User:Cobalamin12/sandbox/Aldehyde deformylating oxygenase
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| Aldehyde oxygenase (deformylating) | |||||||||
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| Identifiers | |||||||||
| EC no. | 4.1.99.5 | ||||||||
| Alt. names | Aldehyde decarbonylase | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
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Aldehyde deformylating oxygenases (ADO) (EC 4.1.99.5) are a family of enzymes which catalyze the oxygenation of medium and long chain aldehydes to alkanes via the removal of a carbonyl group as formate.
- n-aldehyde + O2 + 2 NADPH + H+ → (n-1)-alkane + formate + H2O + 2 NADP+
Aldehyde deformylating oxygenases are found in cyanobacteria as part of the alkane biosynthesis pathway[2]. Their substrates are medium- to long-chain aldehydes formed from acyl-ACP by acyl-ACP reductases (EC 1.2.1.80)[2], commonly of 16 and 18 carbons, but potentially as short as nonanal and decanal[3]. Compared to other aldehyde decarbonylases, such as insect or plant aldehyde decarbonylase, cyanobacterial ADO is unusual in evolving formate rather than CO or CO2, for residing in the cytosol[3]. It is also enzymatically unusual in catalyzing an formally hydrolytic and redox-neutral oxygenation of the substrate[4].
Structure
[edit]
Cyanobacterial aldehyde deformylating oxygenases are cytosolic nonheme di-iron oxygenases, but are much smaller (29 kDa) than other members of the family[3], and share sequence homology with ferritin-like or ribonucleotide reductases[2]. The overall structure is a bundle of 8 alpha-helices coordinating two central iron cofactors via histidine, aspartate and glutamate[2]. The substrate channels lies parallel to the helices and terminates at the di-iron center[2].
Conformational changes during the enzymatic cycle of Synechococcus elongates ADO have been observed[5] (PDB: 4QUW, PDB: 4RC6, PDB: 4RC7, PDB: 4RC8). The binding of the substrate aldehyde displaces two coordinating residues on helix 5 (Glu157 and His160), causing a portion of the helix (residues 144-150) to unwind[5]. The resulting hole in the protein surface exposes the active site, facilitating the entrance of the cosubstrate oxygen[5].
A similar conformational change has been observed for Prochlorococcus marinus ADO (PDB: 4PGI), in which residues 154-165 on helix 5 are unwound in the apoenzyme conformation to facilitate metal entry[1].
Mechanism
[edit]The reaction catalyzed by ADO is unusual in that it is oxygenation reaction which results in the formal hydrolysis, rather than oxidation, of the substrate [4]. The exact mechanism is not completely understood, and current understanding is based on a consensus between mechanistic studies and comparison with similar enzymes. The structurally similar R2 unit of ribonucleotide reductase proceeds via a tyrosyl radical mechanism, but the homologous tyrosine is replaced by phenylalanine in ADO[2].
Mechanistic studies suggest that the aldehyde hydrogen is retained in the formate, the alkane hydrogen derives from the solvent, and one formate oxygen originates from O2[6]. The mechanism is tentatively hypothesized to take place by the following steps[7]:
- The reduced di-iron coordinates oxygen, which oxidizes the iron and forms a peroxide species.
- The peroxide species attacks the aldehyde.
- An electron transfer coupled with cleavage of the peroxo species generates a hemi-acetal radical.
- The terminal C-C bond cleaves homolytically to form the alkyl radical and release formate.
- The alkyl radical is quenched by final electron transfer.
- Two electron transfers restore the reduced state of di-iron and release a molecule of water.
Non-specific formation of alcohols rather than alkanes has also been observed, which would instead correspond to a heterolytic cleavage[7].
Kinetics
[edit]The Km for O2 is 84 ± 9 µM [8]. However, the observed catalytic turnover is extremely inefficient, on the order of kcat = 1 min-1 [3], raising the possibility that the current understanding of the functional role, cofactors, or even substrates of ADO are incorrect. Transgenetically expressed, ADO appears to be dependent on ferredoxin-ferredoxin reductase to deliver reducing equivalents, but the endogenous reducing system is not known[2]. Further, oxygen-independent aldehyde deformylation has also been observed [6].
H2O2 is an inhibitor of cADO, and a ADO-catalase fusion protein exhibits improved turnover. Short-chain aldehydes are also observed to be substrate inhibitors [6].
References
[edit]- ^ a b c d Buer BC, Paul B, Das D, Stuckey JA, Marsh EN (November 2014). "Insights into Substrate and Metal Binding from the Crystal Structure of Cyanobacterial Aldehyde Deformylating Oxygenase with Substrate Bound". ACS Chem. Biol. 9 (11): 2584–2593. doi:10.1021/cb500343j.
- ^ a b c d e f g Schirmer A, Rude M, Li X, Popova E, del Cardayre SB (Jul 2010). "Microbial biosynthesis of alkanes". Science. 329 (5991): 559–562. doi:10.1126/science.1187936.
- ^ a b c d Marsh EN, Waugh MW (Sep 2013). "Aldehyde Decarbonylases: Enigmatic Enzymes of Hydrocarbon Biosynthesis". ACS Catal. 3 (11): 2515–2521. doi:10.1021/cs400637t.
- ^ a b Li N, Nørgaard H, Warui DM, Booker SJ, Krebs C, Bollinger JL Jr (Apr 2011). "Conversion of Fatty Aldehydes to Alka(e)nes and Formate by a Cyanobacterial Aldehyde Decarbonylase: Cryptic Redox by an Unusual Dimetal Oxygenase". J. Am. Chem. Soc. 133 (16): 6158–6161. doi:10.1021/ja2013517.
- ^ a b c Jia C, Li M, Li J, Zhang J, Zhang H, Cao P, Pan X, Lu X, Chang W (Jan 2015). "Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases". Protein & Cell. 6 (1): 55–67. doi:10.1007/s13238-014-0108-2.
- ^ a b c Eser BE, Das D, Han J, Jones PR, Marsh EN (Dec 2013). "Oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor". Biochemistry. 50 (49): 10743–50. doi:10.1021/bi2012417.
- ^ a b Rajakovich LJ, Nørgaard H, Warui DM, Chang W, Li N, Booker SJ, Krebs C, Bollinger JM Jr, Pandelia ME (Aug 2015). "Rapid Reduction of the Diferric-Peroxyhemiacetal Intermediate in Aldehyde-Deformylating Oxygenase by a Cyanobacterial Ferredoxin: Evidence for a Free-Radical Mechanism". J. Am. Chem. Soc. 137 (36): 11695–11709. doi:10.1021/jacs.5b06345.
- ^ Andre C, Kim SW, Yu XH, Shanklin J (Feb 2013). "Fusing catalase to an alkane-producing enzyme maintains enzymatic activity by converting the inhibitory byproduct H2O2 to the cosubstrate O2". Proc. Natl. Acad. Sci. U.S.A. 110 (8): 3191–6. doi:10.1073/pnas.1218769110.
