1
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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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2
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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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3
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Fietze T, Wilk P, Kabinger F, Anoosheh S, Hofer A, Lundin D, Feiler CG, Weiss MS, Loderer C. HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry 2022; 61:1633-1641. [PMID: 35856337 DOI: 10.1021/acs.biochem.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from Rhodobacter sphaeroides reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.
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Affiliation(s)
- Tobias Fietze
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
| | - Piotr Wilk
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany.,Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 31-007, Poland
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Saber Anoosheh
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - Christian G Feiler
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Christoph Loderer
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
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4
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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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5
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Ueno H, Hoshino T, Yano W, Tsukioka S, Suzuki T, Hara S, Ogino Y, Chong KT, Suzuki T, Tsuji S, Itadani H, Yamamiya I, Otsu Y, Ito S, Yonekura T, Terasaka M, Tanaka N, Miyahara S. TAS1553, a small molecule subunit interaction inhibitor of ribonucleotide reductase, exhibits antitumor activity by causing DNA replication stress. Commun Biol 2022; 5:571. [PMID: 35681099 PMCID: PMC9184620 DOI: 10.1038/s42003-022-03516-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/22/2022] [Indexed: 01/03/2023] Open
Abstract
Ribonucleotide reductase (RNR) is composed of two non-identical subunits, R1 and R2, and plays a crucial role in balancing the cellular dNTP pool, establishing it as an attractive cancer target. Herein, we report the discovery of a highly potent and selective small-molecule inhibitor, TAS1553, targeting protein-protein interaction between R1 and R2. TAS1553 is also expected to demonstrate superior selectivity because it does not directly target free radical or a substrate binding site. TAS1553 has shown antiproliferative activity in human cancer cell lines, dramatically reducing the intracellular dATP pool and causing DNA replication stress. Furthermore, we identified SLFN11 as a biomarker that predicts the cytotoxic effect of TAS1553. Oral administration of TAS1553 demonstrated robust antitumor efficacy against both hematological and solid cancer xenograft tumors and also provided a significant survival benefit in an acute myelogenous leukemia model. Our findings strongly support the evaluation of TAS1553 in clinical trials. A small-molecule protein-protein interaction inhibitor of ribonucleotide reductase subunit, TAS1553, is shown to inhibit growth of both hematological and solid cancer xenograft tumors following oral administration in mice.
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6
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Rozman Grinberg I, Martínez-Carranza M, Bimai O, Nouaïria G, Shahid S, Lundin D, Logan DT, Sjöberg BM, Stenmark P. A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Nat Commun 2022; 13:2700. [PMID: 35577776 PMCID: PMC9110341 DOI: 10.1038/s41467-022-30328-1] [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: 09/20/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRibonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria — including well-known pathogens such as Mycobacterium tuberculosis — NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.
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7
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Salvador PJ, Jacobs HB, Alnouri L, Fee A, Utley LM, Mabry M, Krajeck H, Dicksion C, Awad AM. Synthesis and in silico evaluation of novel uridyl sulfamoylbenzoate derivatives as potential anticancer agents targeting M1 subunit of human ribonucleotide reductase (hRRM1). Med Chem Res 2022. [DOI: 10.1007/s00044-021-02840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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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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9
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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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10
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Hasan M, Banerjee I, Rozman Grinberg I, Sjöberg BM, Logan DT. Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy. Front Mol Biosci 2021; 8:713608. [PMID: 34381817 PMCID: PMC8350387 DOI: 10.3389/fmolb.2021.713608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/21/2021] [Indexed: 01/14/2023] Open
Abstract
The essential enzyme ribonucleotide reductase (RNR) is highly regulated both at the level of overall activity and substrate specificity. Studies of class I, aerobic RNRs have shown that overall activity is downregulated by the binding of dATP to a small domain known as the ATP-cone often found at the N-terminus of RNR subunits, causing oligomerization that prevents formation of a necessary α2β2 complex between the catalytic (α2) and radical generating (β2) subunits. In some relatively rare organisms with RNRs of the subclass NrdAi, the ATP-cone is found at the N-terminus of the β subunit rather than more commonly the α subunit. Binding of dATP to the ATP-cone in β results in formation of an unusual β4 tetramer. However, the structural basis for how the formation of the active complex is hindered by such oligomerization has not been studied. Here we analyse the low-resolution three-dimensional structures of the separate subunits of an RNR from subclass NrdAi, as well as the α4β4 octamer that forms in the presence of dATP. The results reveal a type of oligomer not previously seen for any class of RNR and suggest a mechanism for how binding of dATP to the ATP-cone switches off catalysis by sterically preventing formation of the asymmetrical α2β2 complex.
