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Information on EC 4.1.99.5 - aldehyde oxygenase (deformylating) and Organism(s) Prochlorococcus marinus and UniProt Accession Q7V6D4
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4.1.99.5 aldehyde oxygenase (deformylating)IUBMB Comments
Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 and C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents . The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
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Word Map
- 4.1.99.5
-
biofuels
-
decarbonylation
-
acyl-acyl
- punctiforme
- elongatus
- octadecanal
-
di-iron
-
drop-in
-
cados
- heptadecane
-
ferritin-like
- prochlorococcus
-
diferric
-
photodecarboxylase
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petroleum-derived
- biofuel production
The taxonomic range for the selected organisms is: Prochlorococcus marinus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
decarbonylase, aldehyde-deformylating oxygenase, aldehyde deformylating oxygenase, aldehyde decarbonylase, cyanobacterial aldehyde deformylating oxygenase, cado-1593, cyanobacterial aldehyde decarbonylase, cyanobacterial aldehyde-deformylating oxygenase, liado, osado, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
cyanobacterial aldehyde deformylating oxygenase
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aldehyde decarbonylase
-
-
-
-
decarbonylase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
reaction mechanism, overview
a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
proposed mechanism for deformylation of aldehydes by cADO, overview. The rate of alkane formation is the same in D2O or H2O, implying that proton transfer is not a kinetically significant step. When the ratio of protium to deuterium in the product alkane is measured as a function of the mole fraction of D2O, a D2OSIEobs of 2.19 is observed. The SIE is invariant with the mole fraction of D2O, indicating the involvement of a single protic site in the reaction. An iron-bound water molecule is the proton donor to the alkane in the reaction
a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + 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
a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
mechanism of the unusual iron-catalysed decarbonylation reaction
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a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
mechanistic proposal for the oxygen-independent formation of alkanes by the enzyme. In this mechanism the external reducing system functions catalytically to generate a reactive ketyl radical anion and facilitate carbon-carbon bond cleavage
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C-C bond cleavage
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-
-
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PATHWAY SOURCE
PATHWAYS
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-, -, -
SYSTEMATIC NAME
IUBMB Comments
a long-chain aldehyde alkane-lyase
Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 and C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
CAS REGISTRY NUMBER
COMMENTARY
94185-90-7
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
decanal + O2 + 2 NADH + 2 H+
nonane + formate + H2O + 2 NAD+
with reducing system NADH/phenazine
-
-
?
isobutyraldehyde + O2 + 2 NADPH + 2 H+
propane + formate + H2O + 2 NADP+
low activity with the wild-type enzyme, but increased activity with enzyme mutants I127G and I127G/A48G
-
-
?
n-butanal + O2 + 2 NADPH + 2 H+
n-propane + formate + H2O + 2 NADP+
-
-
-
?
n-hexanal + O2 + 2 NADPH + 2 H+
n-pentane + formate + H2O + 2 NADP+
-
-
-
?
n-octadecanal + O2 + 2 NADPH + 2 H+
heptadecane + formate + H2O + 2 NADP+
-
-
-
?
n-undecanal + O2 + 2 NADPH + 2 H+
n-decane + formate + H2O + 2 NADP+
-
-
-
?
nonanal + O2 + 2 NADH + 2 H+
octane + formate + H2O + 2 NAD+
with reducing system NADH/phenazine
-
-
?
octadecanal + O2 + 2 NADH + 2 H+
heptadecane + formate + H2O + 2 NAD+
with reducing system NADH/phenazine
-
-
?
butanal + O2 + 2 NADH + 2 H+
propane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate
GC-MS poduct analysis
-
?
heptanal + O2 + 2 NAD(P)H + 2 H+
hexane + formate + H2O + 2 NAD(P)+
-
with reducing system NADH/phenazine methosulfate or reducing system with NADPH, ferredoxin, and ferredoxin reductase
-
-
?
heptanal + O2 + 2 NADH + 2 H+
hexane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate or reducing system with NADPH, ferredoxin, and ferredoxin reductase
GC-MS poduct analysis
-
?
