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Information on EC 3.1.4.4 - phospholipase D and Organism(s) Streptomyces antibioticus and UniProt Accession Q53728
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3.1.4.4 phospholipase DIUBMB Comments
Also acts on other phosphatidyl esters.
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Word Map
- 3.1.4.4
-
phosphatidic
- diacylglycerol
- pkc
-
liposomal
- doxorubicin
- agonist
-
pegylated
-
phorbol
- phospholipases
-
transphosphatidylation
- 12-myristate
-
adp-ribosylation
- 13-acetate
- pertussis
-
phosphohydrolase
-
arachidonic
- propranolol
- phosphoinositide
-
gtp-binding
- fmlp
-
prelabeled
- anandamide
- rhoa
- 1-butanol
-
endocannabinoids
- staurosporine
-
lysophosphatidic
- pc-plc
-
phosphatidylcholine-specific
-
latissimus
- diglyceride
- pkcalpha
-
phosphatidylinositol-specific
- pseudotuberculosis
- 1,2-diacylglycerol
- arf6
- cannabinoids
-
fmet-leu-phe
-
listening
-
fmlp-stimulated
-
platinum-resistant
- analysis
-
phosphoinositide-specific
- gtpgammas
- synthesis
-
3hcholine
-
hand-foot
-
platinum-sensitive
-
fmlp-induced
- lymphadenitis
- medicine
-
ptdins4,5p2
- molecular biology
- 5-kinase
- agriculture
- biotechnology
The taxonomic range for the selected organisms is: Streptomyces antibioticus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
pld, phospholipase d, nape-pld, phospholipase d1, dermonecrotic toxin, phospholipase d2, pc-pld, pldalpha, rpld1, spo14, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AtPLDalpha1
-
-
-
-
AtPLDalpha2
-
-
-
-
AtPLDbeta1
-
-
-
-
AtPLDbeta2
-
-
-
-
AtPLDdelta
-
-
-
-
AtPLDepsilon
-
-
-
-
AtPLDgamma1
-
-
-
-
AtPLDgamma2
-
-
-
-
AtPLDgamma3
-
-
-
-
AtPLDp1
-
-
-
-
AtPLDp2
-
-
-
-
AtPLDzeta
-
-
-
-
choline phosphatase
-
-
-
-
hPLD1
-
-
-
-
hPLD2
-
-
-
-
lecithinase D
-
-
-
-
lipophosphodiesterase II
-
-
-
-
Meiosis-specific sporulation protein SPO14
-
-
-
-
mPLD1
-
-
-
-
mPLD2
-
-
-
-
Phosphatidylcholine-hydrolyzing phospholipase D1
-
-
-
-
Phosphatidylcholine-hydrolyzing phospholipase D2
-
-
-
-
Phospholipase D1 PHOX and PX containing domain
-
-
-
-
Phospholipase D2 PHOX and PX containing domain
-
-
-
-
PLD
PLD delta
-
-
-
-
PLD epsilon
-
-
-
-
PLD zeta
-
-
-
-
PLD1C
-
-
-
-
PLDalpha
-
-
-
-
PLDalpha3
-
-
-
-
PLDbeta
-
-
-
-
PLDdelta1
-
-
-
-
PLDzeta1
-
-
-
-
PLDzeta2
-
-
-
-
rPLD1
-
-
-
-
rPLD2
-
-
-
-
additional information
-
the enzyme belongs to the PLD superfamily containing two HKD motifs
PLD
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
a phosphatidylcholine + H2O = choline + a phosphatidate
mode of substrate binding, the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview
a phosphatidylcholine + H2O = choline + a phosphatidate
catalytic mechanism, PLD uses a ping-pong type of reaction through the formation of a covalent phosphatidyl-enzyme intermediate, structure-function relationship, and substrate recognition and specificity, overview
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
phosphatidylcholine phosphatidohydrolase
Also acts on other phosphatidyl esters.
