopy, as well as rapid freeze-quench EPR, ENDOR, and PELDOR spectroscopic methods. The data suggest that radical transport occurs via proton-coupled electron transfer (PCET) and that the protein structure has evolved to manage the proton and electron transfer co-ordinates in order to prevent 'off-pathway' reactivity and build-up of oxidised intermediates. Thus, precise design and control over the factors that govern PCET is key to enabling reversible and long-range charge transport by amino acid radicals in RNR.
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40
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Lin Q, Parker MJ, Taguchi AT, Ravichandran K, Kim A, Kang G, Shao J, Drennan CL, Stubbe J. Glutamate 52-β at the α/β subunit interface of Escherichia coli class Ia ribonucleotide reductase is essential for conformational gating of radical transfer. J Biol Chem 2017; 292:9229-9239. [PMID: 28377505 DOI: 10.1074/jbc.m117.783092] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/02/2017] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleoside diphosphate substrates (S) to deoxynucleotides with allosteric effectors (e) controlling their relative ratios and amounts, crucial for fidelity of DNA replication and repair. Escherichia coli class Ia RNR is composed of α and β subunits that form a transient, active α2β2 complex. The E. coli RNR is rate-limited by S/e-dependent conformational change(s) that trigger the radical initiation step through a pathway of 35 Å across the subunit (α/β) interface. The weak subunit affinity and complex nucleotide-dependent quaternary structures have precluded a molecular understanding of the kinetic gating mechanism(s) of the RNR machinery. Using a docking model of α2β2 created from X-ray structures of α and β and conserved residues from a new subclassification of the E. coli Ia RNR (Iag), we identified and investigated four residues at the α/β interface (Glu350 and Glu52 in β2 and Arg329 and Arg639 in α2) of potential interest in kinetic gating. Mutation of each residue resulted in loss of activity and with the exception of E52Q-β2, weakened subunit affinity. An RNR mutant with 2,3,5-trifluorotyrosine radical (F3Y122•) replacing the stable Tyr122• in WT-β2, a mutation that partly overcomes conformational gating, was placed in the E52Q background. Incubation of this double mutant with His6-α2/S/e resulted in an RNR capable of catalyzing pathway-radical formation (Tyr356•-β2), 0.5 eq of dCDP/F3Y122•, and formation of an α2β2 complex that is isolable in pulldown assays over 2 h. Negative stain EM images with S/e (GDP/TTP) revealed the uniformity of the α2β2 complex formed.
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Affiliation(s)
- Qinghui Lin
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | | | | | | | | | | | - Jimin Shao
- From the Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou 310058, China and
| | - Catherine L Drennan
- the Departments of Chemistry and .,Biology, and.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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Dose-biomarker-response modeling of the anticancer effect of ethaselen in a human non-small cell lung cancer xenograft mouse model. Acta Pharmacol Sin 2017; 38:223-232. [PMID: 27917873 DOI: 10.1038/aps.2016.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022] Open
Abstract
Thioredoxin reductase (TrxR) is a component of several redox-sensitive signaling cascades that mediate important biological processes such as cell survival, maturation, growth, migration and inhibition of apoptosis. The expression levels of TrxR1 in some human carcinoma cell lines are nearly 10 times higher than those in normal cells. Ethaselen is a novel antitumor candidate that exerts potent inhibition on non-small cell lung cancer (NSCLC) by targeting TrxR. In this study we explored the relationship between the ethaselen dose and TrxR activity level and the relationship between TrxR degradation and tumor apoptosis in a human lung carcinoma A549 xenograft model. BALB/c nude mice implanted with human NSCLC cell line A54 were administered ethaselen (36, 72, 108 mg·kg-1·d-1, ig) or vehicle for 10 d. The tumor size and TrxR activity levels in tumor tissues were daily recorded and detected. Based on the experimental data, NONMEM 7.2 was used to develop an integrated dose-biomarker-response model for describing the quantitative relationship between ethaselen dose and tumor eradication effects. The time course of TrxR activity levels was modeled using an indirect response model (IDR model), in which the influence of the tumor growth rates on Kin with the linear correction factor γ1 (0.021 d/mm). The drug binding-inhibition effects on Kout was described using a sigmoidal Emax model with Smax (5.95), SC50 (136 mg/kg) and Hill's coefficient γ2 (2.29). The influence of TrxR activity inhibition on tumor eradication was characterized by an Emax model with an Emax (130 mm3/d) and EC50 (0.0676). This model was further validated using a visual predictive check (VPC) and was used to predict the efficacy of different doses. In conclusion, the properties and characteristics of ethaselen acting on TrxR degradation and subsequently resulting in tumor apoptosis are characterized by the IDR model and integrated dose-biomarker-response model with high goodness-of-fit and great predicative ability. This approach shed new light on the detailed processes and mechanism of ethaselen action and may offer a valuable reference for an appropriate dosing regimen for use in further clinical applications.