pentanal + O2 + 2 NADH + 2 H+
butane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate
GC-MS poduct analysis
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
an alkane + formate + H2O + 2 NADP+
-
-
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
an alkane + formate + H2O + 2 NADP+
C-H-bond-formation by enzyme cADO. The enzyme requires O2 to carry out the oxidative deformylation of substrate to form alkane and formate. The formate product derives an O atom from O2 and retains the aldehyde C-H bond, and the terminal methyl group of the alkane product incorporates an H atom from solvent
-
-
?
n-octanal + O2 + 2 NADPH + 2 H+
n-heptane + formate + H2O + 2 NADP+
-
-
-
?
n-octanal + O2 + 2 NADPH + 2 H+
n-heptane + formate + H2O + 2 NADP+
binding of 1-[13C]-octanal to enzyme cADO is monitored by 13C NMR
-
-
?
octadecanal + O2 + 2 NADH + 2 H+
heptadecane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate
GC-MS poduct analysis
-
?
octadecanal + O2 + 2 NADH + 2 H+
heptadecane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate or reducing system with NADPH, ferredoxin, and ferredoxin reductase
-
-
?
octadecanal + O2 + 2 NADH + 2 H+
heptadecane + formate + H2O + 2 NAD+
-
with reducing system NADH/phenazine methosulfate or reducing system with NADPH, ferredoxin, and ferredoxin reductase
GC-MS poduct analysis
-
?
additional information
?
-
substrate specificity, overview. Marked decrease in relative yields of aldehyde and alcohol products are observed as the alkyl chain length is decreased from C9 to C8. The relative yields of the one-carbon-shorter alcohol and aldehyde products are optimal with nonanal and decanal and decrease with shorter and longer alkyl chains
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-
?
additional information
?
-
cyanobacterial aldehyde-deformylating oxygenase (cADO) converts long-chain fatty aldehydes to alkanes via a proposed diferric-peroxo intermediate that carries out the oxidative deformylation of the substrate. The synthetic iron(III)-peroxo complex [FeIII(eta2deltaO2)(TMC)]+ (TMC is tetramethylcyclam) causes a similar transformation in the presence of a suitable H atom donor, thus serving as a functional model for cADO, reaction analysis with undecanal as substrate, detailed overview. Mechanistic studies suggest that the H atom donor can intercept the incipient alkyl radical formed in the oxidative deformylation step in competition with the oxygen rebound step typically used by most oxygenases for forming C-O bonds
-
-
?
additional information
?
-
enzyme assay in anaerobic conditions, quantification of hydrocarbon products by GC-MS
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-
?
additional information
?
-
GC-MS analysis of the volatile alkane products
-
-
?
additional information
?
-
NMR studies of substrate Binding to cADO
-
-
?
additional information
?
-
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natural specificity of cADO to favour reactivity against short-chain over long-chain aldehydes
-
-
?
additional information
?
-
-
the enzyme catalyzes the conversion of Cn fatty aldehydes to formate and the corresponding Cn-1 alk(a/e)nes. This apparently hydrolytic reaction is actually a cryptically redox oxygenation process, in which one O-atom is incorporated from O2 into formate and a protein-based reducing system (NADPH, ferredoxin, and ferredoxin reductase) provides all four electrons needed for the complete reduction of O2, absolute O2 requirement for formate production
-
-
?
additional information
?
-
-
the enzyme catalyzes the unusual hydrolysis of aldehydes to produce alkanes and formate. The reaction requires an external reducing system but does not require oxygen. The enzyme catalyzes aldehyde decarbonylation at a much faster rate under anaerobic conditions, and the oxygen in formate derives from water. Eventhough an oxygen-dependent mechanism may operate in cAD, the oxygen-independent decarbonylation of aldehydes is a general feature of these enzymes
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
an alkane + formate + H2O + 2 NADP+
-
-
-
?
additional information
?
