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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. 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., and Broderick, Joan B. Thu . "Paradigm Shift for Radical S -Adenosyl- l -methionine Reactions: The Organometallic Intermediate Ω Is Central to Catalysis". United States. doi: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
DOI: 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

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Works referencing / citing this record:

Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe–4S] clusters
journal, September 2019

  • Galambas, Amanda; Miller, Jacquelyn; Jones, Morgan
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 24, Issue 6
  • DOI: 10.1007/s00775-019-01708-8

The hidden enzymology of bacterial natural product biosynthesis
journal, June 2019


Radical S-adenosylmethionine maquette chemistry: Cx3Cx2C peptide coordinated redox active [4Fe–4S] clusters
journal, September 2019

  • Galambas, Amanda; Miller, Jacquelyn; Jones, Morgan
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 24, Issue 6
  • DOI: 10.1007/s00775-019-01708-8

The hidden enzymology of bacterial natural product biosynthesis
journal, June 2019


Introduction of d -Amino Acids in Minimalistic Peptide Substrates by an S -Adenosyl- l -Methionine Radical Epimerase
journal, January 2019

  • Vagstad, Anna L.; Kuranaga, Takefumi; Püntener, Salome
  • Angewandte Chemie, Vol. 131, Issue 8
  • DOI: 10.1002/ange.201809508

Introduction of d -Amino Acids in Minimalistic Peptide Substrates by an S -Adenosyl- l -Methionine Radical Epimerase
journal, January 2019

  • Vagstad, Anna L.; Kuranaga, Takefumi; Püntener, Salome
  • Angewandte Chemie International Edition, Vol. 58, Issue 8
  • DOI: 10.1002/anie.201809508

Radical SAM-dependent adenosylation catalyzed by l -tyrosine lyases
journal, January 2019

  • Wu, Yujie; Wu, Runze; Mandalapu, Dhanaraju
  • Organic & Biomolecular Chemistry, Vol. 17, Issue 7
  • DOI: 10.1039/c8ob02906g

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