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

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

doi:10.1038/s41589-018-0061-0

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

Journal Article · Mon Jun 04 00:00:00 EDT 2018 · Nature Chemical Biology

DOI:https://doi.org/10.1038/s41589-018-0061-0· OSTI ID:1466308

Wang, Nan ^[1]; ^[1]; ^[1]; Osipiuk, Jerzy ^[2]; Hatzos-Skintges, Catherine ^[2]; Endres, Michael ^[2]; Chang, Chin-Yuan ^[1]; Babnigg, Gyorgy ^[2]; Joachimiak, Andrzej ^[2]; Phillips, George N. ^[3]; ^[4]

Scripps Research Inst., Jupiter, FL (United States). Dept. of Chemistry
Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division
Rice Univ., Houston, TX (United States). Dept. of Biosciences
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.

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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: Arnold and Mabel Beckman Foundation; Chinese Academy of Sciences (CAS); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1466308

Journal Information:: Nature Chemical Biology, Journal Name: Nature Chemical Biology Journal Issue: 7 Vol. 14; ISSN 1552-4450

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (51)

A Century of Gibberellin Research Hedden, Peter; Sponsel, Valerie Journal of Plant Growth Regulation, Vol. 34, Issue 4 https://doi.org/10.1007/s00344-015-9546-1	journal	October 2015
Titer improvement and pilot-scale production of platensimycin from Streptomyces platensis SB12026 Shi, Jun; Pan, Jian; Liu, Ling Journal of Industrial Microbiology & Biotechnology, Vol. 43, Issue 7 https://doi.org/10.1007/s10295-016-1769-z	journal	April 2016
A general introduction to the biochemistry of mitochondrial fatty acid β-oxidation Houten, Sander Michel; Wanders, Ronald J. A. Journal of Inherited Metabolic Disease, Vol. 33, Issue 5 https://doi.org/10.1007/s10545-010-9061-2	journal	March 2010
Ent-kauranes and other constituents of three Helianthus species Herz, W.; Kulanthaivel, P.; Watanabe, K. Phytochemistry, Vol. 22, Issue 9 https://doi.org/10.1016/0031-9422(83)80036-3	journal	January 1983
Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector MacNeil, Douglas J.; Gewain, Keith M.; Ruby, Carolyn L. Gene, Vol. 111, Issue 1 https://doi.org/10.1016/0378-1119(92)90603-m	journal	February 1992
Platensimycin and platencin: Inspirations for chemistry, biology, enzymology, and medicine Rudolf, Jeffrey D.; Dong, Liao-Bin; Shen, Ben Biochemical Pharmacology, Vol. 133 https://doi.org/10.1016/j.bcp.2016.11.013	journal	June 2017
Antibacterial sulfur-containing platensimycin and platencin congeners from Streptomyces platensis SB12029 Dong, Liao-Bin; Rudolf, Jeffrey D.; Shen, Ben Bioorganic & Medicinal Chemistry, Vol. 24, Issue 24 https://doi.org/10.1016/j.bmc.2016.04.026	journal	December 2016
In vivo instability of platensimycin and platencin: Synthesis and biological evaluation of urea- and carbamate-platensimycin Dong, Liao-Bin; Rudolf, Jeffrey D.; Lin, Li Bioorganic & Medicinal Chemistry, Vol. 25, Issue 6 https://doi.org/10.1016/j.bmc.2017.02.028	journal	March 2017
Inference of Macromolecular Assemblies from Crystalline State Krissinel, Evgeny; Henrick, Kim Journal of Molecular Biology, Vol. 372, Issue 3 https://doi.org/10.1016/j.jmb.2007.05.022	journal	September 2007
Crystal Structure of Bacillus cereus d-Alanyl Carrier Protein Ligase (DltA) in Complex with ATP Osman, Khan Tanjid; Du, Liqin; He, Yujiong Journal of Molecular Biology, Vol. 388, Issue 2 https://doi.org/10.1016/j.jmb.2009.03.040	journal	May 2009
Structural and Functional Studies of Fatty Acyl Adenylate Ligases from E. coli and L. pneumophila Zhang, Zhening; Zhou, Rong; Sauder, J. Michael Journal of Molecular Biology, Vol. 406, Issue 2 https://doi.org/10.1016/j.jmb.2010.12.011	journal	February 2011