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42
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The Cell Killing Mechanisms of Hydroxyurea. Genes (Basel) 2016; 7:genes7110099. [PMID: 27869662 PMCID: PMC5126785 DOI: 10.3390/genes7110099] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/03/2016] [Accepted: 11/09/2016] [Indexed: 11/23/2022] Open
Abstract
Hydroxyurea is a well-established inhibitor of ribonucleotide reductase that has a long history of scientific interest and clinical use for the treatment of neoplastic and non-neoplastic diseases. It is currently the staple drug for the management of sickle cell anemia and chronic myeloproliferative disorders. Due to its reversible inhibitory effect on DNA replication in various organisms, hydroxyurea is also commonly used in laboratories for cell cycle synchronization or generating replication stress. However, incubation with high concentrations or prolonged treatment with low doses of hydroxyurea can result in cell death and the DNA damage generated at arrested replication forks is generally believed to be the direct cause. Recent studies in multiple model organisms have shown that oxidative stress and several other mechanisms may contribute to the majority of the cytotoxic effect of hydroxyurea. This review aims to summarize the progress in our understanding of the cell-killing mechanisms of hydroxyurea, which may provide new insights towards the improvement of chemotherapies that employ this agent.
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Knappenberger AJ, Ahmad MF, Viswanathan R, Dealwis CG, Harris ME. Nucleoside Analogue Triphosphates Allosterically Regulate Human Ribonucleotide Reductase and Identify Chemical Determinants That Drive Substrate Specificity. Biochemistry 2016; 55:5884-5896. [PMID: 27634056 DOI: 10.1021/acs.biochem.6b00594] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Class I ribonucleotide reductase (RR) maintains balanced pools of deoxyribonucleotide substrates for DNA replication by converting ribonucleoside diphosphates (NDPs) to 2'-deoxyribonucleoside diphosphates (dNDPs). Binding of deoxynucleoside triphosphate (dNTP) effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I RR for CDP, UDP, ADP, and GDP substrates. Crystal structures of bacterial and eukaryotic RRs show that dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop (loop 2). Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of RR. However, the functional groups proposed to drive specificity remain untested. Here, we use deoxynucleoside analogue triphosphates to determine the nucleobase functional groups that drive human RR (hRR) specificity. The results demonstrate that the 5-methyl, O4, and N3 groups of dTTP contribute to specificity for GDP. The O6 and protonated N1 of dGTP direct specificity for ADP. In contrast, the unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP. Structural models from X-ray crystallography of eukaryotic RR suggest that the side chain of D287 in loop 2 is involved in binding of dGTP and dTTP, but not dATP/ATP. This feature is consistent with experimental results showing that a D287A mutant of hRR is deficient in allosteric regulation by dGTP and dTTP, but not ATP/dATP. Together, these data define the effector functional groups that are the drivers of human RR specificity and provide constraints for evaluating models of allosteric regulation.
