The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage

Prussia, Gregory A.; Shisler, Krista A.; Zadvornyy, Oleg A.; Streit, Bennett R.; DuBois, Jennifer L.; Peters, John W.

doi:10.1016/j.jbc.2021.100961

The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage

Journal Article · Mon Jul 12 00:00:00 EDT 2021 · Journal of Biological Chemistry

DOI:https://doi.org/10.1016/j.jbc.2021.100961· OSTI ID:1816273

^[1]; Shisler, Krista A. ^[2]; Zadvornyy, Oleg A. ^[2]; ^[3]; DuBois, Jennifer L. ^[3]; Peters, John W. ^[2]

Washington State Univ., Pullman, WA (United States); OSTI
Washington State Univ., Pullman, WA (United States)
Montana State Univ., Bozeman, MT (United States)

The 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) enzyme is the only member of the disulfide oxidoreductase (DSOR) family of enzymes, which are important for reductively cleaving S–S bonds, to have carboxylation activity. 2-KPCC catalyzes the conversion of 2-ketopropyl-coenzyme M to acetoacetate, which is used as a carbon source, in a controlled reaction to exclude protons. A conserved His–Glu motif present in DSORs is key in the protonation step; however, in 2-KPCC, the dyad is substituted by Phe–His. Here, we propose that this difference is important for coupling carboxylation with C–S bond cleavage. We substituted the Phe–His dyad in 2-KPCC to be more DSOR like, replacing the phenylalanine with histidine (F501H) and the histidine with glutamate (H506E), and solved crystal structures of F501H and the double variant F501H_H506E. We found that F501 protects the enolacetone intermediate from protons and that the F501H variant strongly promotes protonation. We also provided evidence for the involvement of the H506 residue in stabilizing the developing charge during the formation of acetoacetate, which acts as a product inhibitor in the WT but not the H506E variant enzymes. Finally, we determined that the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base. Taken together, these results indicate that the 2-KPCC dyad is responsible for selectively promoting carboxylation and inhibiting protonation in the formation of acetoacetate.

View Accepted Manuscript (DOE)

Research Organization:: Washington State Univ., Pullman, WA (United States)

Sponsoring Organization:: USDA; USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0018143

OSTI ID:: 1816273

Journal Information:: Journal of Biological Chemistry, Journal Name: Journal of Biological Chemistry Journal Issue: 2 Vol. 297; ISSN 0021-9258

Publisher:: American Society for Biochemistry and Molecular BiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (24)

