BRENDA - Enzyme Database show
show all sequences of 4.1.99.5

Structural insights into the catalytic mechanism of aldehyde-deformylating oxygenases

Jia, C.; Li, M.; Li, J.; Zhang, J.; Zhang, H.; Cao, P.; Pan, X.; Lu, X.; Chang, W.; Protein Cell 6, 55-67 (2015)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene Synpcc7942_1593, sequence comparisons, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Synechococcus elongatus PCC 7942
Crystallization (Commentary)
Crystallization
Organism
purified recombinant enzyme in both its iron-free and iron-bound forms or with bound substrate, and of mutants Y122F and F86Y/F87Y, sitting drop vapor diffusion method, from reservoir solution of 0.2 mol/l Mg2+, 0.1 mol/l Tris, pH 8.5, 30% w/v PEG 4000, for the iron-bound crystals, 4 mM ferrous ammonium sulfate is added to SeADO protein solutions right before crystallization, and for the substrate-bound enzyme, 0.2mol/l L-proline, 0.1mol/l HEPES, pH 7.1, 25% w/v PEG 1500 is used, 18°C, X-ray diffraction structure determination and analysis at 1.71-2.9 A resolution
Synechococcus elongatus PCC 7942
Engineering
Amino acid exchange
Commentary
Organism
F86Y/F87Y
site-directed mutagenesis, structure comparison with the wild-type enzyme
Synechococcus elongatus PCC 7942
additional information
enzyme structure analysis, comparisons of wild-type and mutant structures, overview
Synechococcus elongatus PCC 7942
Y122F
site-directed mutagenesis, structure comparison with the wild-type enzyme
Synechococcus elongatus PCC 7942
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
di-iron center, Glu144 is one of the iron-coordinating residues and plays a vital role in the catalytic reaction of cADO. The helix, in which Glu144 resides, exhibits two distinct conformations that correlate with the different binding states of the di-iron center in cADO structures. The highly labile feature of cADO di-iron center seems to be responsible for the low enzymatic activity. Six conservative amino acids, loctaed in two EX28-29EX2H motifs, from four helices (Glu32 from helix H1, Glu115 from helix H4, Glu60 and His63 from helix H2, and Glu144 and His147 from helix H5) act as metal ligands. The WT0 structure is characterized by losing the di-iron cluster and by exhibiting a distorted conformation of helix H5. This structure is likely to represent the inactive state of SeADO, as it has lost its cofactor iron
Synechococcus elongatus PCC 7942
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
Synechococcus elongatus PCC 7942
-
an alkane + formate + H2O + 2 NADP+
-
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
Synechococcus elongatus PCC 7942 R2
-
an alkane + formate + H2O + 2 NADP+
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Synechococcus elongatus PCC 7942
Q54764
i.e. Synechococcus elongates strain PCC 7942
-
Synechococcus elongatus PCC 7942 R2
Q54764
i.e. Synechococcus elongates strain PCC 7942
-
Purification (Commentary)
Commentary
Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration, followed by ultrafiltration
Synechococcus elongatus PCC 7942
Reaction
Reaction
Commentary
Organism
a long-chain aldehyde + O2 + 2 NADPH + 2 H+ = an alkane + formate + H2O + 2 NADP+
enzyme structures representing the different states during catalytic reaction
Synechococcus elongatus PCC 7942
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942
an alkane + formate + H2O + 2 NADP+
-
-
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942 R2
an alkane + formate + H2O + 2 NADP+
-
-
-
?
additional information
the in vitro reaction catalyzed by cADO requires both the dioxygen as co-substrate and the presence of a reducing system, which provides four electrons per turnover and can either be biological (ferredoxin, ferredoxin reductase, and NADPH) or chemical (phenazine methosulfate and NADH)
749212
Synechococcus elongatus PCC 7942
?
-
-
-
-
additional information
the in vitro reaction catalyzed by cADO requires both the dioxygen as co-substrate and the presence of a reducing system, which provides four electrons per turnover and can either be biological (ferredoxin, ferredoxin reductase, and NADPH) or chemical (phenazine methosulfate and NADH)
749212
Synechococcus elongatus PCC 7942 R2
?
