BRENDA - Enzyme Database show
show all sequences of 1.14.18.3

Effects of zinc on particulate methane monooxygenase activity and structure

Sirajuddin, S.; Barupala, D.; Helling, S.; Marcus, K.; Stemmler, T.L.; Rosenzweig, A.C.; J. Biol. Chem. 289, 21782-21794 (2014)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization
Organism
purified native enzyme, sitting drop vapour diffusion method, mixing of 0.0025 ml of 20 mg/ml pMMO protein, and 0.0005 ml of 85 mM n-octyl beta-D-thiomaltoside with 0.002 ml of 10% PEG 3000, 200 mM magnesium formate dihydrate, 100 mM sodium cacodylate trihydrate, pH 6.5, at room temperature, 1-4 weeks, for the complex structure, the crystals are soaked in Zn2+ solution, X-ray diffraction structure determination and analysis at 2.6 A resolution
Methylocystis sp.
Inhibitors
Inhibitors
Commentary
Organism
Structure
Zn2+
effects of zinc binding on pMMO in membrane extracts, binding efficiency varies under different consitions, multisite inhibition, detailed overview. Addition of copper to these zinc-loaded membranes results in loss of half the zinc ions
Methylococcus capsulatus
Zn2+
zinc inhibits enzyme pMMO at two sites that are distinct from the copper active site, zinc might inhibit proton transfer in pMMO. Locations for the two zinc inhibition sites: the first is the crystallographic zinc site in the pmoC subunit, a second zinc site is present on the cytoplasmic side of the pmoC subunit
Methylocystis sp.
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
membrane-bound
Methylocystis sp.
16020
-
membrane
membrane-bound
Methylococcus capsulatus
16020
-
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Cu2+
required, preferred metal ion
Methylococcus capsulatus
Cu2+
required
Methylocystis sp.
additional information
metal content of Methylococcus capsulatus (Bath) crude membranes before (as-isolated) and after (apo) cyanide treatment, and of apo-membranes after zinc and zinc/copper loading, overview. When zinc is loaded first, copper can replace one zinc site, which is likely the more accessible pmoC site. The activity of the zinc- and copper-loaded membrane-bound pMMO is 11-18% of the copper-reconstituted membrane-bound pMMO activity. This activity is lower than the 40-60% observed for copper- and zinc-loaded pMMO, even though the metal stoichiometries are similar, which is consistent with zinc occupying the active site when loaded first
Methylococcus capsulatus
additional information
the final model for the zinc-soaked structure included pmoB residues 29-418, pmoA residues 9-252, and pmoC residues 16-210 and 224-256, three polyalanine helices consisting of up to 25 residues, five zinc ions, three copper ions, and one cacodylate molecule
Methylocystis sp.
Zn2+
can replace Cu2+, enzyme-bound, structure analysis, overview. Zinc binding at the pmoC site in the zinc-soaked structure stabilizes pmoC residues 200-210
Methylococcus capsulatus
Zn2+
enzyme bound, structure analysis, overview
Methylocystis sp.
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
100000
-
about
Methylococcus capsulatus
450000
-
about, enzyme complex, native PAGE
Methylocystis sp.
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
methane + quinol + O2
Methylocystis sp.
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylococcus capsulatus
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylococcus capsulatus Bath
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylocystis sp. Rockwell
-
methanol + quinone + H2O
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Methylococcus capsulatus
G1UBD1 AND Q607G3
alpha- and beta-subunits
-
Methylococcus capsulatus Bath
G1UBD1 AND Q607G3
alpha- and beta-subunits
-
Methylocystis sp.
-
-
-
Methylocystis sp. Rockwell
-
-
-
Purification (Commentary)
Commentary
Organism
native enzyme from mebranes by solubilization with n-dodecyl beta-D-maltopyranoside, anion exchange chromatography, and ultrafiltration
Methylocystis sp.
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
methane + duroquinol + O2
-
745305
Methylocystis sp.