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Affiliation(s)
- Mahmudul Hasan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | - Ipsita Banerjee
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | | | - Britt-Marie Sjöberg
- Dept. of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
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11
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Abstract
Metabolism is an important part of tumorigenesis as well as progression. The various cancer metabolism pathways, such as glucose metabolism and glutamine metabolism, directly regulate the development and progression of cancer. The pathways by which the cancer cells rewire their metabolism according to their needs, surrounding environment and host tissue conditions are an important area of study. The regulation of these metabolic pathways is determined by various oncogenes, tumor suppressor genes, as well as various constituent cells of the tumor microenvironment. Expanded studies on metabolism will help identify efficient biomarkers for diagnosis and strategies for therapeutic interventions and countering ways by which cancers may acquire resistance to therapy.
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12
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Song Y, Shvartsman SY. Chemical Embryology Redux: Metabolic Control of Development. Trends Genet 2020; 36:577-586. [PMID: 32532533 PMCID: PMC10947471 DOI: 10.1016/j.tig.2020.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
New studies of metabolic reactions and networks in embryos are making important additions to regulatory models of development, so far dominated by genes and signals. Metabolic control of development is not a new idea and can be traced back to Joseph Needham's 'Chemical Embryology', published in the 1930s. Even though Needham's ideas fell by the wayside with the advent of genetic studies of embryogenesis, they demonstrated that embryos provide convenient models for addressing fundamental questions in biochemistry and are now experiencing a comeback, enabled by the powerful merger of detailed mechanistic studies and systems-level techniques. Here we review recent results from studies that quantified the energy budget of embryogenesis in Drosophila and started to untangle the intricate connections between core anabolic processes and developmental transitions. Dynamic coordination of metabolic, genetic, and signaling networks appears to be essential for seamless progression of development.
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Affiliation(s)
- Yonghyun Song
- Computational Sciences Department, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - 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; Center for Computational Biology, Flatiron Institute - Simons Foundation, New York, NY 10010, USA.
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13
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Chen PC, Masiewicz P, Perez K, Hennig J. Structure-based screening of binding affinities via small-angle X-ray scattering. IUCRJ 2020; 7:644-655. [PMID: 32695411 PMCID: PMC7340254 DOI: 10.1107/s2052252520004169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Protein-protein and protein-ligand interactions often involve conformational changes or structural rearrangements that can be quantified by solution small-angle X-ray scattering (SAXS). These scattering intensity measurements reveal structural details of the bound complex, the number of species involved and, additionally, the strength of interactions if carried out as a titration. Although a core part of structural biology workflows, SAXS-based titrations are not commonly used in drug discovery contexts. This is because prior knowledge of expected sample requirements, throughput and prediction accuracy is needed to develop reliable ligand screens. This study presents the use of the histidine-binding protein (26 kDa) and other periplasmic binding proteins to benchmark ligand screen performance. Sample concentrations and exposure times were varied across multiple screening trials at four beamlines to investigate the accuracy and precision of affinity prediction. The volatility ratio between titrated scattering curves and a common apo reference is found to most reliably capture the extent of structural and population changes. This obviates the need to explicitly model scattering intensities of bound complexes, which can be strongly ligand-dependent. Where the dissociation constant is within 102 of the protein concentration and the total exposure times exceed 20 s, the titration protocol presented at 0.5 mg ml-1 yields affinities comparable to isothermal titration calorimetry measurements. Estimated throughput ranges between 20 and 100 ligand titrations per day at current synchrotron beamlines, with the limiting step imposed by sample handling and cleaning procedures.