Substitution of a conserved catalytic dyad into 2-KPCC causes loss of carboxylation activity Prussia, Gregory A.; Gauss, George H.; Mus, Florence FEBS Letters, Vol. 590, Issue 17 https://doi.org/10.1002/1873-3468.12325	journal	August 2016
Substrate binding and catalysis by glutathione reductase as derived from refined enzyme: Substrate crystal structures at 2Å resolution Karplus, P. Andrew; Schulz, Georg E. Journal of Molecular Biology, Vol. 210, Issue 1 https://doi.org/10.1016/0022-2836(89)90298-2	journal	November 1989
Variations on a theme: the family of FAD-dependent NAD(P)H-(disulphide)-oxidoreductases Pai, Emil F. Current Opinion in Structural Biology, Vol. 1, Issue 5 https://doi.org/10.1016/0959-440X(91)90181-R	journal	October 1991
The catalytic mechanism of glutathione reductase as derived from x-ray diffraction analyses of reaction intermediates. Pai, E. F.; Schulz, G. E. Journal of Biological Chemistry, Vol. 258, Issue 3 https://doi.org/10.1016/S0021-9258(18)33050-3	journal	February 1983
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Flavoprotein Disulfide Reductases: Advances in Chemistry and Function Argyrou, Argyrides; Blanchard, John S. Progress in Nucleic Acid Research and Molecular Biology, Vol. 78, p. 89-142 https://doi.org/10.1016/S0079-6603(04)78003-4	book	June 2004
Glutathione catalysis and the reaction mechanisms of glutathione-dependent enzymes Deponte, Marcel Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1830, Issue 5 https://doi.org/10.1016/j.bbagen.2012.09.018	journal	May 2013
Structural basis for carbon dioxide binding by 2-ketopropyl coenzyme M oxidoreductase/carboxylase Pandey, Arti S.; Mulder, David W.; Ensign, Scott A. FEBS Letters, Vol. 585, Issue 3 https://doi.org/10.1016/j.febslet.2010.12.035	journal	December 2010
Reductive and Oxidative Half-Reactions of Glutathione Reductase from Escherichia coli Rietveld, Patrick; Arscott, L. David; Berry, Alan Biochemistry, Vol. 33, Issue 46 https://doi.org/10.1021/bi00250a043	journal	November 1994
Alternative proton donors/acceptors in the catalytic mechanism of the glutathione reductase of Escherichia coli: the role of histidine-439 and tyrosine-99 Deonarain, Mahendra P.; Berry, Alan; Scrutton, Nigel S. Biochemistry, Vol. 28, Issue 25 https://doi.org/10.1021/bi00451a008	journal	December 1989
Structural Basis for CO ₂ Fixation by a Novel Member of the Disulfide Oxidoreductase Family of Enzymes, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase ^† ^, ^‡ Nocek, Boguslaw; Jang, Se Bok; Jeong, Mi Suk Biochemistry, Vol. 41, Issue 43 https://doi.org/10.1021/bi026580p	journal	October 2002
Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase ^† ^, ^‡ Pandey, Arti S.; Nocek, Boguslaw; Clark, Daniel D. Biochemistry, Vol. 45, Issue 1 https://doi.org/10.1021/bi051518o	journal	January 2006
Characterization of Five Catalytic Activities Associated with the NADPH:2-Ketopropyl-coenzyme M [2-(2-Ketopropylthio)ethanesulfonate] Oxidoreductase/Carboxylase of the Xanthobacter Strain Py2 Epoxide Carboxylase System ^† Clark, Daniel D.; Allen, Jeffrey R.; Ensign, Scott A. Biochemistry, Vol. 39, Issue 6 https://doi.org/10.1021/bi992282p	journal	February 2000
Mechanism of Rubisco: The Carbamate as General Base ^✗ Cleland, W. Wallace; Andrews, T. John; Gutteridge, Steven Chemical Reviews, Vol. 98, Issue 2 https://doi.org/10.1021/cr970010r	journal	April 1998
The structure of the flavoenzyme glutathione reductase Schulz, G. E.; Schirmer, R. H.; Sachsenheimer, W. Nature, Vol. 273, Issue 5658 https://doi.org/10.1038/273120a0	journal	May 1978
Biocatalytic carboxylation Glueck, Silvia M.; Gümüs, Selcuc; Fabian, Walter M. F. Chem. Soc. Rev., Vol. 39, Issue 1 https://doi.org/10.1039/B807875K	journal	January 2010
Mechanism of Inhibition of Aliphatic Epoxide Carboxylation by the Coenzyme M Analog 2-Bromoethanesulfonate Boyd, Jeffrey M.; Clark, Daniel D.; Kofoed, Melissa A. Journal of Biological Chemistry, Vol. 285, Issue 33 https://doi.org/10.1074/jbc.M110.144410	journal	June 2010
The reactive form of a C–S bond–cleaving, CO2-fixing flavoenzyme Streit, Bennett R.; Mattice, Jenna R.; Prussia, Gregory A. Journal of Biological Chemistry, Vol. 294, Issue 13 https://doi.org/10.1074/jbc.RA118.005554	journal	March 2019
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Mechanisms of flavoprotein-catalyzed reactions Ghisla, Sandro; Massey, Vincent European Journal of Biochemistry, Vol. 181, Issue 1 https://doi.org/10.1111/j.1432-1033.1989.tb14688.x	journal	April 1989
Roles of the Redox-Active Disulfide and Histidine Residues Forming a Catalytic Dyad in Reactions Catalyzed by 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase Kofoed, M. A.; Wampler, D. A.; Pandey, A. S. Journal of Bacteriology, Vol. 193, Issue 18 https://doi.org/10.1128/JB.05231-11	journal	July 2011
Aliphatic Epoxide Carboxylation Ensign, Scott A.; Allen, Jeffrey R. Annual Review of Biochemistry, Vol. 72, Issue 1 https://doi.org/10.1146/annurev.biochem.72.121801.161820	journal	June 2003

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The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage

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