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Title: Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme

Abstract

Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.

Authors:
 [1]; ORCiD logo [1]; ORCiD logo [1];  [2];  [2];  [2];  [1];  [2];  [2];  [3]; ORCiD logo [4]
  1. Scripps Research Inst., Jupiter, FL (United States). Dept. of Chemistry
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division
  3. Rice Univ., Houston, TX (United States). Dept. of Biosciences
  4. Scripps Research Inst., Jupiter, FL (United States). Dept. of Chemistry; Scripps Research Inst., Jupiter, FL (United States). Dept of Molecular Medicine; Scripps Research Inst., Jupiter, FL (United States). Natural Products Library Initiative at The Scripps Research Inst.
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH); Chinese Academy of Sciences (CAS); Arnold and Mabel Beckman Foundation
OSTI Identifier:
1466308
Grant/Contract Number:  
AC02-06CH11357; GM094585; GM098248; GM109456; GM114353
Resource Type:
Accepted Manuscript
Journal Name:
Nature Chemical Biology
Additional Journal Information:
Journal Volume: 14; Journal Issue: 7; Journal ID: ISSN 1552-4450
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Wang, Nan, Rudolf, Jeffrey D., Dong, Liao-Bin, Osipiuk, Jerzy, Hatzos-Skintges, Catherine, Endres, Michael, Chang, Chin-Yuan, Babnigg, Gyorgy, Joachimiak, Andrzej, Phillips, George N., and Shen, Ben. Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme. United States: N. p., 2018. Web. doi:10.1038/s41589-018-0061-0.
Wang, Nan, Rudolf, Jeffrey D., Dong, Liao-Bin, Osipiuk, Jerzy, Hatzos-Skintges, Catherine, Endres, Michael, Chang, Chin-Yuan, Babnigg, Gyorgy, Joachimiak, Andrzej, Phillips, George N., & Shen, Ben. Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme. United States. doi:10.1038/s41589-018-0061-0.
Wang, Nan, Rudolf, Jeffrey D., Dong, Liao-Bin, Osipiuk, Jerzy, Hatzos-Skintges, Catherine, Endres, Michael, Chang, Chin-Yuan, Babnigg, Gyorgy, Joachimiak, Andrzej, Phillips, George N., and Shen, Ben. Mon . "Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme". United States. doi:10.1038/s41589-018-0061-0. https://www.osti.gov/servlets/purl/1466308.
@article{osti_1466308,
title = {Natural separation of the acyl-CoA ligase reaction results in a non-adenylating enzyme},
author = {Wang, Nan and Rudolf, Jeffrey D. and Dong, Liao-Bin and Osipiuk, Jerzy and Hatzos-Skintges, Catherine and Endres, Michael and Chang, Chin-Yuan and Babnigg, Gyorgy and Joachimiak, Andrzej and Phillips, George N. and Shen, Ben},
abstractNote = {Acyl-coenzyme A (CoA) ligases catalyze the activation of carboxylic acids via a two-step reaction of adenylation followed by thioesterification. Here, we report the discovery of a non-adenylating acyl-CoA ligase PtmA2 and the functional separation of an acyl-CoA ligase reaction. Both PtmA1 and PtmA2, two acyl-CoA ligases from the biosynthetic pathway of platensimycin and platencin, are necessary for the two steps of CoA activation. Gene inactivation of ptmA1 and ptmA2 resulted in the accumulation of free acid and adenylate intermediates, respectively. Enzymatic and structural characterization of PtmA2 confirmed its ability to only catalyze thioesterification. Structural characterization of PtmA2 revealed it binds both free acid and adenylate substrates and undergoes the established mechanism of domain alternation. Finally, site-directed mutagenesis restored both the adenylation and complete CoA activation reactions. This study challenges the currently accepted paradigm of adenylating enzymes and inspires future investigations on functionally separated acyl-CoA ligases and their ramifications in biology.},
doi = {10.1038/s41589-018-0061-0},
journal = {Nature Chemical Biology},
number = 7,
volume = 14,
place = {United States},
year = {2018},
month = {6}
}

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