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Affiliation(s)
- Andrew J Knappenberger
- Departments of Biochemistry, ‡Pharmacology, and §Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Md Faiz Ahmad
- Departments of Biochemistry, ‡Pharmacology, and §Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Rajesh Viswanathan
- Departments of Biochemistry, ‡Pharmacology, and §Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Chris G Dealwis
- Departments of Biochemistry, ‡Pharmacology, and §Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | - Michael E Harris
- Departments of Biochemistry, ‡Pharmacology, and §Chemistry, Case Western Reserve University , Cleveland, Ohio 44106, United States
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44
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Jang S, Zhou X, Ahn J. Substrate Specificity of SAMHD1 Triphosphohydrolase Activity Is Controlled by Deoxyribonucleoside Triphosphates and Phosphorylation at Thr592. Biochemistry 2016; 55:5635-5646. [PMID: 27588835 DOI: 10.1021/acs.biochem.6b00627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The sterile alpha motif (SAM) and histidine-aspartate (HD) domain containing protein 1 (SAMHD1) constitute a triphosphohydrolase that converts deoxyribonucleoside triphosphates (dNTPs) into deoxyribonucleosides and triphosphates. SAMHD1 exists in multiple states. The monomer and apo- or GTP-bound dimer are catalytically inactive. Binding of dNTP at allosteric site 2 (AS2), adjacent to GTP-binding allosteric site 1 (AS1), induces formation of the tetramer, the catalytically active form. We have developed an enzyme kinetic assay, tailored to control specific dNTP binding at each site, allowing us to determine the kinetic binding parameters of individual dNTPs at both the AS2 and catalytic sites for all possible combinations of dNTP binding at both sites. Here, we show that the apparent Km values of dNTPs at AS2 vary in the order of dCTP < dGTP < dATP < dTTP. Interestingly, dCTP binding at AS2 significantly reduces the dCTP hydrolysis rate, which is restored to a rate comparable to that of other dNTPs upon dGTP, dATP, or dTTP binding at AS2. Strikingly, a phosphomimetic mutant, Thr592Asp SAMHD1 as well as phospho-Thr592, show a significantly altered substrate specificity, with the rate of dCTP hydrolysis being selectively reduced regardless of which dNTP binds at AS2. Furthermore, cyclin A2 binding at the C-terminus of SAMHD1 induces the disassembly of the SAMHD1 tetramer, suggesting an additional layer of SAMHD1 activity modulation by cyclin A2/CDK2 kinase. Together, our results reveal multiple allosteric mechanisms for controlling the rate of dNTP destruction by SAMHD1.
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Affiliation(s)
- Sunbok Jang
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Xiaohong Zhou
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
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45
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Bhattacharya A, Wang Z, White T, Buffone C, Nguyen LA, Shepard CN, Kim B, Demeler B, Diaz-Griffero F, Ivanov DN. Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect. Sci Rep 2016; 6:31353. [PMID: 27511536 PMCID: PMC4980677 DOI: 10.1038/srep31353] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/18/2016] [Indexed: 12/30/2022] Open
Abstract
SAMHD1, a dNTP triphosphohydrolase, contributes to interferon signaling and restriction of retroviral replication. SAMHD1-mediated retroviral restriction is thought to result from the depletion of cellular dNTP pools, but it remains controversial whether the dNTPase activity of SAMHD1 is sufficient for restriction. The restriction ability of SAMHD1 is regulated in cells by phosphorylation on T592. Phosphomimetic mutations of T592 are not restriction competent, but appear intact in their ability to deplete cellular dNTPs. Here we use analytical ultracentrifugation, fluorescence polarization and NMR-based enzymatic assays to investigate the impact of phosphomimetic mutations on SAMHD1 tetramerization and dNTPase activity in vitro. We find that phosphomimetic mutations affect kinetics of tetramer assembly and disassembly, but their effects on tetramerization equilibrium and dNTPase activity are insignificant. In contrast, the Y146S/Y154S dimerization-defective mutant displays a severe dNTPase defect in vitro, but is indistinguishable from WT in its ability to deplete cellular dNTP pools and to restrict HIV replication. Our data suggest that the effect of T592 phosphorylation on SAMHD1 tetramerization is not likely to explain the retroviral restriction defect, and we hypothesize that enzymatic activity of SAMHD1 is subject to additional cellular regulatory mechanisms that have not yet been recapitulated in vitro.