CAS REGISTRY NUMBER
COMMENTARY
9001-87-0
-
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
1,2-dioleoylphosphatidylcholine + inositol
1,2-dioleoylphosphatidylinositol + choline
-
-
-
?
dioleoyl-phosphatidylcholine + cyclohexane-1,2,3-triol
choline + dioleoyl-phosphatidylcyclohexane-2,3-diol
in the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type
-
-
?
dioleoyl-phosphatidylcholine + cyclohexane-1,2,5-triol
choline + dioleoyl-phosphatidylcyclohexane-2,5-diol
in the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type
-
-
?
dioleoyl-phosphatidylcholine + cyclohexane-1,2-diol
choline + dioleoyl-phosphatidylcyclohexane-2-ol
in the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type
-
-
?
dioleoyl-phosphatidylcholine + cyclohexane-1,3-diol
choline + dioleoyl-phosphatidylcyclohexane-3-ol
in the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type
-
-
?
dioleoyl-phosphatidylcholine + cyclohexane-1,4-diol
choline + dioleoyl-phosphatidylcyclohexane-4-ol
-
-
-
?
dioleoyl-phosphatidylcholine + cyclohexanol
choline + dioleoyl-phosphatidylcyclohexane
in the cases of cyclohexanol and of cyclohexane-1,4-diol, the wild-type enzyme generates the corresponding transphosphatidylated products more efficiently than the mutant W187F/Y191R
-
-
?
dioleoyl-phosphatidylcholine + H2O
choline + dioleoyl-phosphatidate
-
-
-
?
dioleoyl-phosphatidylcholine + myo-inositol
?
in the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type
-
-
?
dioleoylphosphatidylcholine + myo-inositol
choline + dioleoylphosphatidylinositol
transphosphatidylation activity of mutant W187D/Y191Y/Y385R enzyme
-
-
?
phosphatidylcholine + myo-inositol
phosphatidylinositol + choline
the wild-type enzyme is capable of synthesizing phosphatidylinositol by transphosphatidylation. Increase in phosphatidylinositol yield is possible by providing excess of solvated myo-inositol, which is achievable at high temperatures due to its highly temperature-dependent solubility, especially by enzyme variants with increased thermostability, e.g. mutant W187D/Y191Y/Y385R
-
-
?
lysophosphatidylcholine + H2O
monoacylglycerophosphate + choline
-
-
-
-
?
phosphatidylcholine + D-arabinose
phosphatidylarabinose + choline
-
-
-
-
?
phosphatidylcholine + D-fructose
phosphatidylfructose + choline
-
-
-
-
?
phosphatidylcholine + D-galactose
phosphatidylgalactose + choline
-
-
-
-
?
phosphatidylcholine + D-glucose
phosphatidylglucose + choline
-
-
-
-
?
phosphatidylcholine + D-mannose
phosphatidylmannose + choline
-
-
-
-
?
phosphatidylcholine + D-xylose
phosphatidylxylose + choline
-
-
-
-
?
phosphatidylcholine + diethyleneglycol
phosphatidyldiethyleneglycol + choline
-
-
-
-
?
phosphatidylcholine + diethyleneglycol monomethyl ester
diethyleneglycol dimethyl phosphatidic acid + choline
-
-
-
-
?
phosphatidylcholine + ethyleneglycol
phosphatidylethyleneglycol + choline
-
-
-
-
?
phosphatidylcholine + ethyleneglycol monomethyl ester
ethyleneglycol monomethyl phosphatidic acid + choline
-
-
-
-
?
phosphatidylcholine + H2O
1,2-diacylglycerophosphate + choline
-
-
-
-
?
phosphatidylcholine + L-sorbose
phosphatidylsorbose + choline
-
-
-
-
?
phosphatidylcholine + triethyleneglycol
phosphatidyltriethyleneglycol + choline
-
-
-
-
?
phosphatidylcholine + triethyleneglycol monomethyl ester
triethyleneglycol trimethyl phosphatidic acid + choline
-
-
-
-
?
