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Information on EC 1.14.15.35 - 6-deoxyerythronolide B hydroxylase and Organism(s) Saccharopolyspora erythraea and UniProt Accession Q00441
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1.14.15.35 6-deoxyerythronolide B hydroxylaseIUBMB Comments
A cytochrome P-450 (heme-thiolate) protein isolated from the bacterium Saccharopolyspora erythraea. The enzyme is involved in the biosynthesis of the antibiotic erythromycin.
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Word Map
- 1.14.15.35
- heme
-
p450cam
- erythromycin
-
p450terp
- dioxygen
-
saccharopolyspora
-
macrolide
-
substrate-bound
- erythraea
-
i-helix
-
1-pyrenebutanol
-
hutchinson
- ketoconazole
- alpha-naphthoflavone
- unconstrained
-
homotropic
-
7-benzyloxyquinoline
-
ferryl
The taxonomic range for the selected organisms is: Saccharopolyspora erythraea
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
+
2
+
2
+
=
+
2
+
+
2
reduced ferredoxin [iron-sulfur] cluster
+
2
+
=
+
2
oxidized ferredoxin [iron-sulfur] cluster
+
Synonyms
p450eryf, cytochrome p450eryf, cyp107a1, 6-deoxyerythronolide b hydroxylase, eryfac, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
6-deoxyerythronolide-B,reduced ferredoxin:oxygen oxidoreductase
A cytochrome P-450 (heme-thiolate) protein isolated from the bacterium Saccharopolyspora erythraea. The enzyme is involved in the biosynthesis of the antibiotic erythromycin.
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
6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
erythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
6-deoxyerythronolide B + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
erythronolide B + oxidized ferredoxin [iron-sulfur] cluster + H2O
C-6 hydroxylation
-
-
?
9-aminophenanthrene + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
? + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
androstenedione + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
? + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
dehydroepiandrostenedione + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
? + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
testosterone + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
? + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
?
(9R)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9R)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(9S)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9S)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(9S)-9-deoxo-9-hydroxy-8,8a-deoxyoleandolide + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
6-hydroxy-8,8a-deoxyoleandolide + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
substrate is identical to 6-deoxyerythronolide B except for the presence of a C13 methyl group. Hydroxylation at a rate approximately 4fold lower than the natural substrate 6-deoxyerythronolide B
-
-
?
6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
erythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
-
?
8,8a-deoxyoleandolide + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
6-hydroxy-8,8a-deoxyoleandolide + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
substrate is identical to 6-deoxyerythronolide B except for the presence of a C13 methyl group. Hydroxylation at a rate approximately 4fold lower than the natural substrate 6-deoxyerythronolide B
-
-
?
6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
erythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
the enzyme is involved in the biosynthesis of the antibiotic erythromycin
-
-
?
6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
erythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
direct involvement of the substrate in O2 activation
-
-
?
(9R)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9R)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
-
?
(9R)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9R)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
hydroxylation at a rate approximately 2fold lower than the natural substrate 6-deoxyerythronolide B
-
-
?
(9S)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9S)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
-
-
-
?
(9S)-9-deoxo-9-hydroxy-6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
(9S)-9-deoxo-9-hydroxyerythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
-
hydroxylation at a rate approximately equal to the natural substrate 6-deoxyerythronolide B
-
-
?
additional information
?
-
enzyme demonstrates cooperative ligand binding and oxidation kinetics
-
-
?
additional information
?
-
the oxidation state dependence originates from differential proton affinities while the electronic state dependence of the reduced oxyferrous heme has its origins in subtle differences in network topologies near the transition state of the initial proton transfer event. Simultaneous diprotonation of the distal oxygen of the reduced oxyferrous heme leads to O-O bond scission, using the combined water network and 6-deoxyerythronolide B substrate protonation agents
-
-
?
additional information
?
-
-
the ethyl substituent at the 13-position of 6-deoxyerythronolide B is important in the affinity of the substrate for the enzyme, possibly by interacting with a hydrophobic active-site residue. Residue Leu76 may be in a position to interact with the C-13 ethyl group
-
-
?
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
6-deoxyerythronolide B + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2
erythronolide B + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
the enzyme is involved in the biosynthesis of the antibiotic erythromycin
-
-
?
