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Information on EC 1.13.11.50 - acetylacetone-cleaving enzyme and Organism(s) Acinetobacter johnsonii and UniProt Accession Q8GNT2
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1.13.11.50 acetylacetone-cleaving enzymeIUBMB Comments
An Fe(II)-dependent enzyme. Forms the first step in the acetylacetone degradation pathway of Acinetobacter johnsonii. While acetylacetone is by far the best substrate, heptane-3,5-dione, octane-2,4-dione, 2-acetylcyclohexanone and ethyl acetoacetate can also act as substrates.
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Word Map
- 1.13.11.50
-
facial
- acinetobacter
- johnsonii
-
nonheme
- methylglyoxal
-
five-coordinate
-
o2-dependent
-
fe2+-dependent
-
dioxygen-dependent
-
six-coordinate
-
bidentate
-
uv-vis
-
ferrous
-
non-native
-
r-groups
-
enzyme-bound
-
enol
-
metal-binding
-
2-his-1-carboxylate
-
ironii
-
high-spin
- environmental protection
The taxonomic range for the selected organisms is: Acinetobacter johnsonii
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
diketone cleaving enzyme, acetylacetone dioxygenase, acetylacetone-cleaving enzyme, diketone dioxygenase, diketone-cleaving dioxygenase, diketone cleaving dioxygenase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
acetylacetone dioxygenase
b-diketone dioxygenase
-
-
-
-
diketone cleaving dioxygenase
diketone cleaving enzyme
Dke1
oxygenase, b-diketone di-
-
-
-
-
acetylacetone dioxygenase
-
-
-
-
diketone cleaving dioxygenase
-
-
-
-
diketone cleaving enzyme
-
-
-
-
Dke1
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pentane-2,4-dione + O2 = acetate + 2-oxopropanal
reaction mechanism
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
reduction
-
-
-
-
oxidation
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
acetylacetone:oxygen oxidoreductase
An Fe(II)-dependent enzyme. Forms the first step in the acetylacetone degradation pathway of Acinetobacter johnsonii. While acetylacetone is by far the best substrate, heptane-3,5-dione, octane-2,4-dione, 2-acetylcyclohexanone and ethyl acetoacetate can also act as substrates.
CAS REGISTRY NUMBER
COMMENTARY
524047-53-8
-
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
pentane-2,4-dione + O2
acetate + 2-oxopropanal
-
-
-
-
?
pentane-2,4-dione + O2
acetate + 2-oxopropanal
-
i.e. acetylacetone
i.e. acetate and acetone
-
?
additional information
?
-
residues Arg80 and Tyr70 promote O2 reduction
-
-
?
additional information
?
-
-
no substrate: 4-hydroxy-4-methyl-2-pentanone, 3-oxobutanoate, quercetin, catechols, 2,4`-dihydroxyacetophenone, ascorbate
-
-
?
additional information
?
-
-
the catalytic reaction proceeds via one common rate-limiting step in the clevage of all substrates accepted by the enzyme
-
-
?
additional information
?
-
-
the enzyme is a mononuclear non-heme iron enzymes, Dke1 active site modelling, overview
-
-
?
additional information
?
-
-
acetylacetone dioxygenase catalyzes the dioxygen-dependent degradation of beta-dicarbonyl compounds
-
-
?
additional information
?
-
-
Dke1 also performs the atypical cleavage of the alpha-keto acid, 4-hydroxyphenylpyruvate, to form 4-hydroxybenzaldehyde as product instead of the homogentisate product found for 4-hydroxyphenylpyruvate with 4-hydroxyphenylpyruvate dioxygenase, EC 1.13.11.27, analysis of the bonding of the alpha-keto acid, 4-hydroxyphenylpyruvate, to ferrous Dke1 using anaerobic Dke1, added ferrous ammonium sulfate, and 4-hydroxyphenylpyruvate at pH 7.0, overview
-
-
?
additional information
?
-
-
Ni(II)-complex-adducts show regioselective oxidative cleavage of the aliphatic C-C bond using dioxygen via the substrate activation mechanism without changing the oxidation state of nickel(II) as similar to the wild type enzyme
-
-
-
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
pentane-2,4-dione + O2
acetate + 2-oxopropanal
-
-
-
-
?
additional information
?
