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Research Article

Generation of a stable, aminotyrosyl radical-induced α2β2 complex of Escherichia coli class Ia ribonucleotide reductase

Ellen C. Minnihan, Nozomi Ando, Edward J. Brignole, Lisa Olshansky, Johnathan Chittuluru, Francisco J. Asturias, Catherine L. Drennan, Daniel G. Nocera, and JoAnne Stubbe
PNAS March 5, 2013 110 (10) 3835-3840; https://doi.org/10.1073/pnas.1220691110
Ellen C. Minnihan
Departments of aChemistry and
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Nozomi Ando
Departments of aChemistry and
bHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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Edward J. Brignole
Departments of aChemistry and
bHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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Lisa Olshansky
Departments of aChemistry and
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Johnathan Chittuluru
cDepartment of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
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Francisco J. Asturias
cDepartment of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
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  • For correspondence: asturias@scripps.edu cdrennan@mit.edu nocera@mit.edu stubbe@mit.edu
Catherine L. Drennan
Departments of aChemistry and
bHoward Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; and
dBiology, and
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  • For correspondence: asturias@scripps.edu cdrennan@mit.edu nocera@mit.edu stubbe@mit.edu
Daniel G. Nocera
Departments of aChemistry and
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  • For correspondence: asturias@scripps.edu cdrennan@mit.edu nocera@mit.edu stubbe@mit.edu
JoAnne Stubbe
Departments of aChemistry and
dBiology, and
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  • For correspondence: asturias@scripps.edu cdrennan@mit.edu nocera@mit.edu stubbe@mit.edu
  1. Edited by Rowena G. Matthews, University of Michigan, Ann Arbor, MI, and approved January 17, 2013 (received for review November 27, 2012)

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Abstract

Ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates to deoxynucleoside diphosphates (dNDPs). The Escherichia coli class Ia RNR uses a mechanism of radical propagation by which a cysteine in the active site of the RNR large (α2) subunit is transiently oxidized by a stable tyrosyl radical (Y•) in the RNR small (β2) subunit over a 35-Å pathway of redox-active amino acids: Y122• ↔ [W48?] ↔ Y356 in β2 to Y731 ↔ Y730 ↔ C439 in α2. When 3-aminotyrosine (NH2Y) is incorporated in place of Y730, a long-lived NH2Y730• is generated in α2 in the presence of wild-type (wt)-β2, substrate, and effector. This radical intermediate is chemically and kinetically competent to generate dNDPs. Herein, evidence is presented that NH2Y730• induces formation of a kinetically stable α2β2 complex. Under conditions that generate NH2Y730•, binding between Y730NH2Y-α2 and wt-β2 is 25-fold tighter (Kd = 7 nM) than for wt-α2|wt-β2 and is cooperative. Stopped-flow fluorescence experiments establish that the dissociation rate constant for the Y730NH2Y-α2|wt-β2 interaction is ∼104-fold slower than for the wt subunits (∼60 s−1). EM and small-angle X-ray scattering studies indicate that the stabilized species is a compact globular α2β2, consistent with the structure predicted by Uhlin and Eklund’s docking model [Uhlin U, Eklund H (1994) Nature 370(6490):533–539]. These results present a structural and biochemical characterization of the active RNR complex “trapped” during turnover, and suggest that stabilization of the α2β2 state may be a regulatory mechanism for protecting the catalytic radical and ensuring the fidelity of its reactivity.

  • conformational equilibria
  • radical transfer
  • unnatural amino acid

Footnotes

  • ↵1N.A., E.J.B., and L.O. contributed equally to this work.

  • ↵2To whom correspondence may be addressed. E-mail: asturias{at}scripps.edu, cdrennan{at}mit.edu, nocera{at}mit.edu, or stubbe{at}mit.edu.
  • Author contributions: E.C.M., N.A., E.J.B., L.O., J.C., F.J.A., C.L.D., D.G.N., and J.S. designed research; E.C.M., N.A., E.J.B., L.O., and J.C. performed research; E.C.M., N.A., E.J.B., L.O., J.C., F.J.A., C.L.D., D.G.N., and J.S. analyzed data; and E.C.M., N.A., E.J.B., and J.S. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1220691110/-/DCSupplemental.

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A stable, radical-induced α2β2 complex of RNR
Ellen C. Minnihan, Nozomi Ando, Edward J. Brignole, Lisa Olshansky, Johnathan Chittuluru, Francisco J. Asturias, Catherine L. Drennan, Daniel G. Nocera, JoAnne Stubbe
Proceedings of the National Academy of Sciences Mar 2013, 110 (10) 3835-3840; DOI: 10.1073/pnas.1220691110

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A stable, radical-induced α2β2 complex of RNR
Ellen C. Minnihan, Nozomi Ando, Edward J. Brignole, Lisa Olshansky, Johnathan Chittuluru, Francisco J. Asturias, Catherine L. Drennan, Daniel G. Nocera, JoAnne Stubbe
Proceedings of the National Academy of Sciences Mar 2013, 110 (10) 3835-3840; DOI: 10.1073/pnas.1220691110
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