DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis

Abstract

Radical S-adenosyl-L-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'- dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only amore » small number (~12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.« less

Authors:
 [1];  [2];  [1];  [2];  [1];  [1];  [1];  [1];  [3];  [3];  [1];  [1];  [4];  [4];  [5]; ORCiD logo [5];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. Department of Chemistry & Biochemistry, Montana State University, Bozeman, Montana 59717, United States
  2. Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
  3. Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
  4. Cassia, LLC, 3030 Bunker Hill Street, Ste. 214, San Diego, California 92109, United States
  5. Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
Publication Date:
Research Org.:
Montana State Univ., Bozeman, MT (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1459248
Alternate Identifier(s):
OSTI ID: 1508581
Grant/Contract Number:  
SC0005404
Resource Type:
Published Article
Journal Name:
Journal of the American Chemical Society
Additional Journal Information:
Journal Name: Journal of the American Chemical Society Journal Volume: 140 Journal Issue: 28; Journal ID: ISSN 0002-7863
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Byer, Amanda S., Yang, Hao, McDaniel, Elizabeth C., Kathiresan, Venkatesan, Impano, Stella, Pagnier, Adrien, Watts, Hope, Denler, Carly, Vagstad, Anna L., Piel, Jörn, Duschene, Kaitlin S., Shepard, Eric M., Shields, Thomas P., Scott, Lincoln G., Lilla, Edward A., Yokoyama, Kenichi, Broderick, William E., Hoffman, Brian M., and Broderick, Joan B. Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. United States: N. p., 2018. Web. doi:10.1021/jacs.8b04061.
Byer, Amanda S., Yang, Hao, McDaniel, Elizabeth C., Kathiresan, Venkatesan, Impano, Stella, Pagnier, Adrien, Watts, Hope, Denler, Carly, Vagstad, Anna L., Piel, Jörn, Duschene, Kaitlin S., Shepard, Eric M., Shields, Thomas P., Scott, Lincoln G., Lilla, Edward A., Yokoyama, Kenichi, Broderick, William E., Hoffman, Brian M., & Broderick, Joan B. Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis. United States. https://doi.org/10.1021/jacs.8b04061
Byer, Amanda S., Yang, Hao, McDaniel, Elizabeth C., Kathiresan, Venkatesan, Impano, Stella, Pagnier, Adrien, Watts, Hope, Denler, Carly, Vagstad, Anna L., Piel, Jörn, Duschene, Kaitlin S., Shepard, Eric M., Shields, Thomas P., Scott, Lincoln G., Lilla, Edward A., Yokoyama, Kenichi, Broderick, William E., Hoffman, Brian M., and Broderick, Joan B. Thu . "Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis". United States. https://doi.org/10.1021/jacs.8b04061.
@article{osti_1459248,
title = {Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis},
author = {Byer, Amanda S. and Yang, Hao and McDaniel, Elizabeth C. and Kathiresan, Venkatesan and Impano, Stella and Pagnier, Adrien and Watts, Hope and Denler, Carly and Vagstad, Anna L. and Piel, Jörn and Duschene, Kaitlin S. and Shepard, Eric M. and Shields, Thomas P. and Scott, Lincoln G. and Lilla, Edward A. and Yokoyama, Kenichi and Broderick, William E. and Hoffman, Brian M. and Broderick, Joan B.},
abstractNote = {Radical S-adenosyl-L-methionine (SAM) enzymes comprise a vast superfamily catalyzing diverse reactions essential to all life through homolytic SAM cleavage to liberate the highly reactive 5'-deoxyadenosyl radical (5'-dAdo·). Our recent observation of a catalytically competent organometallic intermediate Ω that forms during reaction of the radical SAM (RS) enzyme pyruvate formate-lyase activating-enzyme (PFL-AE) was therefore quite surprising, and led to the question of its broad relevance in the superfamily. We now show that Ω in PFL-AE forms as an intermediate under a variety of mixing order conditions, suggesting it is central to catalysis in this enzyme. We further demonstrate that Ω forms in a suite of RS enzymes chosen to span the totality of superfamily reaction types, implicating Ω as essential in catalysis across the RS superfamily. Finally, EPR and electron nuclear double resonance spectroscopy establish that Ω involves an Fe-C5' bond between 5'-dAdo· and the [4Fe-4S] cluster. An analogous organometallic bond is found in the well-known adenosylcobalamin (coenzyme B12) cofactor used to initiate radical reactions via a 5'- dAdo· intermediate. Liberation of a reactive 5'-dAdo· intermediate via homolytic metal-carbon bond cleavage thus appears to be similar for Ω and coenzyme B12. However, coenzyme B12 is involved in enzymes catalyzing only a small number (~12) of distinct reactions, whereas the RS superfamily has more than 100 000 distinct sequences and over 80 reaction types characterized to date. The appearance of Ω across the RS superfamily therefore dramatically enlarges the sphere of bio-organometallic chemistry in Nature.},
doi = {10.1021/jacs.8b04061},
journal = {Journal of the American Chemical Society},
number = 28,
volume = 140,
place = {United States},
year = {2018},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/jacs.8b04061

Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1. Figure 1.: Top, premixed (PFL + SAM), RFQ with PFL-AE. Middle, (PFL-AE + SAM) RFQ with PFL. Bottom, (PFL-AE + PFL) + SAM; the slight increase in g|| suggests a slightly different conformation of Ω. Feature to low field of Ω signal in bottom spectrum due to Cu2+ contamination frommore » Cu wheels used for freezing in RFQ apparatus. Conditions: Freeze-quenched, 500 ms; frequency, 9.374 GHz (top), 9.374 GHz (middle), 9.375 GHz (bottom); modulation, 10 G; T = 40 K. Samples cryoannealed at 150 K to remove a small overlapping signal, see Figure S2.« less

