Structure of a ribonucleotide reductase R2 protein radical

Lebrette, Hugo; Srinivas, Vivek; John, Juliane; Aurelius, Oskar; Kumar, Rohit; Lundin, Daniel; Brewster, Aaron S.; Bhowmick, Asmit; Sirohiwal, Abhishek; Kim, In-Sik; Gul, Sheraz; Pham, Cindy; Sutherlin, Kyle D.; Simon, Philipp; Butryn, Agata; Aller, Pierre; Orville, Allen M.; Fuller, Franklin D.; Alonso-Mori, Roberto; Batyuk, Alexander; Sauter, Nicholas K.; Yachandra, Vittal K.; Yano, Junko; Kaila, Ville I.; Sjöberg, Britt-Marie; Kern, Jan; Roos, Katarina; Högbom, Martin

doi:10.1126/science.adh8160

Structure of a ribonucleotide reductase R2 protein radical

Journal Article · Thu Oct 05 00:00:00 EDT 2023 · Science

DOI:https://doi.org/10.1126/science.adh8160· OSTI ID:2439705

^[1]; ^[2]; ^[2]; Aurelius, Oskar ^[3]; ^[2]; ^[2]; ^[4]; ^[4]; ^[2]; ^[4]; ^[4]; Pham, Cindy ^[4]; ^[4]; ^[4]; ^[5]; Aller, Pierre ^[5]; ^[5]; Fuller, Franklin D. ^[6]; ^[6]; ^[6] more »

Stockholm Univ. (Sweden); Univ. of Toulouse (France); Centre National de la Recherche Scientifique (CNRS) (France)
Stockholm Univ. (Sweden); Arrhenius Laboratories for Natural Sciences, Stockholm (Sweden)
Stockholm Univ. (Sweden); Arrhenius Laboratories for Natural Sciences, Stockholm (Sweden); Lund Univ. (Sweden)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Science and Technology Facilities Council (STFC), Oxford (United Kingdom). Diamond Light Source, Ltd.
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
Uppsala Univ. (Sweden); Sprint Bioscience, Huddinge (Sweden)

Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). Here we present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O–O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 2439705

Journal Information:: Science, Journal Name: Science Journal Issue: 6666 Vol. 382; ISSN 0036-8075

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: English

References (58)