Molecular Basis of the Functional Divergence of Fatty Acyl-AMP Ligase Biosynthetic Enzymes of Mycobacterium tuberculosis Goyal, Aneesh; Verma, Priyanka; Anandhakrishnan, Madhankumar Journal of Molecular Biology, Vol. 416, Issue 2 https://doi.org/10.1016/j.jmb.2011.12.031	journal	February 2012
Adenylate-forming enzymes Schmelz, Stefan; Naismith, James H. Current Opinion in Structural Biology, Vol. 19, Issue 6 https://doi.org/10.1016/j.sbi.2009.09.004	journal	December 2009
Characterization of the Propionyl-CoA Synthetase (PrpE) Enzyme of Salmonella enterica : Residue Lys592 Is Required for Propionyl-AMP Synthesis ^† Horswill, Alexander R.; Escalante-Semerena, Jorge C. Biochemistry, Vol. 41, Issue 7 https://doi.org/10.1021/bi015647q	journal	February 2002
The 1.75 Å Crystal Structure of Acetyl-CoA Synthetase Bound to Adenosine-5‘-propylphosphate and Coenzyme A ^† Gulick, Andrew M.; Starai, Vincent J.; Horswill, Alexander R. Biochemistry, Vol. 42, Issue 10, p. 2866-2873 https://doi.org/10.1021/bi0271603	journal	March 2003
Crystal Structure of 4-Chlorobenzoate:CoA Ligase/Synthetase in the Unliganded and Aryl Substrate-Bound States ^† ^, ^‡ Gulick, Andrew M.; Lu, Xuefeng; Dunaway-Mariano, Debra Biochemistry, Vol. 43, Issue 27, p. 8670-8679 https://doi.org/10.1021/bi049384m	journal	July 2004
Mechanism of 4-Chlorobenzoate:Coenzyme A Ligase Catalysis ^† Wu, Rui; Cao, Jian; Lu, Xuefeng Biochemistry, Vol. 47, Issue 31 https://doi.org/10.1021/bi800698m	journal	August 2008
The Mechanism of Domain Alternation in the Acyl-Adenylate Forming Ligase Superfamily Member 4-Chlorobenzoate: Coenzyme A Ligase ^, Wu, Rui; Reger, Albert S.; Lu, Xuefeng Biochemistry, Vol. 48, Issue 19 https://doi.org/10.1021/bi9002327	journal	May 2009
Conformational Dynamics in the Acyl-CoA Synthetases, Adenylation Domains of Non-ribosomal Peptide Synthetases, and Firefly Luciferase Gulick, Andrew M. ACS Chemical Biology, Vol. 4, Issue 10, p. 811-827 https://doi.org/10.1021/cb900156h	journal	October 2009
Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis Marahiel, Mohamed A.; Stachelhaus, Torsten; Mootz, Henning D. Chemical Reviews, Vol. 97, Issue 7 https://doi.org/10.1021/cr960029e	journal	November 1997
Expression of the Platencin Biosynthetic Gene Cluster in Heterologous Hosts Yielding New Platencin Congeners Smanski, Michael J.; Casper, Jeffrey; Peterson, Ryan M. Journal of Natural Products, Vol. 75, Issue 12 https://doi.org/10.1021/np3005985	journal	November 2012
Strain Prioritization for Natural Product Discovery by a High-Throughput Real-Time PCR Method No authors listed Journal of Natural Products, Vol. 77, Issue 10 https://doi.org/10.1021/np5006168	journal	September 2014
Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria Trivedi, Omita A.; Arora, Pooja; Sridharan, Vijayalakshmi Nature, Vol. 428, Issue 6981 https://doi.org/10.1038/nature02384	journal	March 2004
Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis Arora, Pooja; Goyal, Aneesh; Natarajan, Vivek T. Nature Chemical Biology, Vol. 5, Issue 3 https://doi.org/10.1038/nchembio.143	journal	February 2009
The pimeloyl-CoA synthetase BioW defines a new fold for adenylate-forming enzymes Estrada, Paola; Manandhar, Miglena; Dong, Shi-Hui Nature Chemical Biology, Vol. 13, Issue 6 https://doi.org/10.1038/nchembio.2359	journal	April 2017
PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin Gust, B.; Challis, G. L.; Fowler, K. Proceedings of the National Academy of Sciences, Vol. 100, Issue 4 https://doi.org/10.1073/pnas.0337542100	journal	January 2003