-
-
acetylacetone dioxygenase catalyzes the dioxygen-dependent degradation of beta-dicarbonyl compounds
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron
an interplay of residues Glu98, His104, Glu11 (from the neighbor subunit), and Arg80 is the most important for the Fe2+ transport in and out of the protein. The Fe2+ ion when expelled from the binding site can be trapped at different locations within the enzyme. The neighborhood of residue Glu11 (form the neighbor subunit) is the second most favorable binding site for the Fe2+ ion after the active site
Fe2+
Iron
-
dependent on, metalloenzyme, 1 iron bound per subunit, required for positioning of the substrate and for rendering of the appropriate electronic environment
additional information
Fe2+
sulfate, necessary for enzyme activity. About 0.9 mol Fe2+/mol wild-type enzyme, less than 5% Fe2+ in mutants except 0.27 mol/mol H104E-enzyme and 0.45 mol/mol H104N-enzyme
Fe2+
Dke1 contains an atypical, three-histidine-ligated, mononuclear non-heme Fe2+ center, spectroscopic analysis, overview. Stabilizing effect of Glu98 on the 6C geometry of the metal center, priming it for substrate ligation. Also Thr107 stabilizes the Fe(II) cofactor
Fe2+
-
0.9-1.0 iron atoms per subunit, bound to active enzyme, essential for catalytic activity
Fe2+
-
the Fe(II) coordinating triad is composed of three His residues, geometric and electronic structure of the Fe(II) center, structure and function comparison with other dioxygenases containing a two histidines and a carboxylate coordinating the iron center in a facial triad, overview
Fe2+
-
active site nonheme monoiron(II) center, facially ligated by three histidine residues, overview. Spectral analysis of Dke1 FeII-alpha-keto acid complexes with 4-hydroxyphneylpyruvate, overview
Fe2+
-
nonheme Fe(II) cofactor, distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. In the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination
additional information
-
the enzyme is a mononuclear non-heme iron enzyme, overview
additional information
-
spectrophotometrical monitoring, Fe2+ and Fe3+ coordination, formation of iron(II) enzyme-substrate complexes, and detachment kinetics, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Cu2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
H2O2
1 M H2O2 causes complete loss of enzyme activity in less than 10 min, contains no Fe2+ (probably oxidized to Fe3+), partial reconstitution (40%) with 2 mM Fe2+, 20 mM Tris/HCl buffer, pH 7.5, 25°C
Mn2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
Ni2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
Zn2+
20 mM Tris/HCl buffer, pH 7.5, 25°C, 1.2fold molar excess, reversible inactivation of wild-type and mutant enzyme through competition with Fe2+, substrates 200 microM pentane-2,4-dione, 330 microM quercetin, 330 microM potassium oxalate, 330 microM 3,4-dihydroxyphenylacetate
hexacyanoferrate(III)
-
2.5 mM, 80% decrease in activity within 10 min
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.006
Pentane-2,4-dione
-
wild type enzyme, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
0.0065
Pentane-2,4-dione
-
mutant enzyme E69Q, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
additional information
additional information
kinetic first-order rate constants of substrate ligation and steady-state kinetic studies of wild-type and mutant enzymes, overview
-
additional information
additional information
-
steady-state and single-turnover kinetics of substrate binding and conversion in wild-type Dke1 and mutants, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0043
1,1,1-trifluoro-pentane-2,4-dione
-
native enzyme, using 0.09 mM 1,1,1-trifluoro-pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
0.00043
4,4-difluoro-1-phenyl-1,3-butanedione
-
apparent value at 25°C
0.007
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70A/R80A/E98A
0.033
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70F/R80A/E98A
0.05
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant E98Q
0.074
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant E98A
0.098
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant R80A/E98A
0.1
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant T107A
0.126
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant R80A
0.13
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70A
1.27
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant mutant Y70F
6.6
1,1,1-trifluoro-pentane-2,4-dione
pH 7.5, 25°C, recombinant wild-type enzyme
3.6
Pentane-2,4-dione
-
mutant enzyme E69Q, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
6.6
Pentane-2,4-dione
-
wild type enzyme, using 0.2 mM pentane-2,4-dione in 20 mM Tris/HCl buffer at pH 7.5 and 25°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
as sole carbon source
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
Dke1 also performs the atypical cleavage of the alpha-keto acid, 4-hydroxyphenylpyruvate, to form 4-hydroxybenzaldehyde as product instead of the homogentisate product found for 4-hydroxyphenylpyruvate with 4-hydroxyphenylpyruvate dioxygenase, EC 1.13.11.27, analysis of the bonding of the alpha-keto acid, 4-hydroxyphenylpyruvate, to ferrous Dke1 using anaerobic Dke1, added ferrous ammonium sulfate, and 4-hydroxyphenylpyruvate at pH 7.0, overview. active site was modeling, histidine residues are truncated to methyl imidazole for the model, and constraints imposed by the protein backbone are simulated by fixing the relative positions of the beta-carbons of the backbone. The coordination of the active site is completed with either alpha keto (monoanion) or enolate (dianion) bidentate coordinated 4-hydroxyphenylpyruvate ligand or a monoanionic acetylacetone ligand