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylococcus capsulatus
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylococcus capsulatus Bath
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylocystis sp. Rockwell
methanol + duroquinone + H2O
-
-
-
?
methane + NADH + O2
-
745305
Methylococcus capsulatus
methanol + NAD+ + H2O
-
-
-
?
methane + NADH + O2
-
745305
Methylococcus capsulatus Bath
methanol + NAD+ + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylocystis sp.
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylococcus capsulatus
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylococcus capsulatus Bath
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylocystis sp. Rockwell
methanol + quinone + H2O
-
-
-
?
additional information
methane oxidation activity of apo membrane-bound Methylococcus capsulatus (Bath) pMMO after metal loading using two copper reconstitution methods, overview
745305
Methylococcus capsulatus
?
-
-
-
-
additional information
methane oxidation activity of apo membrane-bound Methylococcus capsulatus (Bath) pMMO after metal loading using two copper reconstitution methods, overview
745305
Methylococcus capsulatus Bath
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
heterotrimer
three pMMO subunits confirmed by mass spectrometry
Methylococcus capsulatus
heterotrimer
three pMMO subunits confirmed by mass spectrometry
Methylocystis sp.
More
three-dimensional structure determination and analysis
Methylocystis sp.
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Methylococcus capsulatus
22
-
assay at room temperature
Methylocystis sp.
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
7.2
assay at
Methylococcus capsulatus
7
7.2
assay at
Methylocystis sp.
Cofactor
Cofactor
Commentary
Organism
Structure
duroquinol
NADH passes electron to duroquinol
Methylococcus capsulatus
duroquinol
-
Methylocystis sp.
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
duroquinol
NADH passes electron to duroquinol
Methylococcus capsulatus
duroquinol
-
Methylocystis sp.
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified native enzyme, sitting drop vapour diffusion method, mixing of 0.0025 ml of 20 mg/ml pMMO protein, and 0.0005 ml of 85 mM n-octyl beta-D-thiomaltoside with 0.002 ml of 10% PEG 3000, 200 mM magnesium formate dihydrate, 100 mM sodium cacodylate trihydrate, pH 6.5, at room temperature, 1-4 weeks, for the complex structure, the crystals are soaked in Zn2+ solution, X-ray diffraction structure determination and analysis at 2.6 A resolution
Methylocystis sp.
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
Zn2+
effects of zinc binding on pMMO in membrane extracts, binding efficiency varies under different consitions, multisite inhibition, detailed overview. Addition of copper to these zinc-loaded membranes results in loss of half the zinc ions
Methylococcus capsulatus
Zn2+
zinc inhibits enzyme pMMO at two sites that are distinct from the copper active site, zinc might inhibit proton transfer in pMMO. Locations for the two zinc inhibition sites: the first is the crystallographic zinc site in the pmoC subunit, a second zinc site is present on the cytoplasmic side of the pmoC subunit
Methylocystis sp.
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
membrane-bound
Methylocystis sp.
16020
-
membrane
membrane-bound
Methylococcus capsulatus
16020
-
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Cu2+
required, preferred metal ion
Methylococcus capsulatus
Cu2+
required
Methylocystis sp.
additional information
metal content of Methylococcus capsulatus (Bath) crude membranes before (as-isolated) and after (apo) cyanide treatment, and of apo-membranes after zinc and zinc/copper loading, overview. When zinc is loaded first, copper can replace one zinc site, which is likely the more accessible pmoC site. The activity of the zinc- and copper-loaded membrane-bound pMMO is 11-18% of the copper-reconstituted membrane-bound pMMO activity. This activity is lower than the 40-60% observed for copper- and zinc-loaded pMMO, even though the metal stoichiometries are similar, which is consistent with zinc occupying the active site when loaded first
Methylococcus capsulatus
additional information
the final model for the zinc-soaked structure included pmoB residues 29-418, pmoA residues 9-252, and pmoC residues 16-210 and 224-256, three polyalanine helices consisting of up to 25 residues, five zinc ions, three copper ions, and one cacodylate molecule
Methylocystis sp.
Zn2+
can replace Cu2+, enzyme-bound, structure analysis, overview. Zinc binding at the pmoC site in the zinc-soaked structure stabilizes pmoC residues 200-210
Methylococcus capsulatus
Zn2+
enzyme bound, structure analysis, overview
Methylocystis sp.