-
-
-
-
n-heptanal + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942
n-hexane + formate + H2O + 2 NADP+
-
-
-
?
n-heptanal + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942 R2
n-hexane + formate + H2O + 2 NADP+
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
enzyme structure analysis, comparisons of wild-type and mutant structures, overview
Synechococcus elongatus PCC 7942
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Synechococcus elongatus PCC 7942
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.2
-
assay at
Synechococcus elongatus PCC 7942
Cofactor
Cofactor
Commentary
Organism
Structure
NADPH
-
Synechococcus elongatus PCC 7942
Cloned(Commentary) (protein specific)
Commentary
Organism
gene Synpcc7942_1593, sequence comparisons, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Synechococcus elongatus PCC 7942
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NADPH
-
Synechococcus elongatus PCC 7942
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant enzyme in both its iron-free and iron-bound forms or with bound substrate, and of mutants Y122F and F86Y/F87Y, sitting drop vapor diffusion method, from reservoir solution of 0.2 mol/l Mg2+, 0.1 mol/l Tris, pH 8.5, 30% w/v PEG 4000, for the iron-bound crystals, 4 mM ferrous ammonium sulfate is added to SeADO protein solutions right before crystallization, and for the substrate-bound enzyme, 0.2mol/l L-proline, 0.1mol/l HEPES, pH 7.1, 25% w/v PEG 1500 is used, 18°C, X-ray diffraction structure determination and analysis at 1.71-2.9 A resolution
Synechococcus elongatus PCC 7942
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
F86Y/F87Y
site-directed mutagenesis, structure comparison with the wild-type enzyme
Synechococcus elongatus PCC 7942
additional information
enzyme structure analysis, comparisons of wild-type and mutant structures, overview
Synechococcus elongatus PCC 7942
Y122F
site-directed mutagenesis, structure comparison with the wild-type enzyme
Synechococcus elongatus PCC 7942
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
di-iron center, Glu144 is one of the iron-coordinating residues and plays a vital role in the catalytic reaction of cADO. The helix, in which Glu144 resides, exhibits two distinct conformations that correlate with the different binding states of the di-iron center in cADO structures. The highly labile feature of cADO di-iron center seems to be responsible for the low enzymatic activity. Six conservative amino acids, loctaed in two EX28-29EX2H motifs, from four helices (Glu32 from helix H1, Glu115 from helix H4, Glu60 and His63 from helix H2, and Glu144 and His147 from helix H5) act as metal ligands. The WT0 structure is characterized by losing the di-iron cluster and by exhibiting a distorted conformation of helix H5. This structure is likely to represent the inactive state of SeADO, as it has lost its cofactor iron
Synechococcus elongatus PCC 7942
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
Synechococcus elongatus PCC 7942
-
an alkane + formate + H2O + 2 NADP+
-
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
Synechococcus elongatus PCC 7942 R2
-
an alkane + formate + H2O + 2 NADP+
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration, followed by ultrafiltration
Synechococcus elongatus PCC 7942
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942
an alkane + formate + H2O + 2 NADP+
-
-
-
?
a long-chain aldehyde + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942 R2
an alkane + formate + H2O + 2 NADP+
-
-
-
?
additional information
the in vitro reaction catalyzed by cADO requires both the dioxygen as co-substrate and the presence of a reducing system, which provides four electrons per turnover and can either be biological (ferredoxin, ferredoxin reductase, and NADPH) or chemical (phenazine methosulfate and NADH)
749212
Synechococcus elongatus PCC 7942
?
-
-
-
-
additional information
the in vitro reaction catalyzed by cADO requires both the dioxygen as co-substrate and the presence of a reducing system, which provides four electrons per turnover and can either be biological (ferredoxin, ferredoxin reductase, and NADPH) or chemical (phenazine methosulfate and NADH)
749212
Synechococcus elongatus PCC 7942 R2
?
