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Literature summary extracted from

  • Buer, B.C.; Paul, B.; Das, D.; Stuckey, J.A.; Marsh, E.N.
    Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound (2014), ACS Chem. Biol., 9, 2584-2593 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.1.99.5 purified recombinant wild-type and mutant L194A in complex with 11-(2-(2-ethoxyethoxy)ethoxy)undecanal, trans-2-nonylcyclopropane-1-carboxylic acid, or stearate, X-ray diffraction structure determination and analysis at 1.60-2.21 A resolution. It appears that the fatty acids are necessary for crystallization. Attempts to crystallize the enzyme in fully metalated form by including Fe2+ or Zn2+ ions in the crystallization buffer together with 11-(2-(2-ethoxyethoxy)ethoxy)undecanal are unsuccessful Prochlorococcus marinus

Protein Variants

EC Number Protein Variants Comment Organism
4.1.99.5 L194A site-directed mutagenesis, the mutant has kinetic properties very similar to the wild-type enzyme Prochlorococcus marinus

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.1.99.5 additional information substrate inhibition might occur with short aldehydes if a second substrate molecule is bound in the channel preventing product release Prochlorococcus marinus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
4.1.99.5 Fe2+ a nonheme di-iron enzyme Prochlorococcus marinus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.1.99.5 a long-chain aldehyde + O2 + 2 NADPH + 2 H+ Prochlorococcus marinus
-
 an alkane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 a long-chain aldehyde + O2 + 2 NADPH + 2 H+ Prochlorococcus marinus MIT 9313
-
 an alkane + formate + H2O + 2 NADP+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.1.99.5 Prochlorococcus marinus Q7V6D4
-
-
4.1.99.5 Prochlorococcus marinus MIT 9313 Q7V6D4
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
4.1.99.5 octadecanal + O2 + 2 NADPH + 2 H+ = heptadecane + formate + H2O + 2 NADP+ the aldehyde proton is retained in formate and one of the oxygen atoms derives from molecular oxygen, whereas the proton in the product alkane derives from the solvent. Initial formation of a diferric intermediate in the cADO catalyzed reaction. Addition of a further electron to this complex is proposed to lead to its breakdown and scission of the C1-C2 bond. A radical mechanism for C1-C2 bond cleavage is supported by the observed ring-opening of cyclopropyl aldehydes and oxiranyl aldehydes designed to act as radical clocks during deformylation by cADO. Structure-function analysis Prochlorococcus marinus
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.1.99.5 a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus an alkane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus MIT 9313 an alkane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 additional information NMR studies of substrate Binding to cADO Prochlorococcus marinus ?
-
 ?
4.1.99.5 additional information NMR studies of substrate Binding to cADO Prochlorococcus marinus MIT 9313 ?
-
 ?
4.1.99.5 n-octadecanal + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus heptadecane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 n-octadecanal + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus MIT 9313 heptadecane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 n-octanal + O2 + 2 NADPH + 2 H+ binding of 1-[13C]-octanal to enzyme cADO is monitored by 13C NMR Prochlorococcus marinus n-heptane + formate + H2O + 2 NADP+
-
 ?
4.1.99.5 n-octanal + O2 + 2 NADPH + 2 H+ binding of 1-[13C]-octanal to enzyme cADO is monitored by 13C NMR Prochlorococcus marinus MIT 9313 n-heptane + formate + H2O + 2 NADP+
-
 ?

Synonyms

EC Number Synonyms Comment Organism
4.1.99.5 aldehyde decarbonylase
-
 Prochlorococcus marinus
4.1.99.5 cADO
-
 Prochlorococcus marinus
4.1.99.5 cyanobacterial aldehyde deformylating oxygenase
-
 Prochlorococcus marinus
4.1.99.5 PMT_1231
-
 Prochlorococcus marinus

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.1.99.5 additional information
-
 additional information low rates of turnover are measured for cADO Prochlorococcus marinus

Cofactor

EC Number Cofactor Comment Organism Structure
4.1.99.5 NADPH
-
 Prochlorococcus marinus

General Information

EC Number General Information Comment Organism
4.1.99.5 additional information residue L194, at the center of the hydrophobic cavity, might serve as a gateway for substrate entry, but L194 does not play a kinetically significant role in limiting substrate access to the active site. Structure of metal-free cADO, overview Prochlorococcus marinus
4.1.99.5 physiological function the nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the deformylation of aliphatic aldehydes to alkanes and formate Prochlorococcus marinus