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Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Kathryn Perez
- Protein Expression and Purification Core Facility, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69126 Heidelberg, Germany
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14
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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: 101] [Impact Index Per Article: 25.3] [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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15
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Ravichandran K, Olshansky L, Nocera DG, Stubbe J. Subunit Interaction Dynamics of Class Ia Ribonucleotide Reductases: In Search of a Robust Assay. Biochemistry 2020; 59:1442-1453. [PMID: 32186371 DOI: 10.1021/acs.biochem.0c00001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides (NDP) to deoxynucleotides (dNDP), in part, by controlling the ratios and quantities of dNTPs available for DNA replication and repair. The active form of Escherichia coli class Ia RNR is an asymmetric α2β2 complex in which α2 contains the active site and β2 contains the stable diferric-tyrosyl radical cofactor responsible for initiating the reduction chemistry. Each dNDP is accompanied by disulfide bond formation. We now report that, under in vitro conditions, β2 can initiate turnover in α2 catalytically under both "one" turnover (no external reductant, though producing two dCDPs) and multiple turnover (with an external reductant) assay conditions. In the absence of reductant, rapid chemical quench analysis of a reaction of α2, substrate, and effector with variable amounts of β2 (1-, 10-, and 100-fold less than α2) yields 3 dCDP/α2 at all ratios of α2:β2 with a rate constant of 8-9 s-1, associated with a rate-limiting conformational change. Stopped-flow fluorescence spectroscopy with a fluorophore-labeled β reveals that the rate constants for subunit association (163 ± 7 μM-1 s-1) and dissociation (75 ± 10 s-1) are fast relative to turnover, consistent with catalytic β2. When assaying in the presence of an external reducing system, the turnover number is dictated by the ratio of α2:β2, their concentrations, and the concentration and nature of the reducing system; the rate-limiting step can change from the conformational gating to a step or steps involving disulfide rereduction, dissociation of the inhibited α4β4 state, or both. The issues encountered with E. coli RNR are likely of importance in all class I RNRs and are central to understanding the development of screening assays for inhibitors of these enzymes.
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Affiliation(s)
- Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lisa Olshansky
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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16
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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17
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Long MJC, Van Hall-Beauvais A, Aye Y. The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase. Curr Opin Chem Biol 2019; 54:10-18. [PMID: 31734537 DOI: 10.1016/j.cbpa.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 02/05/2023]
Abstract
Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of 'omics', we discuss what makes the larger subunit of this enzyme (RNR-α) so interesting, highlighting its emerging cellular interactome based on its unique oligomeric dynamism that dictates its compartment-specific occupations. Linking the history of the field with the multivariable nature of this exceedingly sophisticated enzyme, we further discuss implications of new data pertaining to DNA-damage response, S-phase checkpoints, and ultimately tumor suppression. We hereby hope to provide ideas for those interested in these fields and exemplify conceptual frameworks and tools that are useful to study RNR's broader roles in biology.
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Affiliation(s)
| | - Alexandra Van Hall-Beauvais
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland.
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18
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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: 21] [Impact Index Per Article: 4.2] [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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19
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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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20
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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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21
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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22
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Chang WC, Liu P, Guo Y. Mechanistic Elucidation of Two Catalytically Versatile Iron(II)- and α-Ketoglutarate-Dependent Enzymes: Cases Beyond Hydroxylation. COMMENT INORG CHEM 2018. [DOI: 10.1080/02603594.2018.1509856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei-chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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23
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Fu Y, Long MJC, Wisitpitthaya S, Inayat H, Pierpont TM, Elsaid IM, Bloom JC, Ortega J, Weiss RS, Aye Y. Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3. Nat Chem Biol 2018; 14:943-954. [PMID: 30150681 DOI: 10.1038/s41589-018-0113-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/28/2018] [Indexed: 11/09/2022]
Abstract
Since the origins of DNA-based life, the enzyme ribonucleotide reductase (RNR) has spurred proliferation because of its rate-limiting role in de novo deoxynucleoside-triphosphate (dNTP) biosynthesis. Paradoxically, the large subunit, RNR-α, of this obligatory two-component complex in mammals plays a context-specific antiproliferative role. There is little explanation for this dichotomy. Here, we show that RNR-α has a previously unrecognized DNA-replication inhibition function, leading to growth retardation. This underappreciated biological activity functions in the nucleus, where RNR-α interacts with ZRANB3. This process suppresses ZRANB3's function in unstressed cells, which we show to promote DNA synthesis. This nonreductase function of RNR-α is promoted by RNR-α hexamerization-induced by a natural and synthetic nucleotide of dA/ClF/CLA/FLU-which elicits rapid RNR-α nuclear import. The newly discovered nuclear signaling axis is a primary defense against elevated or imbalanced dNTP pools that can exert mutagenic effects irrespective of the cell cycle.
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Affiliation(s)
- Yuan Fu
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Marcus J C Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Huma Inayat
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | | | - Islam M Elsaid
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Jordana C Bloom
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland.
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24
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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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25
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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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26
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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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27
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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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28
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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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29
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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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30
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Abstract
Ribonucleotide reductases of the class I family are α2β2 tetramers. Like all RNRs they are subject to allosteric control mechanisms affecting activity and specificity. In this issue of Structure, Johansson et al. (2016) present a structural analysis of an unusual mode of activity site regulation.
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Affiliation(s)
- Christopher K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.