additional information
-
Dke1 displays an atypical three-histidine metal binding site. Role of the protein structure in the catalysis of beta-diketone cleavage at the threehistidine metal center of diketone cleaving enzyme by computational methods in correlation with kinetic and mutational analyses. Molecular dynamics simulations, using quantum mechanically deduced parameters for the nonheme Fe(II) cofactor. Distinct organization of the hydrophilic triad in the free and substrate-ligated wild-type enzyme. In the free species, the Fe(II) center is coordinated to three histidines and one glutamate, whereas the substrate-ligated, catalytically competent enzyme-substrate complex has an Fe(II) center with three-histidine coordination, with a small fraction of three-histidine, one-glutamate coordination
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
16607
66430
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homotetramer
tetramer
homotetramer
-
each subunit is organized in a single-domain beta-barrel fold
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
molecular dynamic simulations with wild-type and mutants E88Q, R80A, Y70A of the Fe2+ free protein, of the enzyme with Fe2+ bound in the active site, without and with applying random force, and of the proteins with the metal ion located at the entrance of the water tunnel
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E98Q
H104E
no activity in initial rate assays with substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, small effect on other metal ions
H104N
approximately 1% of the specific activity of wild-type enzyme with substrate pentan-2,4-dione, retains binding affinity for Fe2+ at binding site I, binding seems to be tighter than in wild-type, small effect on other metal ions
H62E
no activity in initial rate assays with substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, small effect on other metal ions
H62N
no activity in initial rate assays with substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, binding disruption of Cu2+, Mn2+, and Ni2+ compared with wild-type
H64D
no activity in initial rate assays with substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, small effect on other metal ions
H64E
no activity in initial rate assays with substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, small effect on other metal ions
H64N
conversion of substrate in a strictly Fe2+-concentration dependent manner, substrate pentan-2,4-dione, no binding of Fe2+ at binding site I, small effect on other metal ions
R80A
Y70A
E69Q
-
lower thermal stability of beta-sheet secondary structure, half catalytic center activity and remarkably silent difference in apparent substrate binding compared to the wild type enzyme
F115A
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme
F119A
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme
F59A
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme
Y70F
-
site-directed mutagenesis, the mutant shows reduced turnover and altered iron binding compared to the wild-type enzyme
additional information
E98Q
an interplay of residues Glu98, His104, Glu11 (from the neighbor subunit), and Arg80 is the most important for the Fe2+ transport in and out of the protein
R80A
mutation causes relocation of Glu11 from neighbor subunit closer to His104, enabling formation of the Glu11(OE1/2)-His104(NE2H/CD2H) H-bond
Y70A
an interplay of residues Glu98, His104, Glu11 (from the neighbor subunit), and Arg80 is the most important for the Fe2+ transport in and out of the protein
additional information
the exchange of 3 histidines in the Fe2+-binding centre shows that these histidines are crucial for for binding Fe2+ and for Fe2+-dependent dioxygenase activity
additional information
-
the exchange of 3 histidines in the Fe2+-binding centre shows that these histidines are crucial for for binding Fe2+ and for Fe2+-dependent dioxygenase activity
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5
-
half-life 308 min in a membrane bioreactor, increase in stability from 5°C to 10°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified, concentrated enzyme is dialyzed twice against 2 mM EDTA in 20 mM Tris/HCl (pH 7.5) to strip off iron, incubation in 2 mM metal ion as sulfate salt plus ascorbate to prevent Fe2+ oxidation, unbound metal ions are removed by 3 cycles of gel filtration using nucleic acid purification column
recombinant Strep-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by affinity chromatography
-
Sepharose Q fast flow column chromatography Superdex 200 gel filtration, Resource Q column chromatography, Nap-5 column gel filtration, and Phenyl Sepharose HP chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of mutant gene vector in Escherichia coli BL21(DE3)
expression of Strep-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
environmental protection
-
biodegradation by the enzyme of the widely used industrial chemical acetylacetone, i.e. 2,4-pentanedione, which has toxic effects, in a membrane bioreactor, determination of operational stability of the enzyme in the reactor at different temperatures, simulations
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Straganz, G.D.; Glieder, A.; Brecker, L.; Ribbons, D.W.; Steiner, W.
