Display options
Cite
Stunkard LM, Benjamin AB, Bower JB, et al. Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*. Chembiochem. 2021;doi: 10.1002/cbic.202100487.
Stunkard, L. M., Benjamin, A. B., Bower, J. B., Huth, T. J., & Lohman, J. R. (2021). Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*. Chembiochem : a European journal of chemical biology, . https://doi.org/10.1002/cbic.202100487
Stunkard, Lee M, et al. "Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*." Chembiochem : a European journal of chemical biology vol. (2021). doi: https://doi.org/10.1002/cbic.202100487
Stunkard LM, Benjamin AB, Bower JB, Huth TJ, Lohman JR. Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*. Chembiochem. 2021 Dec 01; doi: 10.1002/cbic.202100487. Epub 2021 Dec 01. PMID: 34856049.
Copy Download .nbib Format: NLM
Share it on

Chembiochem. 2021 Dec 01; doi: 10.1002/cbic.202100487. Epub 2021 Dec 01.

Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase*.

Chembiochem : a European journal of chemical biology

Lee M Stunkard, Aaron B Benjamin, James B Bower, Tyler J Huth, Jeremy R Lohman

Affiliations

  1. Department of Biochemistry, Purdue University, 175 S. University St., West Lafayette, IN 47907, USA.

PMID: 34856049 DOI: 10.1002/cbic.202100487

Abstract

Methylmalonyl-CoA epimerase (MMCE) is proposed to use general acid-base catalysis, but the proposed catalytic glutamic acids are highly asymmetrical in the active site unlike many other racemases. To gain insight into the puzzling relationships between catalytic mechanism, structure, and substrate preference, we solved Streptomyces coelicolor MMCE structures with substrate or 2-nitropropionyl-CoA, an intermediate/transition state analogue. Both ligand bound structures have a planar methylmalonate/2-nitropropionyl moiety indicating a deprotonated C2 with ≥4 Å distances to either catalytic acid. Both glutamates interact with the carboxylate/nitro group, either directly or through other residues. This suggests the proposed catalytic acids sequentially catalyze proton shifts between C2 and carboxylate of the substrate with an enolate intermediate. In addition, our structures provide a platform to design mutations for expanding substrate scope to support combinatorial biosynthesis.

© 2021 Wiley-VCH GmbH.

Keywords: chirality; conformational changes; isomerases; isosteres; metalloenzymes

References

  1. C. M. Dobson, A. Gradinger, N. Longo, X. Wu, D. Leclerc, J. Lerner-Ellis, M. Lemieux, C. Belair, D. Watkins, D. S. Rosenblatt, R. A. Gravel, Mol. Genet. Metab. 2006, 88, 327-333. - PubMed
  2. F. Gross, M. W. Ring, O. Perlova, J. Fu, S. Schneider, K. Gerth, S. Kuhlmann, A. F. Stewart, Y. Zhang, R. Muller, Chem. Biol. 2006, 13, 1253-1264. - PubMed
  3.   - PubMed
  4. L. C. Dayem, J. R. Carney, D. V. Santi, B. A. Pfeifer, C. Khosla, J. T. Kealey, Biochemistry 2002, 41, 5193-5201; - PubMed
  5. A. F. Marsden, P. Caffrey, J. F. Aparicio, M. S. Loughran, J. Staunton, P. F. Leadlay, Science 1994, 263, 378-380. - PubMed
  6.   - PubMed
  7. D. M. Peter, B. Vogeli, N. S. Cortina, T. J. Erb, Molecules 2016, 21, 517; - PubMed
  8. A. J. Hughes, A. Keatinge-Clay, Chem. Biol. 2011, 18, 165-176. - PubMed
  9. H. A. Crosby, K. C. Rank, I. Rayment, J. C. Escalante-Semerena, Appl. Environ. Microbiol. 2012, 78, 6619-6629. - PubMed
  10. N. L. Pohl, M. Hans, H. Y. Lee, Y. S. Kim, D. E. Cane, C. Khosla, J. Am. Chem. Soc. 2001, 123, 5822-5823. - PubMed
  11.   - PubMed
  12. I. Koryakina, G. J. Williams, ChemBioChem 2011, 12, 2289-2293; - PubMed
  13. I. Koryakina, J. McArthur, S. Randall, M. M. Draelos, E. M. Musiol, D. C. Muddiman, T. Weber, G. J. Williams, ACS Chem. Biol. 2013, 8, 200-208; - PubMed
  14. I. Koryakina, C. Kasey, J. B. McArthur, A. N. Lowell, J. A. Chemler, S. Li, D. A. Hansen, D. H. Sherman, G. J. Williams, ACS Chem. Biol. 2017, 12, 114-123; - PubMed
  15. E. M. Musiol-Kroll, F. Zubeil, T. Schafhauser, T. Hartner, A. Kulik, J. McArthur, I. Koryakina, W. Wohlleben, S. Grond, G. J. Williams, S. Y. Lee, T. Weber, ACS Synth. Biol. 2017, 6, 421-427; - PubMed
  16. S. M. Carpenter, G. J. Williams, ACS Chem. Biol. 2018, 13, 3361-3373; - PubMed
  17. E. Kalkreuter, J. M. CroweTipton, A. N. Lowell, D. H. Sherman, G. J. Williams, J. Am. Chem. Soc. 2019, 141, 1961-1969. - PubMed
  18. J. Q. Fuller, P. F. Leadlay, Biochem. J. 1983, 213, 643-650. - PubMed
  19.   - PubMed
  20. P. F. Leadlay, J. Q. Fuller, Biochem. J. 1983, 213, 635-642; - PubMed
  21. M. Michenfelder, W. E. Hull, J. Retey, Eur. J. Biochem. 1987, 168, 659-667. - PubMed
  22. A. A. McCarthy, H. M. Baker, S. C. Shewry, M. L. Patchett, E. N. Baker, Structure 2001, 9, 637-646. - PubMed
  23.   - PubMed
  24. L. M. Stunkard, B. J. Kick, J. R. Lohman, Biochemistry 2021, 60, 365-372; - PubMed
  25. L. M. Stunkard, A. D. Dixon, T. J. Huth, J. R. Lohman, J. Am. Chem. Soc. 2019, 141, 5121-5124. - PubMed
  26. P. F. Leadlay, Biochem. J. 1981, 197, 413-419. - PubMed
  27. K. Heuberger, H. J. Bailey, P. Burda, A. Chaikuad, E. Krysztofinska, T. Suormala, C. Burer, S. Lutz, B. Fowler, D. S. Froese, W. W. Yue, M. R. Baumgartner, Biochim. Biophys. Acta Mol. Basis Dis. 2019, 1865, 1265-1272. - PubMed
  28. C. M. Perkins, N. J. Rose, R. E. Stenkamp, Inorg. Chim. Acta 1990, 172, 119-125. - PubMed
  29.   - PubMed
  30. T. J. Erb, J. Retey, G. Fuchs, B. E. Alber, J. Biol. Chem. 2008, 283, 32283-32293; - PubMed
  31. R. B. Hamed, J. R. Gomez-Castellanos, D. Sean Froese, E. Krysztofinska, W. W. Yue, C. J. Schofield, ChemBioChem 2016, 17, 471-473. - PubMed

Publication Types

Grant support