-
-
-
-
n-heptanal + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942
n-hexane + formate + H2O + 2 NADP+
-
-
-
?
n-heptanal + O2 + 2 NADPH + 2 H+
-
749212
Synechococcus elongatus PCC 7942 R2
n-hexane + formate + H2O + 2 NADP+
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
enzyme structure analysis, comparisons of wild-type and mutant structures, overview
Synechococcus elongatus PCC 7942
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Synechococcus elongatus PCC 7942
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.2
-
assay at
Synechococcus elongatus PCC 7942
General Information
General Information
Commentary
Organism
evolution
the enzyme belongs to the superfamily of ferritin-like di-iron proteins with conserved sequence of two EX28-29EX2H motifs
Synechococcus elongatus PCC 7942
metabolism
cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in fatty alk(a/e)ne biosynthesis pathway
Synechococcus elongatus PCC 7942
additional information
Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. The helix, in which Glu144 resides, exhibits two distinct conformations that correlate with the different binding states of the di-iron center in cADO structures. Enzyme structure analysis, comparisons of wild-type and mutant structures, overview. A continuous tube-shaped non-protein electron density, resembling a lipid molecule, is observed close to the di-iron center in all structures but the Y122F structure, a hydrophobic substrate channel in SeADO is described
Synechococcus elongatus PCC 7942
physiological function
cyanobacterial aldehyde-deformylating oxygenase (cADO) catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne with low activity due to a highly labile feature of cADO di-iron center
Synechococcus elongatus PCC 7942
General Information (protein specific)
General Information
Commentary
Organism
evolution
the enzyme belongs to the superfamily of ferritin-like di-iron proteins with conserved sequence of two EX28-29EX2H motifs
Synechococcus elongatus PCC 7942
metabolism
cyanobacterial aldehyde-deformylating oxygenase (cADO), which catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne, is a key enzyme in fatty alk(a/e)ne biosynthesis pathway
Synechococcus elongatus PCC 7942
additional information
Glu144, one of the iron-coordinating residues, plays a vital role in the catalytic reaction of cADO. The helix, in which Glu144 resides, exhibits two distinct conformations that correlate with the different binding states of the di-iron center in cADO structures. Enzyme structure analysis, comparisons of wild-type and mutant structures, overview. A continuous tube-shaped non-protein electron density, resembling a lipid molecule, is observed close to the di-iron center in all structures but the Y122F structure, a hydrophobic substrate channel in SeADO is described
Synechococcus elongatus PCC 7942
physiological function
cyanobacterial aldehyde-deformylating oxygenase (cADO) catalyzes the conversion of Cn fatty aldehyde to its corresponding Cn-1 alk(a/e)ne with low activity due to a highly labile feature of cADO di-iron center
Synechococcus elongatus PCC 7942
Other publictions for EC 4.1.99.5
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
747409
Wang
Identification of residues im ...
Synechococcus elongatus PCC 7942, Synechococcus elongatus PCC 7942 R2, Synechocystis sp. PCC 6803
BMC Biotechnol.
17
31-39
2017
-
-
-
-
21
-
-
8
-
2
-
3
-
9
-
-
-
-
-
-
-
-
11
1
-
-
-
28
-
-
-
1
-
-
-
-
-
-
1
-
21
-
-
-
-
8
-
2
-
3
-
-
-
-
-
-
-
-
11
1
-
-
-
28
-
-
-
-
-
2
2
-
9
9
748564
Patrikainen
Comparison of orthologous cya ...
Nostoc punctiforme, Nostoc punctiforme ATCC 29133 / PCC 73102, Prochlorococcus marinus, Prochlorococcus marinus MIT 9313, Synechococcus sp. RS9917, Synechocystis sp. PCC 6803
Metab. Eng. Commun.
5
9-18
2017
-
-
4
-
5
-
-
-
-
-
-
6
-
13
-
-
-
-
-
-
-
-
30
-
-
-
-
-
-
-
-
4
-
-
-
-
-
4
4
-
5
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
30
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
746976
Park
Crystal structures of aldehyd ...
Limnothrix redekei, Limnothrix redekei KNUA012, Oscillatoria sp. KNUA011
Biochem. Biophys. Res. Commun.
477
395-400
2016
-
2
2
2
-
-
-
-
-
-
-
3
-
5
-
-
-
-
-
-
-
-
6
2
2
-
-
-
2
-
-
2
-
-
-
-
2
2
2
2
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
6
2
2
-
-
-
2
-
-
-
-
4
4
-
-
-
747351
Bao
Structure-oriented substrate ...