phosphatidylethanolamine + H2O
1,2-diacylglycerophosphate + ethanolamine
-
-
-
-
r
phospholipid + alcohol
phospholipid + alcohol
-
transphosphaditylation
-
-
?
dioleoyl-phosphatidylcholine + myo-inositol
phosphatidylinositol + choline
-
-
the 187H/191Y/385R mutant generates 1-phosphatidylinositol more than 3-phosphatidylinositol, whereas 187T/191Y/385R generates 1-phosphatidylinositol less than 3-phosphatidylinositol
-
?
dioleoyl-phosphatidylcholine + myo-inositol
phosphatidylinositol + choline
-
the FRY mutant generates 1(3)-phosphatidylinositol and 4(6)-phosphatidylinositol, but not 2-phosphatidylinositol and 5-phosphatidylinositol
-
?
phospholipid + H2O
phosphatidic acid + alcohol
-
phosphoric ester hydrolysis
-
-
?
additional information
?
-
transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine). Transphosphatidylation with L- and D-serine gives phosphatidyl-L- and D-serine, respectively. Synthesis of phosphatidylinositol by bacterial enzyme is unsuccessful is likely the low affinity of the enzyme toward myo-inositol, a bulky molecule causing steric hindrances in the active site
-
-
?
additional information
?
-
-
PLD performs two different reactions: a hydrolytic reaction and a transphosphatidylation reaction, the latter with a primary alcohol, both pathway share a common intermediate, mechanism, overview
-
-
?
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
phospholipid + alcohol
phospholipid + alcohol
-
transphosphaditylation
-
-
?
phospholipid + H2O
phosphatidic acid + alcohol
-
phosphoric ester hydrolysis
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.5
dioleoyl-phosphatidylcholine
wild-type, Vmax: 4700 micromol/min/mg
3
dioleoyl-phosphatidylcholine
mutant W187F/Y191R, Vmax: 1.8 micromol/min/mg
0.0015
dioleoyl-phosphatidylcholine
wild type enzyme, in sodium acetate buffer (50 mM, pH 5.6), at 37°C
0.003
dioleoyl-phosphatidylcholine
mutant enzyme 187F/191R/385Y, in sodium acetate buffer (50 mM, pH 5.6), at 37°C
0.0015
phosphatidylcholine
-
wild type enzyme, in sodium acetate buffer (50 mM, pH 5.6), at 37°C
0.0043
phosphatidylcholine
-
mutant enzyme 187H/191Y/385R, in sodium acetate buffer (50 mM, pH 5.6), at 37°C
0.0043
phosphatidylcholine
-
mutant enzyme 187T/191Y/385R, in sodium acetate buffer (50 mM, pH 5.6), at 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.0204 - 0.0233
transphosphatidylation activities of mutant enzmes, pH 5.6, 30°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and a common catalytic mechanism
additional information
change of the PLD structure upon phospholipid binding, conformational change of the gate-like structure formed by the two loops around Y126 and G381, residues, W187, Y191 and Y385 are responsible for head group specificity, structure overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D40H/T291Y
site-directed mutagenesis of residues D40 and T291 located within dynamic surface loops, the mutant is able to synthesize phosphatidylinositol by transphosphatidylation
D40H/W187D/Y191Y/R329G/Y385R
random mutagenesis of mutant W187D/Y191Y/Y385R, the resulting mutant shows increased thermostability compared to the wild-type enzyme and transphosphatidylation with myo-inositol and phosphocholine
D40H/W187D/Y191Y/T291Y/R329G/Y385R
random mutagenesis of mutant W187D/Y191Y/Y385R, the resulting mutant shows increased thermostability compared to the wild-type enzyme and transphosphatidylation with myo-inositol and phosphocholine
D40H/W187D/Y191Y/T291Y/Y385R
random mutagenesis of mutant W187D/Y191Y/Y385R, the resulting mutant shows increased thermostability compared to the wild-type enzyme and transphosphatidylation with myo-inositol and phosphocholine
W187D/Y191Y/T291Y/R329G/Y385R
random mutagenesis of mutant W187D/Y191Y/Y385R, the resulting mutant shows increased thermostability compared to the wild-type enzyme and transphosphatidylation with myo-inositol and phosphocholine
W187D/Y191Y/Y385R
W187F/Y191R
mutant enzyme is able to synthesize phosphatidylinositol using dioleoyl-phosphatidylcholine and myo-inositol as a substrate, the mutant enzyme generates a mixture of structural isomers of phosphatidylinositol with the phosphatidyl groups connected at different positions of the inositol ring. In the cases of 1,2-diols, triols, and myo-inositol mutant W187F/Y191R generates the corresponding transphosphatidylated products more efficiently than wild-type. The phosphatidylcholine-hydrolyzing activity of the mutant PLD is much lower than that of the wild-type enzyme (Km higher, Vmax much lower than wild-type). Mutant enzyme is able to transphosphatidylate various cyclohexanols with a preference for bulkier compounds