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31
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Abstract
X-ray scattering is uniquely suited to the study of disordered systems and thus has the potential to provide insight into dynamic processes where diffraction methods fail. In particular, while X-ray crystallography has been a staple of structural biology for more than half a century and will continue to remain so, a major limitation of this technique has been the lack of dynamic information. Solution X-ray scattering has become an invaluable tool in structural and mechanistic studies of biological macromolecules where large conformational changes are involved. Such systems include allosteric enzymes that play key roles in directing metabolic fluxes of biochemical pathways, as well as large, assembly-line type enzymes that synthesize secondary metabolites with pharmaceutical applications. Furthermore, crystallography has the potential to provide information on protein dynamics via the diffuse scattering patterns that are overlaid with Bragg diffraction. Historically, these patterns have been very difficult to interpret, but recent advances in X-ray detection have led to a renewed interest in diffuse scattering analysis as a way to probe correlated motions. Here, we will review X-ray scattering theory and highlight recent advances in scattering-based investigations of protein solutions and crystals, with a particular focus on complex enzymes.
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Affiliation(s)
- Steve P Meisburger
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - William C Thomas
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
| | - Nozomi Ando
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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32
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Lou M, Liu Q, Ren G, Zeng J, Xiang X, Ding Y, Lin Q, Zhong T, Liu X, Zhu L, Qi H, Shen J, Li H, Shao J. Physical interaction between human ribonucleotide reductase large subunit and thioredoxin increases colorectal cancer malignancy. J Biol Chem 2017; 292:9136-9149. [PMID: 28411237 DOI: 10.1074/jbc.m117.783365] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/11/2017] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase (RR) is the rate-limiting enzyme in DNA synthesis, catalyzing the reduction of ribonucleotides to deoxyribonucleotides. During each enzymatic turnover, reduction of the active site disulfide in the catalytic large subunit is performed by a pair of shuttle cysteine residues in its C-terminal tail. Thioredoxin (Trx) and glutaredoxin (Grx) are ubiquitous redox proteins, catalyzing thiol-disulfide exchange reactions. Here, immunohistochemical examination of clinical colorectal cancer (CRC) specimens revealed that human thioredoxin1 (hTrx1), but not human glutaredoxin1 (hGrx1), was up-regulated along with human RR large subunit (RRM1) in cancer tissues, and the expression levels of both proteins were correlated with cancer malignancy stage. Ectopically expressed hTrx1 significantly increased RR activity, DNA synthesis, and cell proliferation and migration. Importantly, inhibition of both hTrx1 and RRM1 produced a synergistic anticancer effect in CRC cells and xenograft mice. Furthermore, hTrx1 rather than hGrx1 was the efficient reductase for RRM1 regeneration. We also observed a direct protein-protein interaction between RRM1 and hTrx1 in CRC cells. Interestingly, besides the known two conserved cysteines, a third cysteine (Cys779) in the RRM1 C terminus was essential for RRM1 regeneration and binding to hTrx1, whereas both Cys32 and Cys35 in hTrx1 played a counterpart role. Our findings suggest that the up-regulated RRM1 and hTrx1 in CRC directly interact with each other and promote RR activity, resulting in enhanced DNA synthesis and cancer malignancy. We propose that the RRM1-hTrx1 interaction might be a novel potential therapeutic target for cancer treatment.
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Affiliation(s)
- Meng Lou
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qian Liu
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | | | | | - Xueping Xiang
- the Department of Pathology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China, and
| | | | - Qinghui Lin
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tingting Zhong
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xia Liu
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lijun Zhu
- Key Laboratory of Precision Diagnosis and Treatment for Hepatobiliary and Pancreatic Tumor of Zhejiang Province, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Hongyan Qi
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Shen
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Haoran Li
- Takeda Pharmaceuticals International Company, Cambridge, Massachusetts 02139
| | - Jimin Shao
- From the Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, Research Center for Air Pollution and Health, Zhejiang University School of Medicine, Hangzhou 310058, China,
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33
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Foskolou IP, Jorgensen C, Leszczynska KB, Olcina MM, Tarhonskaya H, Haisma B, D'Angiolella V, Myers WK, Domene C, Flashman E, Hammond EM. Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication. Mol Cell 2017; 66:206-220.e9. [PMID: 28416140 PMCID: PMC5405111 DOI: 10.1016/j.molcel.2017.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 02/13/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target. RRM2B is induced in response to hypoxia in both cell models and patient datasets RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity
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Affiliation(s)
- Iosifina P Foskolou
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Christian Jorgensen
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Monica M Olcina
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Hanna Tarhonskaya
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Bauke Haisma
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - William K Myers
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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34
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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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35
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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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36
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Crona M, Codó P, Jonna VR, Hofer A, Fernandes AP, Tholander F. A ribonucleotide reductase inhibitor with deoxyribonucleoside-reversible cytotoxicity. Mol Oncol 2016; 10:1375-1386. [PMID: 27511871 DOI: 10.1016/j.molonc.2016.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
Ribonucleotide Reductase (RNR) is the sole enzyme that catalyzes the reduction of ribonucleotides into deoxyribonucleotides. Even though RNR is a recognized target for antiproliferative molecules, and the main target of the approved drug hydroxyurea, few new leads targeted to this enzyme have been developed. We have evaluated a recently identified set of RNR inhibitors with respect to inhibition of the human enzyme and cellular toxicity. One compound, NSC73735, is particularly interesting; it is specific for leukemia cells and is the first identified compound that hinders oligomerization of the mammalian large RNR subunit. Similar to hydroxyurea, it caused a disruption of the cell cycle distribution of cultured HL-60 cells. In contrast to hydroxyurea, the disruption was reversible, indicating higher specificity. NSC73735 thus defines a potential lead candidate for RNR-targeted anticancer drugs, as well as a chemical probe with better selectivity for RNR inhibition than hydroxyurea.
