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Enzyme Nomenclature
Information on EC 1.13.11.49 - chlorite O2-lyase
Word Map on EC 1.13.11.49
- 1.13.11.49
- perchlorate
- chlorate
-
perchlorate-reducing
- dechloromonas
-
dismutases
- clo2
-
dismutation
-
high-spin
-
low-spin
-
dissimilatory
- defluvii
- nitrospira
-
chlorate-reducing
- dechloratans
-
candidatus
- ideonella
-
hypochlorite
- aromatica
- azospira
- environmental protection
- molecular biology
- biotechnology
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Specify your search results
The expected taxonomic range for this enzyme is: Bacteria, Archaea
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EC NUMBER 
COMMENTARY 
1.13.11.49
-
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RECOMMENDED NAME
GeneOntology No.
chlorite O2-lyase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
chloride + O2 = chlorite
reaction occurs in the reverse direction in chlorate- and perchlorate-reducing bacteria. There is no activity when chlorite is replaced by hydrogen peroxide, perchlorate, chlorate or nitrite. The term 'chlorite dismutase' is misleading as the reaction does not involve dismutation/disproportionation. Contains iron and protoheme IX
-
-
-
chloride + O2 = chlorite
reaction mechanism and active site structure, Arg173 plays a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction, overview
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
chloride:oxygen oxidoreductase
Reaction occurs in the reverse direction in chlorate- and perchlorate-reducing bacteria. There is no activity when chlorite is replaced by hydrogen peroxide, perchlorate, chlorate or nitrite. The term 'chlorite dismutase' is misleading as the reaction does not involve dismutation/disproportionation. Contains iron and protoheme IX.
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CAS REGISTRY NUMBER
COMMENTARY
190208-21-0
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Dechlorosoma sp.
strain KJ, strain JM, strain HZ, strain PDX. High activity in anaerobically grown bacteria, very low activity in aerobically grown bacteria
-
-
strain KJ, strain JM, strain HZ, strain PDX. High activity in anaerobically grown bacteria, very low activity in aerobically grown bacteria
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
-
the enzyme is the terminal enzyme involved in the perchlorate reduction pathway
physiological function
additional information
evolution
-
The chlorite dismutases (C-family proteins) are a widespread family of heme-binding proteins
evolution
-
The chlorite dismutases (C-family proteins) are a widespread family of heme-binding proteins
-
malfunction
-
the W155F mutation of the enzyme appears to disturb both the relatively higher heme affinity and pentameric oligomerization state common to the wild-type enzyme, mutant W156F, and mutant W227F
malfunction
-
a Staphylococcus aureus strain with an inactivated hemQ gene is generated and shown to be a slow growing small colony variant under aerobic but not anaerobic conditions. The DELTAhemQ mutant accumulates coproporphyrin specifically under aerobic conditions. Phenotypes, overview
malfunction
-
a Staphylococcus aureus strain with an inactivated hemQ gene is generated and shown to be a slow growing small colony variant under aerobic but not anaerobic conditions. The DELTAhemQ mutant accumulates coproporphyrin specifically under aerobic conditions. Phenotypes, overview
-
physiological function
-
the enzyme detoxifies the chlorite that results from chlorate respiration in bacteria and would otherwise accumulate in the cell and kill the organism. The reaction must be fast in order to serve its biological function: the homopentameric enzyme from Dechloromonas aromatica is one of the fastest and most efficient chlorite O2-lyases yet studied. The enzyme can support the generation of tens-of-millimolar O2 on the millisecond timescale
physiological function
-
the enzyme detoxifies the chlorite that results from chlorate respiration in bacteria and would otherwise accumulate in the cell and kill the organism. Nitrobacter has a limited chlorite resistance, which enables it to persist and even oxidize nitrite in the presence of low concentrations of chlorate
physiological function
-
similar substrate role for heme or porphyrin, with possible sensor-regulator functions for the protein
physiological function
-
similar substrate role for heme or porphyrin, with possible sensor-regulator functions for the protein
-
additional information
-
active and inactive enzyme forms dependent on the protonation status, overview
additional information
Candidatus Nitrospira defluvii is a key nitrifier in biological wastewater treatment, molecular mechanism of chlorite detoxification, overview. The residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins
additional information
-
the enzyme is capable of approximately 17000 turnovers per heme before undergoing irreversible inactivation due to oxidative damage to the heme
additional information
-
conformational and thermal stability of recombinant dimeric Cld from Nitrobacter winogradskyi, overview
additional information
-
conformational and thermal stability of recombinant pentameric Cld from Nitrospira defluvii, overview
additional information
-
despite a truncated N-terminal domain in each subunit, the dimeric enzyme is a highly efficient chlorite dismutase. Subunit interface and active site structures, structure modeling, overview
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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
chloride + O2
chlorite
-
chlorite dismutase catalyzes O2 release from chlorite with exquisite efficiency and specificity
-
-
r
chloride + O2
chlorite
-
chlorite dismutase catalyzes O2 release from chlorite with exquisite efficiency and specificity, the protonation state of the heme environment influences dioxygen formation. The reaction proceeds via an acid-base transition with pKa of 8.7, spectroscopic properties, ligand binding affinities, and steady-state kinetics, unique structure-activity model, overview
-
-
r
chloride + O2
chlorite
chlorite dismutase is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen
-
-
r
chloride + O2
chlorite
Arg173 plays a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction, mechanism, overview. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation
-
-
r
chlorite
chloride + O2
-
-
reaction provides oxygen for aerobic benzene biodegradation
-
?
