Literature DB >> 32217749

Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex.

Gyunghoon Kang1,2, Alexander T Taguchi3, JoAnne Stubbe4,3, Catherine L Drennan5,2,3.   

Abstract

Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide reduction reaction in all RNRs requires the generation of a transient active site thiyl radical, and in class I RNRs, this process involves a long-range radical transfer between two subunits, α and β. Because of the transient subunit association, an atomic resolution structure of an active α2β2 RNR complex has been elusive. We used a doubly substituted β2, E52Q/(2,3,5)-trifluorotyrosine122-β2, to trap wild-type α2 in a long-lived α2β2 complex. We report the structure of this complex by means of cryo-electron microscopy to 3.6-angstrom resolution, allowing for structural visualization of a 32-angstrom-long radical transfer pathway that affords RNR activity.
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Year:  2020        PMID: 32217749      PMCID: PMC7774503          DOI: 10.1126/science.aba6794

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  46 in total

1.  MolProbity: More and better reference data for improved all-atom structure validation.

Authors:  Christopher J Williams; Jeffrey J Headd; Nigel W Moriarty; Michael G Prisant; Lizbeth L Videau; Lindsay N Deis; Vishal Verma; Daniel A Keedy; Bradley J Hintze; Vincent B Chen; Swati Jain; Steven M Lewis; W Bryan Arendall; Jack Snoeyink; Paul D Adams; Simon C Lovell; Jane S Richardson; David C Richardson
Journal:  Protein Sci       Date:  2017-11-27       Impact factor: 6.725

2.  Function of the diiron cluster of Escherichia coli class Ia ribonucleotide reductase in proton-coupled electron transfer.

Authors:  Bigna Wörsdörfer; Denise A Conner; Kenichi Yokoyama; Jovan Livada; Mohammad Seyedsayamdost; Wei Jiang; Alexey Silakov; JoAnne Stubbe; J Martin Bollinger; Carsten Krebs
Journal:  J Am Chem Soc       Date:  2013-05-31       Impact factor: 15.419

3.  Photochemical Rescue of a Conformationally Inactivated Ribonucleotide Reductase.

Authors:  Brandon L Greene; JoAnne Stubbe; Daniel G Nocera
Journal:  J Am Chem Soc       Date:  2018-11-12       Impact factor: 15.419

4.  PELDOR spectroscopy with DOPA-beta2 and NH2Y-alpha2s: distance measurements between residues involved in the radical propagation pathway of E. coli ribonucleotide reductase.

Authors:  Mohammad R Seyedsayamdost; Clement T Y Chan; Veronica Mugnaini; JoAnne Stubbe; Marina Bennati
Journal:  J Am Chem Soc       Date:  2007-11-30       Impact factor: 15.419

5.  Quantifying the local resolution of cryo-EM density maps.

Authors:  Alp Kucukelbir; Fred J Sigworth; Hemant D Tagare
Journal:  Nat Methods       Date:  2013-11-10       Impact factor: 28.547

6.  Hydrogen bond network between amino acid radical intermediates on the proton-coupled electron transfer pathway of E. coli α2 ribonucleotide reductase.

Authors:  Thomas U Nick; Wankyu Lee; Simone Kossmann; Frank Neese; JoAnne Stubbe; Marina Bennati
Journal:  J Am Chem Soc       Date:  2014-12-29       Impact factor: 15.419

7.  New tools for automated high-resolution cryo-EM structure determination in RELION-3.

Authors:  Jasenko Zivanov; Takanori Nakane; Björn O Forsberg; Dari Kimanius; Wim Jh Hagen; Erik Lindahl; Sjors Hw Scheres
Journal:  Elife       Date:  2018-11-09       Impact factor: 8.140

8.  Real-space refinement in PHENIX for cryo-EM and crystallography.

Authors:  Pavel V Afonine; Billy K Poon; Randy J Read; Oleg V Sobolev; Thomas C Terwilliger; Alexandre Urzhumtsev; Paul D Adams
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-05-30       Impact factor: 7.652