MolProbity: More and better reference data for improved all-atom structure validation: PROTEIN SCIENCE.ORG Williams, Christopher J.; Headd, Jeffrey J.; Moriarty, Nigel W. Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3330	journal	November 2017
Hydroxyurea and hydroxamic acid derivatives as antitumor drugs Saban, Nina; Bujak, Maro Cancer Chemotherapy and Pharmacology, Vol. 64, Issue 2 https://doi.org/10.1007/s00280-009-0991-z	journal	April 2009
Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access Grāve, Kristīne; Lambert, Wietske; Berggren, Gustav JBIC Journal of Biological Inorganic Chemistry, Vol. 24, Issue 6 https://doi.org/10.1007/s00775-019-01703-z	journal	August 2019
Electron Spin Resonance of the Iron-containing Protein B2 from Ribonucleotide Reductase Ehrenberg, Anders; Reichard, Peter Journal of Biological Chemistry, Vol. 247, Issue 11 https://doi.org/10.1016/S0021-9258(19)45166-1	journal	June 1972
Orientation of the Tyrosyl Radical in Salmonella typhimurium Class Ib Ribonucleotide Reductase Determined by High Field EPR of R2F Single Crystals Galander, Marcus; Uppsten, Malin; Uhlin, Ulla Journal of Biological Chemistry, Vol. 281, Issue 42 https://doi.org/10.1016/S0021-9258(19)84089-9	journal	October 2006
Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site Logan, Derek T.; Su, Xiao-Dong; Åberg, Anders Structure, Vol. 4, Issue 9 https://doi.org/10.1016/S0969-2126(96)00112-8	journal	September 1996
Low barrier hydrogen bonds in protein structure and function Kemp, M. Trent; Lewandowski, Eric M.; Chen, Yu Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1869, Issue 1 https://doi.org/10.1016/j.bbapap.2020.140557	journal	January 2021
Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality Cooley, Richard B.; Arp, Daniel J.; Karplus, P. Andrew Journal of Molecular Biology, Vol. 404, Issue 2 https://doi.org/10.1016/j.jmb.2010.09.034	journal	November 2010
Are Short, Low-Barrier Hydrogen Bonds Unusually Strong? Perrin, Charles L. Accounts of Chemical Research, Vol. 43, Issue 12 https://doi.org/10.1021/ar100097j	journal	December 2010
Crystal Structure of the Di-iron/Radical Protein of Ribonucleotide Reductase from Corynebacterium ammoniagenes^, Högbom, Martin; Huque, Yasmin; Sjöberg, Britt-Marie Biochemistry, Vol. 41, Issue 4 https://doi.org/10.1021/bi011429l	journal	December 2001
Structure of Salmonella typhimurium nrdF Ribonucleotide Reductase in Its Oxidized and Reduced Forms ^† ^, ^‡ Eriksson, Mathias; Jordan, Albert; Eklund, Hans Biochemistry, Vol. 37, Issue 38 https://doi.org/10.1021/bi981380s	journal	September 1998
Radical Initiation in the Class I Ribonucleotide Reductase: Long-Range Proton-Coupled Electron Transfer? Stubbe, JoAnne; Nocera, Daniel G.; Yee, Cyril S. Chemical Reviews, Vol. 103, Issue 6 https://doi.org/10.1021/cr020421u	journal	June 2003
Biochemistry and Theory of Proton-Coupled Electron Transfer Migliore, Agostino; Polizzi, Nicholas F.; Therien, Michael J. Chemical Reviews, Vol. 114, Issue 7 https://doi.org/10.1021/cr4006654	journal	January 2014
A Tyrosyl−Dimanganese Coupled Spin System is the Native Metalloradical Cofactor of the R2F Subunit of the Ribonucleotide Reductase of Corynebacterium ammoniagenes Cox, Nicholas; Ogata, Hideaki; Stolle, Patrick Journal of the American Chemical Society, Vol. 132, Issue 32 https://doi.org/10.1021/ja1036995	journal	August 2010
A Hot Oxidant, 3-NO ₂ Y ₁₂₂ Radical, Unmasks Conformational Gating in Ribonucleotide Reductase Yokoyama, Kenichi; Uhlin, Ulla; Stubbe, JoAnne Journal of the American Chemical Society, Vol. 132, Issue 43 https://doi.org/10.1021/ja1069344	journal	November 2010
Function of the Diiron Cluster of Escherichia coli Class Ia Ribonucleotide Reductase in Proton-Coupled Electron Transfer Wörsdörfer, Bigna; Conner, Denise A.; Yokoyama, Kenichi Journal of the American Chemical Society, Vol. 135, Issue 23 https://doi.org/10.1021/ja401342s	journal	May 2013
Redox-Linked Structural Changes in Ribonucleotide Reductase Offenbacher, A. R.; Vassiliev, I. R.; Seyedsayamdost, M. R. Journal of the American Chemical Society, Vol. 131, Issue 22 https://doi.org/10.1021/ja901908j	journal	May 2009
Radicals in Biology: Your Life Is in Their Hands Stubbe, JoAnne; Nocera, Daniel G. Journal of the American Chemical Society, Vol. 143, Issue 34 https://doi.org/10.1021/jacs.1c05952	journal	August 2021
Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography Nichols, Derek A.; Hargis, Jacqueline C.; Sanishvili, Ruslan Journal of the American Chemical Society, Vol. 137, Issue 25 https://doi.org/10.1021/jacs.5b00749	journal	June 2015
Redox-Linked Conformational Control of Proton-Coupled Electron Transfer: Y122 in the Ribonucleotide Reductase β2 Subunit Offenbacher, Adam R.; Burns, Lori A.; Sherrill, C. David The Journal of Physical Chemistry B, Vol. 117, Issue 28 https://doi.org/10.1021/jp404757r	journal	July 2013
Hydrogen Atom Transfer in Ribonucleotide Reductase (RNR) Siegbahn, Per E. M.; Eriksson, Leif; Himo, Fahmi The Journal of Physical Chemistry B, Vol. 102, Issue 51 https://doi.org/10.1021/jp9827835	journal	November 1998
Proton-Coupled Electron Transfer and Redox-Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II Barry, Bridgette A.; Chen, Jun; Keough, James The Journal of Physical Chemistry Letters, Vol. 3, Issue 4 https://doi.org/10.1021/jz2014117	journal	February 2012
Three-dimensional structure of the free radical protein of ribonucleotide reductase Nordlund, Pär; Sjöberg, Britt-Marie; Eklund, Hans Nature, Vol. 345, Issue 6276 https://doi.org/10.1038/345593a0	journal	June 1990
Femtosecond X-ray protein nanocrystallography Chapman, Henry N.; Fromme, Petra; Barty, Anton Nature, Vol. 470, Issue 7332, p. 73-77 https://doi.org/10.1038/nature09750	journal	February 2011
Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers Hattne, Johan; Echols, Nathaniel; Tran, Rosalie Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2887	journal	March 2014
CHARMM36m: an improved force field for folded and intrinsically disordered proteins Huang, Jing; Rauscher, Sarah; Nawrocki, Grzegorz Nature Methods, Vol. 14, Issue 1 https://doi.org/10.1038/nmeth.4067	journal	November 2016
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers Fuller, Franklin D.; Gul, Sheraz; Chatterjee, Ruchira Nature Methods, Vol. 14, Issue 4 https://doi.org/10.1038/nmeth.4195	journal	February 2017
Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens Srinivas, Vivek; Lebrette, Hugo; Lundin, Daniel Nature, Vol. 563, Issue 7731 https://doi.org/10.1038/s41586-018-0653-6	journal	October 2018
Metallation and mismetallation of iron and manganese proteins in vitro and in vivo: the class I ribonucleotide reductases as a case study Cotruvo, Jr, Joseph A.; Stubbe, JoAnne Metallomics, Vol. 4, Issue 10 https://doi.org/10.1039/c2mt20142a	journal	January 2012
Long-range proton-coupled electron transfer in the Escherichia coli class Ia ribonucleotide reductase Reece, Steven Y.; Seyedsayamdost, Mohammad R. Essays in Biochemistry, Vol. 61, Issue 2 https://doi.org/10.1042/EBC20160072	journal	May 2017
Scalable molecular dynamics on CPU and GPU architectures with NAMD Phillips, James C.; Hardy, David J.; Maia, Julio D. C. The Journal of Chemical Physics, Vol. 153, Issue 4 https://doi.org/10.1063/5.0014475	journal	July 2020
Efficient growth inhibition of Bacillus anthracis by knocking out the ribonucleotide reductase tyrosyl radical Torrents, E.; Sahlin, M.; Biglino, D. Proceedings of the National Academy of Sciences, Vol. 102, Issue 50, p. 17946-17951 https://doi.org/10.1073/pnas.0506410102	journal	December 2005
Displacement of the tyrosyl radical cofactor in ribonucleotide reductase obtained by single-crystal high-field EPR and 1.4-A x-ray data Hogbom, M.; Galander, M.; Andersson, M. Proceedings of the National Academy of Sciences, Vol. 100, Issue 6 https://doi.org/10.1073/pnas.0536684100	journal	March 2003
Generation of a stable, aminotyrosyl radical-induced 2 2 complex of Escherichia coli class Ia ribonucleotide reductase Minnihan, E. C.; Ando, N.; Brignole, E. J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 10 https://doi.org/10.1073/pnas.1220691110	journal	February 2013
Protein structural ensembles are revealed by redefining X-ray electron density noise Lang, P. T.; Holton, J. M.; Fraser, J. S. Proceedings of the National Academy of Sciences, Vol. 111, Issue 1 https://doi.org/10.1073/pnas.1302823110	journal	December 2013
Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical Blaesi, Elizabeth J.; Palowitch, Gavin M.; Hu, Kai Proceedings of the National Academy of Sciences, Vol. 115, Issue 40 https://doi.org/10.1073/pnas.1811993115	journal	September 2018
Residues Important for Radical Stability in Ribonucleotide Reductase from Escherichia coli Ormö, Mats; Regnström, Karin; Wang, Zhigang Journal of Biological Chemistry, Vol. 270, Issue 12 https://doi.org/10.1074/jbc.270.12.6570	journal	March 1995
Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily Lundin, Daniel; Poole, Anthony M.; Sjöberg, Britt-Marie Journal of Biological Chemistry, Vol. 287, Issue 24 https://doi.org/10.1074/jbc.M112.367458	journal	June 2012
Rapid X-ray Photoreduction of Dimetal-Oxygen Cofactors in Ribonucleotide Reductase Sigfridsson, Kajsa G. V.; Chernev, Petko; Leidel, Nils Journal of Biological Chemistry, Vol. 288, Issue 14 https://doi.org/10.1074/jbc.M112.438796	journal	February 2013
Crystal Structural Studies of Changes in the Native Dinuclear Iron Center of Ribonucleotide Reductase Protein R2 from Mouse Strand, Kari R.; Karlsen, Solveig; Kolberg, Matthias Journal of Biological Chemistry, Vol. 279, Issue 45 https://doi.org/10.1074/jbc.M407346200	journal	November 2004
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Radiation damage in macromolecular crystallography: what is it and why should we care? Garman, Elspeth F. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910008656	journal	March 2010
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Data Exploration Toolkit for serial diffraction experiments Zeldin, Oliver B.; Brewster, Aaron S.; Hattne, Johan Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 2 https://doi.org/10.1107/S1399004714025875	journal	January 2015
Online_DPI : a web server to calculate the diffraction precision index for a protein structure Kumar, K. S. Dinesh; Gurusaran, M.; Satheesh, S. N. Journal of Applied Crystallography, Vol. 48, Issue 3 https://doi.org/10.1107/S1600576715006287	journal	April 2015
XFEL diffraction: developing processing methods to optimize data quality Sauter, Nicholas K. Journal of Synchrotron Radiation, Vol. 22, Issue 2 https://doi.org/10.1107/S1600577514028203	journal	January 2015
The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source Sierra, Raymond G.; Batyuk, Alexander; Sun, Zhibin Journal of Synchrotron Radiation, Vol. 26, Issue 2 https://doi.org/10.1107/S1600577519001577	journal	February 2019
Do we see what we should see? Describing non-covalent interactions in protein structures including precision Gurusaran, Manickam; Shankar, Mani; Nagarajan, Raju IUCrJ, Vol. 1, Issue 1 https://doi.org/10.1107/S2052252513031485	journal	December 2013
Improving signal strength in serial crystallography with DIALS geometry refinement Brewster, Aaron S.; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 9 https://doi.org/10.1107/S2059798318009191	journal	September 2018
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Structural Basis for Activation of Class Ib Ribonucleotide Reductase Boal, A. K.; Cotruvo, J. A.; Stubbe, J. Science, Vol. 329, Issue 5998 https://doi.org/10.1126/science.1190187	journal	August 2010
Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex Kang, Gyunghoon; Taguchi, Alexander T.; Stubbe, JoAnne Science, Vol. 368, Issue 6489 https://doi.org/10.1126/science.aba6794	journal	March 2020
Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets Greene, Brandon L.; Kang, Gyunghoon; Cui, Chang Annual Review of Biochemistry, Vol. 89, Issue 1 https://doi.org/10.1146/annurev-biochem-013118-111843	journal	June 2020
“Strong” Hydrogen Bonds in Chemistry and Biology Perrin, Charles L.; Nielson, Jennifer B. Annual Review of Physical Chemistry, Vol. 48, Issue 1 https://doi.org/10.1146/annurev.physchem.48.1.511	journal	October 1997
HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures Ho, Bosco K.; Gruswitz, Franz BMC Structural Biology, Vol. 8, Issue 1 https://doi.org/10.1186/1472-6807-8-49	journal	January 2008
Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography John, Juliane; Aurelius, Oskar; Srinivas, Vivek eLife, Vol. 11 https://doi.org/10.7554/eLife.79226	journal	September 2022

Similar Records

A stable Fe{sup III}-Fe{sup IV} replacement of tyrosyl radical in a class I ribonucleotide reductase

Journal Article · Fri May 20 00:00:00 EDT 2005 · Biochemical and Biophysical Research Communications · OSTI ID:20709197

Structures of the Yeast Ribonucleotide Reductase Rnr2 and Rnr4 Homodimers

Journal Article · Sun Mar 07 23:00:00 EST 2010 · Biochemistry-US · OSTI ID:1008708

Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis

Journal Article · Mon Mar 11 00:00:00 EDT 2019 · Biochemistry · OSTI ID:1544859

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Structure of a ribonucleotide reductase R2 protein radical

Citation Formats

References (58)

Similar Records

Related Subjects