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Affiliation(s)
- Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Zhonghua Wang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Tommy White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura A Nguyen
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Caitlin N Shepard
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA.,School of Pharmacy, Kyunghee University, Seoul, South Korea
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dmitri N Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
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Misko TA, Wijerathna SR, Radivoyevitch T, Berdis AJ, Ahmad MF, Harris ME, Dealwis CG. Inhibition of yeast ribonucleotide reductase by Sml1 depends on the allosteric state of the enzyme. FEBS Lett 2016; 590:1704-12. [PMID: 27155231 DOI: 10.1002/1873-3468.12207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 11/05/2022]
Abstract
Sml1 is an intrinsically disordered protein inhibitor of Saccharomyces cerevisiae ribonucleotide reductase (ScRR1), but its inhibition mechanism is poorly understood. RR reduces ribonucleoside diphosphates to their deoxy forms, and balances the nucleotide pool. Multiple turnover kinetics show that Sml1 inhibition of dGTP/ADP- and ATP/CDP-bound ScRR follows a mixed inhibition mechanism. However, Sml1 cooperatively binds to the ES complex in the dGTP/ADP form, whereas with ATP/CDP, Sml1 binds weakly and noncooperatively. Gel filtration and mutagenesis studies indicate that Sml1 does not alter the oligomerization equilibrium and the CXXC motif is not involved in the inhibition. The data suggest that Sml1 is an allosteric inhibitor.
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Affiliation(s)
- Tessianna A Misko
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Sanath R Wijerathna
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic Foundation, OH, USA
| | | | - Md Faiz Ahmad
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Chris G Dealwis
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
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47
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Clark AK, Wilder JH, Grayson AW, Johnson QR, Lindsay RJ, Nellas RB, Fernandez EJ, Shen T. The Promiscuity of Allosteric Regulation of Nuclear Receptors by Retinoid X Receptor. J Phys Chem B 2016; 120:8338-45. [PMID: 27110634 DOI: 10.1021/acs.jpcb.6b02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The promiscuous protein retinoid X receptor (RXR) displays essential allosteric regulation of several members in the nuclear hormone receptor superfamily via heterodimerization and (anti)cooperative binding of cognate ligands. Here, the structural basis of the positive allostery of RXR and constitutive androstane receptor (CAR) is revealed. In contrast, a similar computational approach had previously revealed the mechanism for negative allostery in the complex of RXR and thyroid receptor (TR). By comparing the positive and negative allostery of RXR complexed with CAR and TR respectively, we reported the promiscuous allosteric control involving RXR. We characterize the allosteric mechanism by expressing the correlated dynamics of selected residue-residue contacts which was extracted from atomistic molecular dynamics simulation and statistical analysis. While the same set of residues in the binding pocket of RXR may initiate the residue-residue interaction network, RXR uses largely different sets of contacts (only about one-third identical) and allosteric modes to regulate TR and CAR. The promiscuity of RXR control may originate from multiple factors, including (1) the frustrated fit of cognate ligand 9c to the RXR binding pocket and (2) the different ligand-binding features of TR (loose) versus CAR (tight) to their corresponding cognate ligands.
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Affiliation(s)
| | | | | | - Quentin R Johnson
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Richard J Lindsay
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Ricky B Nellas
- Institute of Chemistry, University of the Philippines Diliman , Quezon City, Philippines
| | | | - Tongye Shen
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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