6-deoxyerythronolide B + reduced ferredoxin [iron-sulfur] cluster + H+ + O2
erythronolide B + oxidized ferredoxin [iron-sulfur] cluster + H2O
C-6 hydroxylation
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
cytochrome P450
-
enzyme contains cytochrome P-450 in the low spin state with absorption maxima at 416, 532, and 565 nm, respectively
-
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ketoconazole
wild-type and mutant A245S show type-II binding. Mutant A245T shows type-I binding
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.326
dehydroepiandrostenedione
wild-type, pH 7.5, 37°C, S50 value, Hill coefficient 1.55
0.278
testosterone
wild-type, pH 7.5, 37°C, S50 value, Hill coefficient 1.64
0.0115
(9R)-9-deoxo-9-hydroxy-6-deoxyerythronolide B
-
pH 7.3, 35°C
0.0103
9-aminophenanthrene
wild-type, pH 7.5, 37°C, S50 value, Hill coefficient 1.9
0.0312
9-aminophenanthrene
mutant A245T, pH 7.5, 37°C, S50 value, Hill coefficient 1.7
0.261
androstenedione
wild-type, pH 7.5, 37°C, S50 value, Hill coefficient 1.2
0.277
androstenedione
mutant A245T, pH 7.5, 37°C, S50 value, Hill coefficient 1.09
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the Er gene cluster from Actinopolyspora erythraea strain YIM90600 shares high identity and similarity with the one of Saccharopolyspora erythraea strain NRRL2338, except for two absent genes, eryBI and eryG, correlation of genotype and chemotype
metabolism
the enzyme is involved in the biosynthetic pathway of the final erythronolide product, erythronolid A, pathway overview
physiological function
the enzyme is involved in the biosynthesis of the antibiotic erythromycin
physiological function
-
targeted gene diruption leads to production of 6-deoxyerythromycin A
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
molecular dynamics and hybrid quantum mechanics/molecular mechanics analysis. Two water networks exist around the active site, the one found in the crystal structure involving E360 and an alternative one involving E244. The first proton transfer that converts the peroxo to the hydroperoxo intermediate proceeds via the E244 water network with direct involvement of the 5-OH group of the substrate. For the second proton transfer, the computed barriers for the rate-limiting homolytic O-O cleavage are similar for the E360 and E244 pathways, and hence both glutamate residues may serve as proton source in this step
NMR studies on lgad binding. Binding of 9-aminophenanthrene and testosterone occurs with apparent negative homotropic cooperativity for testosterone and positive homotropic cooperativity for 9-aminophenanthrene with Hill-equation-derived dissociation constants of 4 and 200 microM, respectively. Binding occurs on intermediate and fast chemical exhange time scales, respectively. The 15N-Phe NMR resonances most affected are the same in each titration, suggesting that the two ligands contact the same phenylalanines within the active site of P450eryF
sitting drop vapor diffusion crystallization, crystal structures of the ferrous dioxygen complex of wild-type enzyme and its mutants, A245S and A245T
to 2.2 A resolution. The substrate is positioned with the macrolide ring perpendicular to the heme plane and contacts seven hydrophobic residues and three solvent molecules. The substrate participates in a network of hydrogen bonds that may provide a proton shuttle pathway in the oxygen cleavage reaction
modeling of the substrate-binding pocket with ketoconazole bound shos that the secondary nitrogen of the azole ring is coordinated to the heme iron, and nearby regions are positioned in the active site similarly to 6-deoxyerythronolide B, the remainder of the molecule extends into the active site pocket, which is occupied by water in the 6-deoxyerythronolide B complex. The large water-binding pocket in the P450eryF active site appears to provide flexibility in substrate binding and allows for molecules that are larger than 6-deoxyerythronolide B to be accommodated in the active site
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A245S
A245T
A245S
-
about 10fold decrease in affinity for 6-deoxyerythronolide B, and 6fold decrease in specific affinity
A245T
-
about 10fold decrease in affinity for 6-deoxyerythronolide B, and 1000fold decrease in specific affinity
additional information
A245S
activity is decreased by 84%, the active site structure including water is essentially unchanged with the exception that the OH group of Ser245 points toward the I-helix cleft to make new H-bonds with water 63 and the carbonyl group of the Ala241
A245S
significantly increased activity with substrates testosterone and 7-benzyloxyquinoline. Contrary to wild-type, binding to inhibitor ketoconazole follows type II
A245T
increased activity with substrate 7-benzyloxyquinoline. Like wild-type, type-II binding to inhibitor ketoconazole
additional information
construction of an erythronolide H-producing Saccharopolyspora erythraea mutant via gene complementation is not successful. Construction of en eryF deletion mutant strainEX105 from strain ZL2001 and complementation by Actinopolyspora erythraea eryF expression
additional information
-
construction of an erythronolide H-producing Saccharopolyspora erythraea mutant via gene complementation is not successful. Construction of en eryF deletion mutant strainEX105 from strain ZL2001 and complementation by Actinopolyspora erythraea eryF expression
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
isolation of two forms, P-4501 and P-45011, by hydroxylapatite chromatography, having a P-450 content of 17.5 and 15.2 nmol/mg of protein, respectively
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene eryF, genetic structure, sequence comparison, recombinant expression of His6-tagged enzyme in Saccharopolyspora erythraea strain ZL2001
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nagano, S.; Cupp-Vickery, J.R.; Poulos, T.L.