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
100000
-
about
Methylococcus capsulatus
450000
-
about, enzyme complex, native PAGE
Methylocystis sp.
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
methane + quinol + O2
Methylocystis sp.
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylococcus capsulatus
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylococcus capsulatus Bath
-
methanol + quinone + H2O
-
-
?
methane + quinol + O2
Methylocystis sp. Rockwell
-
methanol + quinone + H2O
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
native enzyme from mebranes by solubilization with n-dodecyl beta-D-maltopyranoside, anion exchange chromatography, and ultrafiltration
Methylocystis sp.
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
methane + duroquinol + O2
-
745305
Methylocystis sp.
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylococcus capsulatus
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylococcus capsulatus Bath
methanol + duroquinone + H2O
-
-
-
?
methane + duroquinol + O2
-
745305
Methylocystis sp. Rockwell
methanol + duroquinone + H2O
-
-
-
?
methane + NADH + O2
-
745305
Methylococcus capsulatus
methanol + NAD+ + H2O
-
-
-
?
methane + NADH + O2
-
745305
Methylococcus capsulatus Bath
methanol + NAD+ + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylocystis sp.
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylococcus capsulatus
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylococcus capsulatus Bath
methanol + quinone + H2O
-
-
-
?
methane + quinol + O2
-
745305
Methylocystis sp. Rockwell
methanol + quinone + H2O
-
-
-
?
additional information
methane oxidation activity of apo membrane-bound Methylococcus capsulatus (Bath) pMMO after metal loading using two copper reconstitution methods, overview
745305
Methylococcus capsulatus
?
-
-
-
-
additional information
methane oxidation activity of apo membrane-bound Methylococcus capsulatus (Bath) pMMO after metal loading using two copper reconstitution methods, overview
745305
Methylococcus capsulatus Bath
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
heterotrimer
three pMMO subunits confirmed by mass spectrometry
Methylococcus capsulatus
heterotrimer
three pMMO subunits confirmed by mass spectrometry
Methylocystis sp.
More
three-dimensional structure determination and analysis
Methylocystis sp.
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
22
-
assay at room temperature
Methylococcus capsulatus
22
-
assay at room temperature
Methylocystis sp.
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
7.2
assay at
Methylococcus capsulatus
7
7.2
assay at
Methylocystis sp.
General Information
General Information
Commentary
Organism
additional information
nano-LC-ESI-MS/MS analysis for protein identification of purified Methylocystis sp. str. Rockwell pMMO. The final model for the zinc-soaked structure included pmoB residues 29-418, pmoA residues 9-252, and pmoC residues 16-210 and 224-256, three polyalanine helices consisting of up to 25 residues, five zinc ions, three copper ions, and one cacodylate molecule
Methylocystis sp.
General Information (protein specific)
General Information
Commentary
Organism
additional information
nano-LC-ESI-MS/MS analysis for protein identification of purified Methylocystis sp. str. Rockwell pMMO. The final model for the zinc-soaked structure included pmoB residues 29-418, pmoA residues 9-252, and pmoC residues 16-210 and 224-256, three polyalanine helices consisting of up to 25 residues, five zinc ions, three copper ions, and one cacodylate molecule
Methylocystis sp.
Other publictions for EC 1.14.18.3
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)
744037
Cao
Quantum refinement does not s ...
Methylococcus capsulatus, Methylococcus capsulatus Bath
Angew. Chem. Int. Ed. Engl.
57
162 -166
2018
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2
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13
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1
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1
1
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744688
Wang
Alkane oxidation methane mono ...
Methylococcus capsulatus, Methylococcus capsulatus Bath
Chem. Rev.
117
8574-8621
2017
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13
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744923
Wang
An improved protocol with a h ...
uncultured Alphaproteobacteria bacterium, uncultured gamma proteobacterium
FEMS Microbiol. Ecol.
93
fiw244
2017
-
4
2
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2
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2
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745389
Ross
A tale of two methane monooxy ...