Synechococcus elongatus PCC 7942, Synechococcus elongatus PCC 7942 R2
Biotechnol. Biofuels
9
185
2016
-
-
1
-
13
-
-
7
-
-
-
2
-
6
-
-
1
-
-
-
-
-
14
-
1
-
-
8
1
-
-
1
-
-
-
-
-
1
1
-
13
-
-
-
-
7
-
-
-
2
-
-
-
1
-
-
-
-
14
-
1
-
-
8
1
-
-
-
-
2
2
-
8
8
747353
Zhang
Microbial synthesis of propan ...
Prochlorococcus marinus, Prochlorococcus marinus MIT 9313
Biotechnol. Biofuels
9
80
2016
-
-
1
-
3
-
-
-
-
-
-
2
-
7
-
-
-
-
-
-
-
-
4
-
1
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
3
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
4
-
1
-
-
-
-
-
-
-
-
1
1
-
-
-
747081
Warui
Efficient delivery of long-ch ...
Nostoc punctiforme, Nostoc punctiforme ATCC 29133 / PCC 73102
Biochemistry
54
1006-1015
2015
-
-
-
-
-
-
-
-
-
-
-
2
-
9
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
1
-
-
-
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-
1
-
-
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-
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-
-
-
2
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
748027
Rajakovich
Rapid reduction of the diferr ...
Nostoc punctiforme, Nostoc punctiforme ATCC 29133 / PCC 73102
J. Am. Chem. Soc.
137
11695-11709
2015
-
-
-
-
-
-
-
-
-
1
-
2
-
8
-
-
-
1
-
-
-
-
10
-
1
-
-
-
1
-
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2
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-
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-
2
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-
-
-
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1
-
2
-
-
-
-
-
-
-
-
10
-
1
-
-
-
1
-
-
-
-
1
1
-
-
-
748032
Shokri
Conversion of aldehyde to alk ...
Prochlorococcus marinus, Prochlorococcus marinus MIT 9313
J. Am. Chem. Soc.
137
7686-7691
2015
-
1
-
-
-
-
-
-
-
1
-
2
-
6
-
-
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1
-
-
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8
1
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1
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1
-
1
-
-
-
-
-
-
-
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1
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2
-
-
-
-
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8
1
-
-
-
-
-
-
-
-
-
2
2
-
-
-
749051
Hayashi
Role of cysteine residues in ...
Nostoc punctiforme, Nostoc punctiforme ATCC 29133 / PCC 73102
PLoS ONE
10
e0122217
2015
-
-
1
-
8
-
-
1
-
1
-
2
-
7
-
-
1
-
-
-
-
-
10
-
1
-
5
-
-
-
-
1
-
-
-
-
-
1
1
-
8
-
-
-
-
1
-
1
-
2
-
-
-
1
-
-
-
-
10
-
1
-
5
-
-
-
-
-
-
3
3
-
-
-
749212
Jia
Structural insights into the ...
Synechococcus elongatus PCC 7942, Synechococcus elongatus PCC 7942 R2
Protein Cell
6
55-67
2015
-
-
1
1
3
-
-
-
-
1
-
2
-
6
-
-
1
1
-
-
-
-
6
1
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
1
3
-
-
-
-
-
-
1
-
2
-
-
-
1
-
-
-
-
6
1
1
-
-
-
1
-
-
-
-
4
4
-
-
-
726552
Das
Mechanistic insights from reac ...
Nostoc punctiforme
ACS Chem. Biol.
9
570-577
2014
-
-
1
-
-
-
1
-
-
1
-
1
-
2
-
-
1
1
-
-
-
-
6
-
1
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-
3
1
-
-
2
-
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-
1
2
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1
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1
-
1
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1
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-
6
-
1
-
-
3
1
-
-
-
-
1
1
-
-
-
746597
Buer
Insights into substrate and m ...
Prochlorococcus marinus, Prochlorococcus marinus MIT 9313
ACS Chem. Biol.
9
2584-2593
2014
-
-
-
1
1
-
1
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Conversion of fatty aldehydes ...
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Production of propane and othe ...
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Pandelia
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Probing the mechanism of cyano ...
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727001
Li
Evidence for only oxygenative ...
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715300
Li
Conversion of fatty aldehydes ...
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726957
Eser
Oxygen-independent alkane form ...
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Schirmer
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Alkane biosynthesis by decarbo ...
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