BRENDA - Enzyme Database

Structural insights into the binding of lauric acid to CYP107L2 from Streptomyces avermitilis

Han, S.; Pham, T.V.; Kim, J.H.; Lim, Y.R.; Park, H.G.; Jeong, D.; Yun, C.H.; Chun, Y.J.; Kang, L.W.; Kim, D.; Biochem. Biophys. Res. Commun. 482, 902-908 (2017)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
1.14.13.185
gene cyp107l2, recombinant expression of His-tagged enzyme in Escherichia coli
Streptomyces avermitilis
1.14.15.33
gene cyp107l2, recombinant expression of His-tagged enzyme in Escherichia coli
Streptomyces avermitilis
Crystallization (Commentary)
EC Number
Crystallization
Organism
1.14.13.185
purified recombinant ligand-free CYP107L2 and its complex with lauric acid, (1) sitting drop vapor diffusion method, mixing of 500 nl of 12 mg/ml protein solution with 500 nl of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, for complex crystals lauric acid in a 1:10 M ratio, and equilibration against 0.05 ml of reservoir solution, 14C, 30 days, (2) hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution with 0.001 ml of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, and equilibration against 0.05 ml of reservoir solution, X-ray diffraction structure determination and analysis at 2.5-2.6 A resolution
Streptomyces avermitilis
1.14.15.33
purified recombinant ligand-free CYP107L2 and its complex with lauric acid, (1) sitting drop vapor diffusion method, mixing of 500 nl of 12 mg/ml protein solution with 500 nl of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, for complex crystals lauric acid in a 1:10 M ratio, and equilibration against 0.05 ml of reservoir solution, 14C, 30 days, (2) hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution with 0.001 ml of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, and equilibration against 0.05 ml of reservoir solution, X-ray diffraction structure determination and analysis at 2.5-2.6 A resolution
Streptomyces avermitilis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
Streptomyces avermitilis
-
novapikromyin + 2 NADP+ + 2 H2O
-
-
?
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
Streptomyces avermitilis ATCC 31267
-
novapikromyin + 2 NADP+ + 2 H2O
-
-
?
1.14.13.185
narbomycin + NADPH + H+ + O2
Streptomyces avermitilis
-
pikromycin + NADP+ + H2O
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
Streptomyces avermitilis
-
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
Streptomyces avermitilis ATCC 31267
-
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
Streptomyces avermitilis
-
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
Streptomyces avermitilis ATCC 31267
-
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
1.14.13.185
Streptomyces avermitilis
Q82LM3
-
-
1.14.13.185
Streptomyces avermitilis ATCC 31267
Q82LM3
-
-
1.14.15.33
Streptomyces avermitilis
Q82LM3
-
-
1.14.15.33
Streptomyces avermitilis ATCC 31267
Q82LM3
-
-
Purification (Commentary)
EC Number
Commentary
Organism
1.14.13.185
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Streptomyces avermitilis
1.14.15.33
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Streptomyces avermitilis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.14.13.185
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis
?
-
-
-
-
1.14.13.185
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis ATCC 31267
?
-
-
-
-
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis
novapikromyin + 2 NADP+ + 2 H2O
-
-
-
?
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis ATCC 31267
novapikromyin + 2 NADP+ + 2 H2O
-
-
-
?
1.14.13.185
narbomycin + NADPH + H+ + O2
-
744239
Streptomyces avermitilis
pikromycin + NADP+ + H2O
-
-
-
?
1.14.15.33
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis
?
-
-
-
-
1.14.15.33
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis ATCC 31267
?
-
-
-
-
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis ATCC 31267
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
-
744239
Streptomyces avermitilis
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
-
744239
Streptomyces avermitilis ATCC 31267
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
1.14.13.185
monomer
1 * 43000, recombinant His-tagged enzyme, SDS-PAGE and crystal structure analysis
Streptomyces avermitilis
1.14.15.33
monomer
1 * 43000, recombinant His-tagged enzyme, SDS-PAGE and crystal structure analysis
Streptomyces avermitilis
Cofactor
EC Number
Cofactor
Commentary
Organism
Structure
1.14.13.185
cytochrome P450
-
Streptomyces avermitilis
1.14.13.185
heme
CYP107L2 shows a low-spin state of heme. Heme is sandwiched between helices I and L in the conserved way of P450 structures. The I-helix crosses the center of CYP107L2 in a slightly bent form over the heme structure, while helices F and G are stacked onto the I-helix to form a wide-open substrate-binding cavity just above the heme moiety
Streptomyces avermitilis
1.14.13.185
NADPH
-
Streptomyces avermitilis
1.14.15.33
cytochrome P450
-
Streptomyces avermitilis
1.14.15.33
ferredoxin [iron-sulfur] cluster
-
Streptomyces avermitilis
1.14.15.33
heme
CYP107L2 shows a low-spin state of heme. Heme is sandwiched between helices I and L in the conserved way of P450 structures. The I-helix crosses the center of CYP107L2 in a slightly bent form over the heme structure, while helices F and G are stacked onto the I-helix to form a wide-open substrate-binding cavity just above the heme moiety
Streptomyces avermitilis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
1.14.13.185
gene cyp107l2, recombinant expression of His-tagged enzyme in Escherichia coli
Streptomyces avermitilis
1.14.15.33
gene cyp107l2, recombinant expression of His-tagged enzyme in Escherichia coli
Streptomyces avermitilis
Cofactor (protein specific)
EC Number
Cofactor
Commentary
Organism
Structure
1.14.13.185
cytochrome P450
-
Streptomyces avermitilis
1.14.13.185
heme