-
-
natural specificity of cADO to favour reactivity against short-chain over long-chain aldehydes
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
-
di-iron centre, coordinated by two histidine residues and four carboxylates from glutamate side chains
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
substrate inhibition might occur with short aldehydes if a second substrate molecule is bound in the channel preventing product release
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
the rate of alkane formation is the same in D2O or H2O, implying that proton transfer is not a kinetically significant step. When the ratio of protium to deuterium in the product alkane is measured as a function of the mole fraction of D2O, a D2OSIEobs of 2.19 is observed. The SIE is invariant with the mole fraction of D2O, indicating the involvement of a single protic site in the reaction. An iron-bound water molecule is the proton donor to the alkane in the reaction
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
low rates of turnover are measured for cADO
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
structurally, the cADO enzyme belongs to the family of ferritin-like nonheme diiron-carboxylate enzymes that include methane monooxygenase (MMO), class I ribonucleotide reductase (RNR), and stearoyl-acyl carrier protein ?9-desaturase (DELTA9D), all of which share a common Fe2(His)2(O2CR)4 active site
physiological function
additional information
physiological function
enzyme ADO natively catalyzes the conversion of long-chain aldehydes into corresponding alkanes. To convert short-chain isobutyraldehyde into propane efficiently, the substrate specificity of ADO has to be modified for the utilization of the short-chain aldehydes
physiological function
the nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the deformylation of aliphatic aldehydes to alkanes and formate
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
additional information
solvent isotope effects on alkane formation by cyanobacterial aldehyde deformylating oxygenase and their mechanistic implications, overview
additional information
the synthetic iron(III)-peroxo complex [FeIII(eta2deltaO2)(TMC)]+ (TMC is tetramethylcyclam) causes a similar transformation in the presence of a suitable H atom donor, thus serving as a functional model for cADO, reaction analysis with undecanal with [FeIII(TMC)(delta2deltaO2)]+, detailed overview
additional information
-
the definitive reaffirmation of the oxygenative nature of the reaction implies that the enzyme, initially designated as aldehyde decarbonylase when the C1-derived coproduct is thought to be carbon monoxide rather than formate, should be redesignated as aldehyde-deformylating oxygenase, ADO
additional information
-
the enzyme shows a mainly alpha helical architecture, with a ferritin-like four-helix bundle. The latter contains the di-iron centre, coordinated by two histidine residues and four carboxylates from glutamate side chains. Substrates access the active site through a tunnel-like hydrophobic pocket. Active site structure analysis from crystal structure, PDB ID 20C5
additional information
-
the very low activity of the enzyme appears to result from inhibition by the ferredoxin reducing system used in the assay and the low solubility of the substrate
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A134F
site-directed mutagenesis, the mutant shows slightly increased activity compared to wild-type
I127G
site-directed mutagenesis, increased activity compared to wild-type
I127G/A48G
site-directed mutagenesis, increased activity compared to wild-type
L194A
site-directed mutagenesis, the mutant has kinetic properties very similar to the wild-type enzyme
A134F
-
site-directed mutagenesis, the mutant has the same global architecture as wild-type enzyme, the mutant shows highly reduced activity with the majority of long-chain aldehyde substrates tested. the A134F variant displays an approximate fourfold increase in the rate of butanal consumption and approximately sixfold increase in pentanal consumption compared to wild-type enzyme, the mutant generates enhanced levels of propane production in whole-cell biotransformations compared to wild-type cADO
V41Y
-
site-directed mutagenesis, the mutant has the same global architecture as wild-type enzyme, the mutant shows highly reduced activity with the majority of long-chain aldehyde substrates tested
V41Y/A134F
-
site-directed mutagenesis, the double mutant shows reduced activity with long-chain aldehyde substrates and increased activity with short-chain aldehyde substrates like the single mutants
additional information
additional information