Acetylacetone-cleaving enzyme Dke1: a novel C-C-bond-cleaving enzyme from Acinetobacter johnsonii
Biochem. J.
369
573-581
2003
Acinetobacter johnsonii
Straganz, G.; Brecker, L.; Weber, H.J.; Steiner, W.; Ribbons, D.W.
A novel beta-diketone-cleaving enzyme from Acinetobacter johnsonii: acetylacetone 2,3-oxygenase
Biochem. Biophys. Res. Commun.
297
232-236
2002
Acinetobacter johnsonii
Hofer, H.; Steiner, W.
Fast determination of operational stability of the soluble acetylacetone-cleaving enzyme Dke1 in an enzyme membrane reactor
Appl. Microbiol. Biotechnol.
1
1-12
2005
Acinetobacter johnsonii
Grogan, G.
Emergent mechanistic diversity of enzyme-catalysed beta-diketone cleavage
Biochem. J.
388
721-730
2005
Acinetobacter johnsonii
Straganz, G.; Slavica, A.; Hofer, H.; Mandl, U.; Steiner, W.; Nidetzky, B.
Integrated approach for production of recombinant acetylacetone dioxygenase from Acinetobacter johnsonii
Biocatal. Biotransform.
23
261-269
2005
Acinetobacter johnsonii
-
Straganz, G.D.; Nidetzky, B.
Reaction coordinate analysis for beta-diketone cleavage by the non-heme Fe2+-dependent dioxygenase Dke1
J. Am. Chem. Soc.
127
12306-12314
2005
Acinetobacter johnsonii
Straganz, G.D.; Egger, S.; Aquino, G.; DAuria, S.; Nidetzky, B.
Exploring the cupin-type metal-coordinating signature of acetylacetone dioxygenase Dke1 with site-directed mutagenesis: Catalytic reaction profile and Fe2+ binding stability of Glu-69->Gln mutant
J. Mol. Catal. B
39
171-178
2006
Acinetobacter johnsonii
-
Leitgeb, S.; Straganz, G.D.; Nidetzky, B.
Biochemical characterization and mutational analysis of the mononuclear non-haem Fe2+ site in Dke1, a cupin-type dioxygenase from Acinetobacter johnsonii
Biochem. J.
418
403-411
2009
Acinetobacter johnsonii (Q8GNT2), Acinetobacter johnsonii
Diebold, A.R.; Neidig, M.L.; Moran, G.R.; Straganz, G.D.; Solomon, E.I.
The three-his triad in Dke1: comparisons to the classical facial triad
Biochemistry
49
6945-6952
2010
Acinetobacter johnsonii
Straganz, G.D.; Diebold, A.R.; Egger, S.; Nidetzky, B.; Solomon, E.I.
Kinetic and CD/MCD spectroscopic studies of the atypical, three-His-ligated, non-heme Fe2+ center in diketone dioxygenase: the role of hydrophilic outer shell residues in catalysis
Biochemistry
49
996-1004
2010
Acinetobacter johnsonii (Q8GNT2)
Diebold, A.R.; Straganz, G.D.; Solomon, E.I.
Spectroscopic and computational studies of alpha-keto acid binding to Dke1: understanding the role of the facial triad and the reactivity of beta-diketones
J. Am. Chem. Soc.
133
15979-15991
2011
Acinetobacter johnsonii
Brkic, H.; Buongiorno, D.; Ramek, M.; Straganz, G.; Tomic, S.
Dke1--structure, dynamics, and function: a theoretical and experimental study elucidating the role of the binding site shape and the hydrogen-bonding network in catalysis
J. Biol. Inorg. Chem.
17
801-815
2012
Acinetobacter johnsonii
Brkic, H.
Insight of the iron binding and transport in Dke1 - A molecular dynamics study
Croat. Chem. Acta
88
297-306
2015
Acinetobacter johnsonii (Q8GNT2)
-
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