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Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound.

Buer BC, Paul B, Das D, Stuckey JA, Marsh EN
ACS Chem Biol 9 2584-93 (2014)
Related entries: 4pg0, 4pg1, 4pgk, 4tw3

Cited: 13 times
EuropePMC logo PMID: 25222710

Abstract

The nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the highly unusual deformylation of aliphatic aldehydes to alkanes and formate. We have determined crystal structures for the enzyme with a long-chain water-soluble aldehyde and medium-chain carboxylic acid bound to the active site. These structures delineate a hydrophobic channel that connects the solvent with the deeply buried active site and reveal a mode of substrate binding that is different from previously determined structures with long-chain fatty acids bound. The structures also identify a water channel leading to the active site that could facilitate the entry of protons required in the reaction. NMR studies examining 1-[(13)C]-octanal binding to cADO indicate that the enzyme binds the aldehyde form rather than the hydrated form. Lastly, the fortuitous cocrystallization of the metal-free form of the protein with aldehyde bound has revealed protein conformation changes that are involved in binding iron.

Reviews - 4pgi mentioned but not cited (1)

  1. Recent advances in the improvement of cyanobacterial enzymes for bioalkane production. Hayashi Y, Arai M. Microb Cell Fact 21 256 (2022)

Articles - 4pgi mentioned but not cited (4)

  1. Structure-oriented substrate specificity engineering of aldehyde-deformylating oxygenase towards aldehydes carbon chain length. Bao L, Li JJ, Jia C, Li M, Lu X. Biotechnol Biofuels 9 185 (2016)
  2. Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound. Buer BC, Paul B, Das D, Stuckey JA, Marsh EN. ACS Chem Biol 9 2584-2593 (2014)
  3. Structural insights into catalytic mechanism and product delivery of cyanobacterial acyl-acyl carrier protein reductase. Gao Y, Zhang H, Fan M, Jia C, Shi L, Pan X, Cao P, Zhao X, Chang W, Li M. Nat Commun 11 1525 (2020)
  4. Identification of residues important for the activity of aldehyde-deformylating oxygenase through investigation into the structure-activity relationship. Wang Q, Bao L, Jia C, Li M, Li JJ, Lu X. BMC Biotechnol 17 31 (2017)


Reviews citing this publication (2)

  1. Enzymes for fatty acid-based hydrocarbon biosynthesis. Herman NA, Zhang W. Curr Opin Chem Biol 35 22-28 (2016)
  2. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. J Biol Inorg Chem 22 221-235 (2017)

Articles citing this publication (6)

  1. A consensus-guided approach yields a heat-stable alkane-producing enzyme and identifies residues promoting thermostability. Shakeel T, Gupta M, Fatma Z, Kumar R, Kumar R, Singh R, Sharma M, Jade D, Gupta D, Fatma T, Yazdani SS. J Biol Chem 293 9148-9161 (2018)
  2. Comparison of orthologous cyanobacterial aldehyde deformylating oxygenases in the production of volatile C3-C7 alkanes in engineered E. coli. Patrikainen P, Carbonell V, Thiel K, Aro EM, Kallio P. Metab Eng Commun 5 9-18 (2017)
  3. Identification of non-conserved residues essential for improving the hydrocarbon-producing activity of cyanobacterial aldehyde-deformylating oxygenase. Kudo H, Hayashi Y, Arai M. Biotechnol Biofuels 12 89 (2019)
  4. Hydrocarbon Desaturation in Cyanobacterial Thylakoid Membranes Is Linked With Acclimation to Suboptimal Growth Temperatures. Vuorio E, Thiel K, Fitzpatrick D, Huokko T, Kämäräinen J, Dandapani H, Aro EM, Kallio P. Front Microbiol 12 781864 (2021)
  5. Ferritin-Like Proteins: A Conserved Core for a Myriad of Enzyme Complexes. Banerjee R, Srinivas V, Lebrette H. Subcell Biochem 99 109-153 (2022)
  6. On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all-Atom Molecular Dynamics Investigation in Water Solution. Pietra F. Chem Biodivers 14 (2017)


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