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Affiliation(s)
- Mikael Crona
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Paula Codó
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | | | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Aristi P Fernandes
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Fredrik Tholander
- Department of Medicinal Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.
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37
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Wisitpitthaya S, Zhao Y, Long MJC, Li M, Fletcher EA, Blessing WA, Weiss RS, Aye Y. Cladribine and Fludarabine Nucleotides Induce Distinct Hexamers Defining a Common Mode of Reversible RNR Inhibition. ACS Chem Biol 2016; 11:2021-32. [PMID: 27159113 DOI: 10.1021/acschembio.6b00303] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The enzyme ribonucleotide reductase (RNR) is a major target of anticancer drugs. Until recently, suicide inactivation in which synthetic substrate analogs (nucleoside diphosphates) irreversibly inactivate the RNR-α2β2 heterodimeric complex was the only clinically proven inhibition pathway. For instance, this mechanism is deployed by the multifactorial anticancer agent gemcitabine diphosphate. Recently reversible targeting of RNR-α-alone coupled with ligand-induced RNR-α-persistent hexamerization has emerged to be of clinical significance. To date, clofarabine nucleotides are the only known example of this mechanism. Herein, chemoenzymatic syntheses of the active forms of two other drugs, phosphorylated cladribine (ClA) and fludarabine (FlU), allow us to establish that reversible inhibition is common to numerous drugs in clinical use. Enzyme inhibition and fluorescence anisotropy assays show that the di- and triphosphates of the two nucleosides function as reversible (i.e., nonmechanism-based) inhibitors of RNR and interact with the catalytic (C site) and the allosteric activity (A site) sites of RNR-α, respectively. Gel filtration, protease digestion, and FRET assays demonstrate that inhibition is coupled with formation of conformationally diverse hexamers. Studies in 293T cells capable of selectively inducing either wild-type or oligomerization-defective mutant RNR-α overexpression delineate the central role of RNR-α oligomerization in drug activity, and highlight a potential resistance mechanism to these drugs. These data set the stage for new interventions targeting RNR oligomeric regulation.
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Affiliation(s)
- Somsinee Wisitpitthaya
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yi Zhao
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Marcus J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Minxing Li
- Department
of Biomedical Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Elaine A. Fletcher
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - William A. Blessing
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Robert S. Weiss
- Department
of Biomedical Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones. Structure 2016; 24:906-17. [PMID: 27133024 DOI: 10.1016/j.str.2016.03.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/22/2022]
Abstract
Ribonucleotide reductases (RNRs) reduce ribonucleotides to deoxyribonucleotides. Their overall activity is stimulated by ATP and downregulated by dATP via a genetically mobile ATP cone domain mediating the formation of oligomeric complexes with varying quaternary structures. The crystal structure and solution X-ray scattering data of a novel dATP-induced homotetramer of the Pseudomonas aeruginosa class I RNR reveal the structural bases for its unique properties, namely one ATP cone that binds two dATP molecules and a second one that is non-functional, binding no nucleotides. Mutations in the observed tetramer interface ablate oligomerization and dATP-induced inhibition but not the ability to bind dATP. Sequence analysis shows that the novel type of ATP cone may be widespread in RNRs. The present study supports a scenario in which diverse mechanisms for allosteric activity regulation are gained and lost through acquisition and evolutionary erosion of different types of ATP cone.
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