Methylococcus capsulatus, Methylococcus capsulatus Bath., Methylococcus capsulatus Bath, Methylocystis sp., Methylocystis sp. M, Methylocystis sp. Rockwell, Methylosinus trichosporium
J. Biol. Inorg. Chem.
22
307-319
2017
1
-
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1
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2
6
-
3
-
22
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2
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9
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2
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1
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2
1
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2
6
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3
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9
-
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6
6
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745453
Zhang
Coupled effects of methane mo ...
Methylosinus trichosporium
J. Environ. Sci.
52
49-57
2017
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1
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1
1
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745536
Nguyen
A novel methanotroph in the g ...
Methylomonas sp., Methylomonas sp. EMGL16-1
J. Microbiol.
55
775-782
2017
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2
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746420
Zhang
-
Low-temperature biological ac ...
Methylococcus capsulatus, Methylococcus capsulatus Bath, Methylocystis sp., Methylocystis sp. Rockwell, Methylosinus trichosporium
Rev. Environ. Sci. Biotechnol.
16
611-623
2017
-
1
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3
5
-
2
-
18
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5
1
3
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2
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3
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1
-
3
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3
5
-
2
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5
1
3
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2
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2
2
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745067
Itoyama
Possible peroxo state of the ...
Methylococcus capsulatus, Methylococcus capsulatus Bath
Inorg. Chem.
55
2771-2775
2016
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1
1
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13
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1
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1
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1
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1
1
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745730
Larsen
Transcriptomic profiling of M ...
Methylococcus capsulatus, Methylococcus capsulatus Bath., Methylococcus capsulatus Bath
MicrobiologyOpen
5
254-267
2016
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1
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5
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16
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1
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5
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1
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1
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5
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1
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5
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1
2
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745857
Blanchette
Printable enzyme-embedded mat ...
Methylococcus capsulatus, Methylococcus capsulatus Bath
Nat. Commun.
7
11900
2016
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1
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1
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13
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4
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1
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744405
Pham
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744325
Culpepper
Structure and protein-protein ...
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Biochemistry
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2014
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Identification of the valence ...
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2014
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1
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745305
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Effects of zinc on particulat ...
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2014
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745721
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Mutagenesis of the hydrocarbo ...
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Microbiology
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2014
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Culpepper
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Extremophiles
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2012
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Co-localization of particulate ...
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Culpepper
Evidence for oxygen binding at ...
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728079
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Bacteriohemerythrin bolsters t ...
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716108
Chan
Overexpression and purificatio ...
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Methods Enzymol.
495
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716109
Smith
Metal reconstitution of partic ...
Methylococcus capsulatus, Methylococcus capsulatus Bath
Methods Enzymol.
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2011
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716110
Miyaji
Particulate methane monooxygen ...
Methylosinus trichosporium
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2011
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726954
Smith
Crystal structure and characte ...
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Biochemistry
50
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2011
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712040
Iguchi
Soluble and particulate methan ...
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2010
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Dunfield
Methylocapsa aurea sp. nov., a ...
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701759
Zhang
The methane monooxygenase intr ...
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3
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703343
Himes
Copper-dioxygen complex mediat ...
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Angel
In situ measurement of methane ...
Soil bacterium
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2009
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Miyaji
-
Hydrogen peroxide as an effect ...
Methylosinus trichosporium OB3b
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2009
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705544
Rastogi
Novel methanotroph diversity e ...
uncultured bacterium
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Chan
Controlled oxidation of hydroc ...
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686085
Ng
Probing the hydrophobic pocket ...
Methylococcus capsulatus
ChemBioChem
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2008
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Baani
Two isozymes of particulate me ...
Methylocystis sp., Methylocystis sp. Sc2
Proc. Natl. Acad. Sci. USA
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2008
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Tumanova
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The binuclear iron site of mem ...
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1
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702170
Rosenzweig
The metal centres of particula ...
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Biochem. Soc. Trans.
36
1134-1137
2008
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702501
Gvozdev
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Purification and properties of ...
Methylococcus capsulatus, Methylococcus capsulatus M
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35
161-169
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706752
Anthony
A tribute to Howard Dalton and ...
Methylococcus capsulatus
Sci. Prog.
91
401-415
2008
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1
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1
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-
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Balasubramanian
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