CYP107L2 shows a low-spin state of heme. Heme is sandwiched between helices I and L in the conserved way of P450 structures. The I-helix crosses the center of CYP107L2 in a slightly bent form over the heme structure, while helices F and G are stacked onto the I-helix to form a wide-open substrate-binding cavity just above the heme moiety
Streptomyces avermitilis
1.14.13.185
NADPH
-
Streptomyces avermitilis
1.14.15.33
cytochrome P450
-
Streptomyces avermitilis
1.14.15.33
ferredoxin [iron-sulfur] cluster
-
Streptomyces avermitilis
1.14.15.33
heme
CYP107L2 shows a low-spin state of heme. Heme is sandwiched between helices I and L in the conserved way of P450 structures. The I-helix crosses the center of CYP107L2 in a slightly bent form over the heme structure, while helices F and G are stacked onto the I-helix to form a wide-open substrate-binding cavity just above the heme moiety
Streptomyces avermitilis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
1.14.13.185
purified recombinant ligand-free CYP107L2 and its complex with lauric acid, (1) sitting drop vapor diffusion method, mixing of 500 nl of 12 mg/ml protein solution with 500 nl of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, for complex crystals lauric acid in a 1:10 M ratio, and equilibration against 0.05 ml of reservoir solution, 14C, 30 days, (2) hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution with 0.001 ml of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, and equilibration against 0.05 ml of reservoir solution, X-ray diffraction structure determination and analysis at 2.5-2.6 A resolution
Streptomyces avermitilis
1.14.15.33
purified recombinant ligand-free CYP107L2 and its complex with lauric acid, (1) sitting drop vapor diffusion method, mixing of 500 nl of 12 mg/ml protein solution with 500 nl of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, for complex crystals lauric acid in a 1:10 M ratio, and equilibration against 0.05 ml of reservoir solution, 14C, 30 days, (2) hanging drop vapor diffusion method, mixing of 0.001 ml of 12 mg/ml protein solution with 0.001 ml of reservoir solution containing 0.17 M ammonium sulfate, 0.085 M sodium cacodylate, pH 6.5, 25.5% w/v PEG 8000, and 15% v/v glycerol, and equilibration against 0.05 ml of reservoir solution, X-ray diffraction structure determination and analysis at 2.5-2.6 A resolution
Streptomyces avermitilis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
Streptomyces avermitilis
-
novapikromyin + 2 NADP+ + 2 H2O
-
-
?
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
Streptomyces avermitilis ATCC 31267
-
novapikromyin + 2 NADP+ + 2 H2O
-
-
?
1.14.13.185
narbomycin + NADPH + H+ + O2
Streptomyces avermitilis
-
pikromycin + NADP+ + H2O
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
Streptomyces avermitilis
-
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
Streptomyces avermitilis ATCC 31267
-
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
Streptomyces avermitilis
-
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
Streptomyces avermitilis ATCC 31267
-
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
1.14.13.185
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Streptomyces avermitilis
1.14.15.33
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Streptomyces avermitilis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
1.14.13.185
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis
?
-
-
-
-
1.14.13.185
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis ATCC 31267
?
-
-
-
-
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis
novapikromyin + 2 NADP+ + 2 H2O
-
-
-
?
1.14.13.185
narbomycin + 2 NADPH + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis ATCC 31267
novapikromyin + 2 NADP+ + 2 H2O
-
-
-
?
1.14.13.185
narbomycin + NADPH + H+ + O2
-
744239
Streptomyces avermitilis
pikromycin + NADP+ + H2O
-
-
-
?
1.14.15.33
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis
?
-
-
-
-
1.14.15.33
additional information
no catalytic activity with lauric acid. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Residue Glu40 and Leu382 in the CYP107L2 complex with lauric acid show significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. Binding structure of enzyme, lauric acid and pikromycin, overview
744239
Streptomyces avermitilis ATCC 31267
?
-
-
-
-
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
-
?
1.14.15.33
narbomycin + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + 2 O2
-
744239
Streptomyces avermitilis ATCC 31267
novapikromyin + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
-
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
-
744239
Streptomyces avermitilis
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
1.14.15.33
narbomycin + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
-
744239
Streptomyces avermitilis ATCC 31267
pikromycin + oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
1.14.13.185
monomer
1 * 43000, recombinant His-tagged enzyme, SDS-PAGE and crystal structure analysis
Streptomyces avermitilis
1.14.15.33
monomer
1 * 43000, recombinant His-tagged enzyme, SDS-PAGE and crystal structure analysis
Streptomyces avermitilis
General Information
EC Number
General Information
Commentary
Organism
1.14.13.185
physiological function
CYP107L1 catalyzes the hydroxylation of narbomycin to produce pikromycin and novapikromycin
Streptomyces avermitilis
1.14.15.33
physiological function
CYP107L1 catalyzes the hydroxylation of narbomycin to produce pikromycin and novapikromycin
Streptomyces avermitilis
General Information (protein specific)
EC Number
General Information
Commentary
Organism
1.14.13.185
physiological function
CYP107L1 catalyzes the hydroxylation of narbomycin to produce pikromycin and novapikromycin
Streptomyces avermitilis
1.14.15.33
physiological function
CYP107L1 catalyzes the hydroxylation of narbomycin to produce pikromycin and novapikromycin
Streptomyces avermitilis