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Literature summary for 4.1.99.5 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
Search for more literature for 4.1.99.5

Crystallization (Commentary)

Crystallization (Comment) Organism
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

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

Inhibitors

Inhibitors Comment Organism Structure
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

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism UniProt Comment Textmining
Prochlorococcus marinus Q7V6D4
-
-
Prochlorococcus marinus MIT 9313 Q7V6D4
-
-

Reaction

Reaction Comment Organism Reaction ID
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)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus an alkane + formate + H2O + 2 NADP+
-
 ?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus MIT 9313 an alkane + formate + H2O + 2 NADP+
-
 ?
additional information NMR studies of substrate Binding to cADO Prochlorococcus marinus ?
-
 ?
additional information NMR studies of substrate Binding to cADO Prochlorococcus marinus MIT 9313 ?
-
 ?
n-octadecanal + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus heptadecane + formate + H2O + 2 NADP+
-
 ?
n-octadecanal + O2 + 2 NADPH + 2 H+
-
 Prochlorococcus marinus MIT 9313 heptadecane + formate + H2O + 2 NADP+
-
 ?
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+
-
 ?
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

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

Turnover Number [1/s]

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

Cofactor

Cofactor Comment Organism Structure
NADPH
-
 Prochlorococcus marinus

General Information

General Information Comment Organism
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
physiological function the nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the deformylation of aliphatic aldehydes to alkanes and formate Prochlorococcus marinus