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2 Schwer, B.; Bunkenborg, J.; Verdin, R. O. Proceedings of the National Academy of Sciences, Vol. 103, Issue 27 https://doi.org/10.1073/pnas.0603968103	journal	June 2006
Dedicated ent-kaurene and ent-atiserene synthases for platensimycin and platencin biosynthesis Smanski, M. J.; Yu, Z.; Casper, J. Proceedings of the National Academy of Sciences, Vol. 108, Issue 33 https://doi.org/10.1073/pnas.1106919108	journal	August 2011
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444910045749	journal	March 2011
Sir2-Dependent Activation of Acetyl-CoA Synthetase by Deacetylation of Active Lysine Starai, V. J.; Celic, I.; Cole, R. N. Science, Vol. 298, Issue 5602, p. 2390-2392 https://doi.org/10.1126/science.1077650	journal	December 2002
Amino Acid Biosynthesis and its Regulation Umbarger, H. E. Annual Review of Biochemistry, Vol. 47, Issue 1 https://doi.org/10.1146/annurev.bi.47.070178.002533	journal	June 1978
Aminoacyl-tRNA Synthesis Ibba, Michael; Söll, Dieter Annual Review of Biochemistry, Vol. 69, Issue 1 https://doi.org/10.1146/annurev.biochem.69.1.617	journal	June 2000
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. International Union of Crystallography (IUCr) https://doi.org/10.17863/cam.52329	journalarticle	January 2008
Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector MacNeil, Douglas J.; Gewain, Keith M.; Ruby, Carolyn L. Gene, Vol. 111, Issue 1 https://doi.org/10.1016/0378-1119(92)90603-M	journal	February 1992
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Biosynthetic Origin of the Ether Ring in Platensimycin Rudolf, Jeffrey D.; Dong, Liao-Bin; Manoogian, Karina Journal of the American Chemical Society, Vol. 138, Issue 51 https://doi.org/10.1021/jacs.6b09818	journal	December 2016
Production of selenomethionine-labeled proteins in two-liter plastic bottles for structure determination Stols, Lucy; Millard, Cynthia Sanville; Dementieva, Irina Journal of Structural and Functional Genomics, Vol. 5, Issue 1/2 https://doi.org/10.1023/B:JSFG.0000029196.87615.6e	journal	March 2004
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
The structural biology of biosynthetic megaenzymes Weissman, Kira J. Nature Chemical Biology, Vol. 11, Issue 9 https://doi.org/10.1038/nchembio.1883	journal	August 2015
Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters Wang, Menglu; Moynié, Lucile; Harrison, Peter J. Nature Chemical Biology, Vol. 13, Issue 6 https://doi.org/10.1038/nchembio.2361	journal	April 2017
A genetically amenable platensimycin- and platencin-overproducer as a platform for biosynthetic explorations: a showcase of PtmO4, a long-chain acyl-CoA dehydrogenase Rudolf, Jeffrey D.; Dong, Liao-Bin; Huang, Tingting Molecular BioSystems, Vol. 11, Issue 10 https://doi.org/10.1039/C5MB00303B	journal	January 2015
Explorations of catalytic domains in non-ribosomal peptide synthetase enzymology Hur, Gene H.; Vickery, Christopher R.; Burkart, Michael D. Natural Product Reports, Vol. 29, Issue 10 https://doi.org/10.1039/c2np20025b	journal	January 2012
Crystal Structure of DltA: IMPLICATIONS FOR THE REACTION MECHANISM OF NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATION DOMAINS Yonus, Huma; Neumann, Piotr; Zimmermann, Stephan Journal of Biological Chemistry, Vol. 283, Issue 47 https://doi.org/10.1074/jbc.M800557200	journal	September 2008
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8 https://doi.org/10.1107/S0907444906019949	journal	July 2006
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Molecular replacement with MOLREP Vagin, Alexei; Teplyakov, Alexei Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042589	journal	December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011

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