installation of a recombinant hydrocarbon production system in Escherichia coli strain BL21(DE3)DELTAyqhDDELTAahr for production of n-alkanes by a combinant ion of four enzymes, i.e. aldehyde deformylating oxygenase (from Prochlorococcus marinus, wild-type and mutant A134F), ferredoxin (from Synechocystis), phosphopantetheinyl transferase (from Bacillus subtilis) and carboxylic acid reductase (from Mycobacterium marinum), method optimization and evaluation, overview. GC-MS analysis of the volatile alkanes produced. Comparison of ADO orthologues from different origins in hydrocarbon biosynthesis in vivo
additional information
screening for Prochlorococcus marinus enzyme ADO mutants generated by engineering the active center to accommodate branched-chain isobutyraldehyde, identification of two ADO mutants, I127G and I127G/A48G, which exhibit higher catalytic activity for isobutyraldehyde and 3fold improved propane productivity compared to wild-type, propane biosynthesis generation
additional information
-
alteration of the enzyme's substrate specificity by engineering of active site residues involved in substrate binding, residues V41 and A134, adjacent to the C9 position of the ligand, might influence fatty acid binding, overview
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
solvent isotope effects on alkane formation by the enzyme have mechanistic implications
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His-tagged enzyme from Escherichia coli strain BL21(DE3) by anion exchange chromatography and dialysis
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of N-terminally His-tagged enzyme in Escherichia coli strain BL21(DE3)
gene PMT1231, recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain BW25113(DE3) DELTA13
recombinant expression of codon-optimized His-tagged enzyme in Escherichia coli strain BL21(DE3)DELTAyqhDDELTAahr, simultaneous coexpression with four enzymes required in the alkane pathway: aldehyde deformylating oxygenase (from Prochlorococcus marinus), ferredoxin (from Synechocystis), phosphopantetheinyl transferase (from Bacillus subtilis) and carboxylic acid reductase (from Mycobacterium marinum), expression analysis
overexpression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biofuel production
the conversion of long-chain fatty aldehydes to corresponding alkanes, that is catalyzed by cyanobacterial aldehyde-deformylating oxygenase (cADO), is probably useful for production of biofuel
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Aukema, K.G.; Makris, T.M.; Stoian, S.A.; Richman, J.E.; Muenck, E.; Lipscomb, J.D.; Wackett, L.P.
Cyanobacterial aldehyde deformylase oxygenation of aldehydes yields n-1 aldehydes and alcohols in addition to alkanes
ACS Catal.
3
2228-2238
2013
Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT 9313 (Q7V6D4)
Eser, B.E.; Das, D.; Han, J.; Jones, P.R.; Marsh, E.N.
Oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor
Biochemistry
50
10743-10750
2011
Nostoc punctiforme, Prochlorococcus marinus, Prochlorococcus marinus MIT9313, Synechococcus sp., Synechocystis sp.
Li, N.; Chang, W.C.; Warui, D.M.; Booker, S.J.; Krebs, C.; Bollinger, J.M.
Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases
Biochemistry
51
7908-7916
2012
Prochlorococcus marinus
Khara, B.; Menon, N.; Levy, C.; Mansell, D.; Das, D.; Marsh, E.N.; Leys, D.; Scrutton, N.S.
Production of propane and other short-chain alkanes by structure-based engineering of ligand specificity in aldehyde-deformylating oxygenase
ChemBioChem
14
1204-1208
2013
Prochlorococcus marinus, Prochlorococcus marinus MIT9313
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
ACS Chem. Biol.
9
2584-2593
2014
Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT 9313 (Q7V6D4)
Waugh, M.W.; Marsh, E.N.
Solvent isotope effects on alkane formation by cyanobacterial aldehyde deformylating oxygenase and their mechanistic implications
Biochemistry
53
5537-5543
2014
Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT9313 (Q7V6D4)
Zhang, L.; Liang, Y.; Wu, W.; Tan, X.; Lu, X.
Microbial synthesis of propane by engineering valine pathway and aldehyde-deformylating oxygenase
Biotechnol. Biofuels
9
80
2016
Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT 9313 (Q7V6D4)
Shokri, A.; Que, L.
Conversion of aldehyde to alkane by a peroxoiron(III) complex a functional model for the cyanobacterial aldehyde-deformylating oxygenase
J. Am. Chem. Soc.
137
7686-7691
2015
Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT 9313 (Q7V6D4)
Patrikainen, P.; Carbonell, V.; Thiel, K.; Aro, E.M.; Kallio, P.
Comparison of orthologous cyanobacterial aldehyde deformylating oxygenases in the production of volatile C3-C7 alkanes in engineered E. coli
Metab. Eng. Commun.
5
9-18
2017
Nostoc punctiforme (B2J1M1), Nostoc punctiforme ATCC 29133 / PCC 73102 (B2J1M1), Prochlorococcus marinus (Q7V6D4), Prochlorococcus marinus MIT 9313 (Q7V6D4), Synechococcus sp. RS9917 (A3Z5H6), Synechocystis sp. PCC 6803 (Q55688)
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