Crystal structures of the ferrous dioxygen complex of wild-type cytochrome P450eryF and its mutants, A245S and A245T: investigation of the proton transfer system in P450eryF
J. Biol. Chem.
280
22102-22107
2005
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea NRRL 2338 (Q00441)
Shafiee, A.; Hutchinson, C.R.
Macrolide antibiotic biosynthesis: isolation and properties of two forms of 6-deoxyerythronolide B hydroxylase from Saccharopolyspora erythraea (Streptomyces erythreus)
Biochemistry
26
6204-6210
1987
Saccharopolyspora erythraea
Andersen, J.F.; Tatsuta, K.; Gunji, H.; Ishiyama, T.; Hutchinson, C.R.
Substrate specificity of 6-deoxyerythronolide B hydroxylase, a bacterial cytochrome P450 of erythromycin A biosynthesis
Biochemistry
32
1905-1913
1993
Saccharopolyspora erythraea
Roberts, A.G.; Diaz, M.D.; Lampe, J.N.; Shireman, L.M.; Grinstead, J.S.; Dabrowski, M.J.; Pearson, J.T.; Bowman, M.K.; Atkins, W.M.; Campbell, A.P.
NMR studies of ligand binding to P450(eryF) provides insight into the mechanism of cooperativity
Biochemistry
45
1673-1684
2006
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea NRRL 2338 (Q00441)
Khan, K.K.; Halpert, J.R.
7-Benzyloxyquinoline oxidation by P450eryF A245T: finding of a new fluorescent substrate probe
Chem. Res. Toxicol.
15
806-814
2002
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea NRRL 2338 (Q00441)
Harris, D.L.
Oxidation and electronic state dependence of proton transfer in the enzymatic cycle of cytochrome P450eryF
J. Inorg. Biochem.
91
568-585
2002
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea NRRL 2338 (Q00441)
Sen, K.; Thiel, W.
Role of two alternate water networks in compound I formation in P450eryF
J. Phys. Chem. B
118
2810-2820
2014
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea, Saccharopolyspora erythraea NRRL 2338 (Q00441)
Cupp-Vickery, J.R.; Poulos, T.L.
Structure of cytochrome P450eryF involved in erythromycin biosynthesis
Nat. Struct. Biol.
2
144-153
1995
Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea NRRL 2338 (Q00441)
Weber, J.M.; Leung, J.O.; Swanson, S.J.; Idler, K.B.; McAlpine, J.B.
An erythromycin derivative produced by targeted gene disruption in Saccharopolyspora erythraea
Science
252
114-117
1991
Saccharopolyspora erythraea
Cupp-Vickery, J.R.; Poulos, T.L.
Structure of cytochrome P450eryF: substrate, inhibitors, and model compounds bound in the active site
Steroids
62
112-116
1997
Saccharopolyspora erythraea
Chen, D.; Feng, J.; Huang, L.; Zhang, Q.; Wu, J.; Zhu, X.; Duan, Y.; Xu, Z.
Identification and characterization of a new erythromycin biosynthetic gene cluster in Actinopolyspora erythraea YIM90600, a novel erythronolide-producing halophilic actinomycete isolated from salt field
PLoS ONE
9
e108129
2014
Actinopolyspora erythraea (A0A099D4T8), Actinopolyspora erythraea YIM90600 (A0A099D4T8), Saccharopolyspora erythraea (Q00441), Saccharopolyspora erythraea, Saccharopolyspora erythraea NRRL2338 (Q00441)
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