9.  Convergent allostery in ribonucleotide reductase.

Authors:  William C Thomas; F Phil Brooks; Audrey A Burnim; John-Paul Bacik; JoAnne Stubbe; Jason T Kaelber; James Z Chen; Nozomi Ando
Journal:  Nat Commun       Date:  2019-06-14       Impact factor: 14.919

10.  EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.

Authors:  Benjamin A Barad; Nathaniel Echols; Ray Yu-Ruei Wang; Yifan Cheng; Frank DiMaio; Paul D Adams; James S Fraser
Journal:  Nat Methods       Date:  2015-08-17       Impact factor: 28.547

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  33 in total

1.  Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase.

Authors:  Clorice R Reinhardt; Pengfei Li; Gyunghoon Kang; JoAnne Stubbe; Catherine L Drennan; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2020-07-28       Impact factor: 15.419

2.  Gated Proton Release during Radical Transfer at the Subunit Interface of Ribonucleotide Reductase.

Authors:  Chang Cui; Brandon L Greene; Gyunghoon Kang; Catherine L Drennan; JoAnne Stubbe; Daniel G Nocera
Journal:  J Am Chem Soc       Date:  2020-12-23       Impact factor: 15.419

3.  A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.

Authors:  Markel Martínez-Carranza; Venkateswara Rao Jonna; Daniel Lundin; Margareta Sahlin; Lars-Anders Carlson; Newal Jemal; Martin Högbom; Britt-Marie Sjöberg; Pål Stenmark; Anders Hofer
Journal:  J Biol Chem       Date:  2020-09-03       Impact factor: 5.157

4.  Substrate recognition induces sequential electron transfer across subunits in the nitrogenase-like DPOR complex.

Authors:  Elliot I Corless; Brian Bennett; Edwin Antony
Journal:  J Biol Chem       Date:  2020-07-31       Impact factor: 5.157

Review 5.  Carbon-fluorine bond cleavage mediated by metalloenzymes.

Authors:  Yifan Wang; Aimin Liu
Journal:  Chem Soc Rev       Date:  2020-06-08       Impact factor: 54.564

6.  Pterostilbene inhibits hepatocellular carcinoma proliferation and HBV replication by targeting ribonucleotide reductase M2 protein.

Authors:  Rui Wang; Zhijian Xu; Jiaping Tian; Qian Liu; Jingwen Dong; Lijuan Guo; Boning Hai; Xia Liu; Hangping Yao; Zhi Chen; Junjie Xu; Lijun Zhu; Haiyi Chen; Tingjun Hou; Weiliang Zhu; Jimin Shao
Journal:  Am J Cancer Res       Date:  2021-06-15       Impact factor: 6.166

7.  Glutamate Mediates Proton-Coupled Electron Transfer Between Tyrosines 730 and 731 in Escherichia coli Ribonucleotide Reductase.

Authors:  Clorice R Reinhardt; Elvira R Sayfutyarova; Jiayun Zhong; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2021-04-15       Impact factor: 15.419

8.  Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers.

Authors:  Kelsey R Miller; Saborni Biswas; Andrew Jasniewski; Alec H Follmer; Ankita Biswas; Therese Albert; Sinan Sabuncu; Emile L Bominaar; Michael P Hendrich; Pierre Moënne-Loccoz; A S Borovik
Journal:  J Am Chem Soc       Date:  2021-02-02       Impact factor: 15.419

9.  Computing Proton-Coupled Redox Potentials of Fluorotyrosines in a Protein Environment.

Authors:  Clorice R Reinhardt; Raquel Sequeira; Cecilia Tommos; Sharon Hammes-Schiffer
Journal:  J Phys Chem B       Date:  2020-12-30       Impact factor: 2.991

Review 10.  Ferric iron reductases and their contribution to unicellular ferrous iron uptake.

Authors:  Timothy J Cain; Aaron T Smith
Journal:  J Inorg Biochem       Date:  2021-02-25       Impact factor: 4.155

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