W187N/Y191Y/Y385R
mutant generates phosphatidylinositol as a mixture of 1-phosphatidylinositol and 3-phosphatidylinositol in the ratio of 76/24
W187N/Y191Y/Y385R/G186T
W187X/Y191X/Y385X
mutations are introduced in the pld gene at the positions corresponding to three amino acid residues that might be involved in substrate recognition, and the mutated genes are expressed in Escherichia coli. High-throughput screening of approximately 10000 colonies for phosphatidylinositol-synthesizing activity identifies 25 phosphatidylinositol-synthesizing mutant PLDs
Y385R
-
the mutation contributes to the selectivity for the 1(3)-PI synthesis
additional information
W187D/Y191Y/Y385R
site-directed mutagenesis, the mutant is able to synthesize phosphatidylinositol by transphosphatidylation, thermostabilization of enzyme mutant W187D/Y191Y/Y385R, termed DYR, is attempted by rational design based on deletion of the D40 loop, generating two variants, DELTA37-45 DYR and DELTA38-46 DYR PLD. DELTA38-46 DYR shows highest thermostability as its activity half-life at 70°C proves 11.7 and 8.0 times longer than that of the DYR mutant and mutant DELTA37-45 DYR, respectively, molecular dynamics, overview
W187D/Y191Y/Y385R
site-directed mutagenesis, the mutant synthesizes phosphatidylinositol from myo-inositol and phosphocholine by transphosphatidylation
W187N/Y191Y/Y385R/G186T
mutant generates phosphatidylinositol as a mixture of 1-phosphatidylinositol and 3-phosphatidylinositol in the ratio of 87/13 and of 97/3 at 20°C, respectively
W187N/Y191Y/Y385R/G186T
mutant generates phosphatidylinositol as a mixture of 1-phosphatidylinositol and 3-phosphatidylinositol in the ratio of 93/7 at 37°C and of 97/3 at 20°C, respectively
additional information
increased thermostability of mutant enzymes, especially those with D40H/T291Y mutation, compared to the wild-type enzyme, molecular dynamics analysis and molecular dynamics simulation, overview
additional information
protein engineering to create enzyme variants that can synthesize phosphatidylinositol from phosphatidylcholine and myo-inositol by transphosphatidylation by site-directed saturation mutagenesis at positions suspected to be involved in substrate recognition, namely Trp187, Tyr191 and Tyr385, high-throughput screening. Three variants (187D/191Y/385R, 187A/191Y/385R and 187M/191Y/385R) selectively produced 1(3)-phosphatidylinositol over the other phosphatidylinositol isomers
additional information
-
the 187H/191Y/385R mutant generates 1-phosphatidylinositol more than 3-phosphatidylinositol, whereas 187T/191Y/385R generates 1-phosphatidylinositol less than 3-phosphatidylinositol
additional information
-
the phosphatidylcholine-hydrolyzing activity of the mutant PLD 187F/191R/385Y is much lower than that of the wild-type enzyme, the mutant enzyme is able to transphosphatidylate various cyclohexanols with a preference for bulkier compounds
additional information
the phosphatidylcholine-hydrolyzing activity of the mutant PLD 187F/191R/385Y is much lower than that of the wild-type enzyme, the mutant enzyme is able to transphosphatidylate various cyclohexanols with a preference for bulkier compounds
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
65
increased thermostability of mutant enzymes, especially those with D40H/T291Y mutation, compared to the wild-type enzyme, half-lives lie between 20 and 40 min, molecular dynamics analysis and molecular dynamics simulation, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3), subcloning in Escherichia coli strain DH5alpha-FT
gene pld, expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
mutants are expressed in Escherichia coli
PLD DNA and amino acid sequence determination, comparison, and analysis
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview
synthesis
-
creation of a high performance PLD with superior transphosphatidylation activity and low hydrolysis activity can be very useful for the synthesis of phospholipids used in pharmaceuticals, foods, cosmetics, and other industries
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Suzuki, A.; Kakuno, K.; Iwasaki, Y.; Yamane, T.
Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus
Acta Crystallogr. Sect. D
55
317-319
1999
Streptomyces antibioticus
Shimbo, K.; Iwasaki,Y.; Yamane, T.; Ina,K.
Purification and properties of phospholipase D from Streptomyces antibioticus
Biosci. Biotechnol. Biochem.
57
1946-1948
1993
Streptomyces antibioticus
-
Masayama, A.; Takahashi, T.; Tsukada, K.; Nishikawa, S.; Takahashi, R.; Adachi, M.; Koga, K.; Suzuki, A.; Yamane, T.; Nakano, H.; Iwasaki, Y.
Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis
ChemBioChem
9
974-981
2008
Streptomyces antibioticus, Streptomyces antibioticus (Q53728)
Masayama, A.; Tsukada, K.; Ikeda, C.; Nakano, H.; Iwasaki, Y.
Isolation of phospholipase D mutants having phosphatidylinositol-synthesizing activity with positional specificity on myo-inositol
ChemBioChem
10
559-564
2009
Streptomyces antibioticus
Uesugi, Y.; Hatanaka, T.
Phospholipase D mechanism using Streptomyces PLD
Biochim. Biophys. Acta
1791
962-969
2009
Streptomyces antibioticus, Streptomyces cinnamoneus, Streptomyces halstedii, Streptomyces septatus, Streptomyces sp. (P84147)
Damnjanovic, J.; Nakano, H.; Iwasaki, Y.
Deletion of a dynamic surface loop improves stability and changes kinetic behavior of phosphatidylinositol-synthesizing Streptomyces phospholipase D
Biotechnol. Bioeng.
111
674-682
2014
Streptomyces antibioticus (Q53728), Streptomyces antibioticus
Damnjanovic, J.; Iwasaki, Y.
Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering
J. Biosci. Bioeng.
116
271-280
2013
Actinomadura sp., Streptomyces chromofuscus, Streptomyces cinnamoneus, Brassica oleracea (O82549), Saccharomyces cerevisiae (P36126), Homo sapiens (Q13393), Streptomyces antibioticus (Q53728), Saccharomyces cerevisiae ATCC 204508 (P36126), Actinomadura sp. 362
Damnjanovic, J.; Takahashi, R.; Suzuki, A.; Nakano, H.; Iwasaki, Y.
Improving thermostability of phosphatidylinositol-synthesizing Streptomyces phospholipase D
Protein Eng. Des. Sel.
25
415-424
2012
Streptomyces antibioticus (Q53728)
Damnjanovic, J.; Kuroiwa, C.; Tanaka, H.; Ishida, K.; Nakano, H.; Iwasaki, Y.
Directing positional specificity in enzymatic synthesis of bioactive 1-phosphatidylinositol by protein engineering of a phospholipase D
Biotechnol. Bioeng.
113
62-71
2016
Streptomyces antibioticus (Q53728), Streptomyces antibioticus
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