Save / Share:

Works referenced in this record:

[FeFe]-Hydrogenase Cyanide Ligands Derived From S-Adenosylmethionine-Dependent Cleavage of Tyrosine
journal, January 2010

  • Driesener, Rebecca C.; Challand, Martin R.; McGlynn, Shawn E.
  • Angewandte Chemie International Edition, Vol. 49, Issue 9
  • DOI: 10.1002/anie.200907047

[FeFe]-Hydrogenase Maturation: HydG-Catalyzed Synthesis of Carbon Monoxide
journal, July 2010

  • Shepard, Eric M.; Duffus, Benjamin R.; George, Simon J.
  • Journal of the American Chemical Society, Vol. 132, Issue 27
  • DOI: 10.1021/ja1012273

Radical S -Adenosylmethionine Enzymes
journal, January 2014

  • Broderick, Joan B.; Duffus, Benjamin R.; Duschene, Kaitlin S.
  • Chemical Reviews, Vol. 114, Issue 8
  • DOI: 10.1021/cr4004709

Biochemical and Kinetic Characterization of Radical S -Adenosyl- l -methionine Enzyme HydG
journal, November 2013

  • Driesener, Rebecca C.; Duffus, Benjamin R.; Shepard, Eric M.
  • Biochemistry, Vol. 52, Issue 48
  • DOI: 10.1021/bi401143s

Radical Carbon Skeleton Rearrangements:  Catalysis by Coenzyme B 12 -Dependent Mutases
journal, June 2003


Post-translational activation introduces a free radical into pyruvate formate-lyase.
journal, March 1984

  • Knappe, J.; Neugebauer, F. A.; Blaschkowski, H. P.
  • Proceedings of the National Academy of Sciences, Vol. 81, Issue 5
  • DOI: 10.1073/pnas.81.5.1332

Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond
journal, May 2016


Advanced paramagnetic resonance spectroscopies of iron–sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM)
journal, June 2015

  • Cutsail, George E.; Telser, Joshua; Hoffman, Brian M.
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
  • DOI: 10.1016/j.bbamcr.2015.01.025

The Structure–Function Linkage Database
journal, November 2013

  • Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1130

Unexpected electron transfer mechanism upon AdoMet cleavage in radical SAM proteins
journal, August 2009

  • Nicolet, Y.; Amara, P.; Mouesca, J. -M.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 35
  • DOI: 10.1073/pnas.0904385106

Spectroscopic Evidence for the Participation of an Allylic Analogue of the 5‘-Deoxyadenosyl Radical in the Reaction of Lysine 2,3-Aminomutase
journal, October 1999

  • Magnusson, Olafur Th.; Reed, George H.; Frey, Perry A.
  • Journal of the American Chemical Society, Vol. 121, Issue 41
  • DOI: 10.1021/ja9925507

The role of S-adenosylmethionine in the lysine 2,3-aminomutase reaction.
journal, November 1987


Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5′-dAdo• “Free Radical” Is Never Free
journal, May 2015

  • Horitani, Masaki; Byer, Amanda S.; Shisler, Krista A.
  • Journal of the American Chemical Society, Vol. 137, Issue 22
  • DOI: 10.1021/jacs.5b00498

Generation of the Glycyl Radical of the Anaerobic Escherichia coli Ribonucleotide Reductase Requires a Specific Activating Enzyme
journal, February 1995

  • Sun, Xueyin; Eliasson, Rolf; Pontis, Elisabet
  • Journal of Biological Chemistry, Vol. 270, Issue 6
  • DOI: 10.1074/jbc.270.6.2443

Structural Insights into Radical Generation by the Radical SAM Superfamily
journal, March 2011

  • Vey, Jessica L.; Drennan, Catherine L.
  • Chemical Reviews, Vol. 111, Issue 4
  • DOI: 10.1021/cr9002616

Regioselectivity in the Homolytic Cleavage of S-Adenosylmethionine
journal, December 2010


Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis
journal, March 2018

  • Dong, Min; Kathiresan, Venkatesan; Fenwick, Michael K.
  • Science, Vol. 359, Issue 6381
  • DOI: 10.1126/science.aao6595

Radical S -Adenosyl Methionine Epimerases: Regioselective Introduction of Diverse D -Amino Acid Patterns into Peptide Natural Products
journal, June 2014

  • Morinaka, Brandon I.; Vagstad, Anna L.; Helf, Maximilian J.
  • Angewandte Chemie International Edition, Vol. 53, Issue 32
  • DOI: 10.1002/anie.201400478

Lysine 2,3‐aminomutase: is adenosylmethionine a poor man's adenosylcobalamin?
journal, May 1993


Pyruvate Formate-lyase, Evidence for an Open Conformation Favored in the Presence of Its Activating Enzyme
journal, June 2010

  • Peng, Yi; Veneziano, Susan E.; Gillispie, Gregory D.
  • Journal of Biological Chemistry, Vol. 285, Issue 35
  • DOI: 10.1074/jbc.M109.096875

Lysine 2,3-Aminomutase
journal, April 1970


Chemistry and Enzymology of Vitamin B 12
journal, June 2005


Structural basis for glycyl radical formation by pyruvate formate-lyase activating enzyme
journal, October 2008

  • Vey, J. L.; Yang, J.; Li, M.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 42
  • DOI: 10.1073/pnas.0806640105

The Radical SAM Superfamily
journal, January 2008

  • Frey, Perry A.; Hegeman, Adrian D.; Ruzicka, Frank J.
  • Critical Reviews in Biochemistry and Molecular Biology, Vol. 43, Issue 1
  • DOI: 10.1080/10409230701829169

Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.