chlorite
chloride + O2
-
-
reaction provides oxygen for aerobic benzene biodegradation
-
?
chlorite
chloride + O2
catalytic mechanism via ferryl species and ClO--anion
-
-
?
chlorite
chloride + O2
catalytic mechanism via ferryl species and ClO--anion
-
-
?
chlorite
chloride + O2
-
-
highly specific (no 18O from 18O-labeled water), no other side products with 18O-labeled ClO2- detectable
-
?
chlorite
chloride + O2
-
the heme enzyme rapidly converts chlorite to chloride and O2, suggesting a simple approach to overcoming both the technical difficulties in the systematic variation of the O2 concentration and its modest solubility
-
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
chlorite
chloride + O2
-
-
water is not involved in the O2-building reaction (no inclusion of 18O-isotope from labeled water)
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
chlorite
chloride + O2
-
-
water is not involved in the O2-building reaction (no inclusion of 18O-isotope from labeled water)
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
additional information
?
-
-
PitA possesses both chlorite dismutase-related (N-terminus) and antibiotic biosynthesis monooxygenase-related (C-terminus) activities
-
-
-
additional information
?
-
-
PitA possesses both chlorite dismutase-related (N-terminus) and antibiotic biosynthesis monooxygenase-related (C-terminus) activities
-
-
-
additional information
?
-
-
although its sequence is highly similar to functional chlorite dismutases, the HemQ protein has no steady state reactivity with chlorite, very modest reactivity with H2O2 or peracetic acid, and no observable transient intermediates
-
-
-
additional information
?
-
-
HemQ uses heme or porphyrin-like organic molecules as substrates. At pH 6.8, the enzyme exhibits relatively weak peroxidase activity with the reductant 2,2'-azino-bis[3-ethylbenzthiazoline-6-sulfonic acid], kinetics, overview
-
-
-
additional information
?
-
-
although its sequence is highly similar to functional chlorite dismutases, the HemQ protein has no steady state reactivity with chlorite, very modest reactivity with H2O2 or peracetic acid, and no observable transient intermediates
-
-
-
additional information
?
-
-
HemQ uses heme or porphyrin-like organic molecules as substrates. At pH 6.8, the enzyme exhibits relatively weak peroxidase activity with the reductant 2,2'-azino-bis[3-ethylbenzthiazoline-6-sulfonic acid], kinetics, overview
-
-
-
additional information
additional information
-
-
2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) is a diagnostic for peroxidase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant peroxidase reactivity products, only in the presence of oxidant peroxyacetic acid peroxidase reactivity products are obtained (1.6 equivalents per mol oxidant)
-
?
additional information
additional information
-
-
guaiacol is a diagnostic for peroxidase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant peroxidase reactivity products, only in the presence of oxidant peroxyacetic acid peroxidase reactivity products are obtained (1.6 equivalents per mol oxidant)
-
?
additional information
additional information
-
-
monochlorodimedone is a diagnostic for halogenation reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no halogenation is observed, not even when Cl-, Br-, or I- are added in excess (10 mM) under the same conditions or when oxidants such as peroxyacetic acid or H2O2 are added
-
?
additional information
additional information
-
-
peroxyacetic acid with chlorite
in excess of peroxyacetic acid the formation of two high-valent ferryl intermediates can be observed with stopped-flow UV-vis spectrophotometry in 0.1 M sodium phosphate buffer, pH 7.0, 10°C and with electron paramagnetic resonance in 20% ethylene glycol, 80% 0.010 M phosphate buffer, pH 7.14, addition of substrate and enzyme at 4°C, flash freezing in liquid N2 for analysis
-
-
additional information
additional information
-
-
thioanisole is a diagnostic for peroxygenase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant sulfoxide products that would point to peroxygenase reactivity, only in the presence of oxidant peroxyacetic acid sulfoxide formation is observed (0.247 sulfoxide per mol oxidant)
-
?
additional information
additional information
-
-
2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) is a diagnostic for peroxidase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant peroxidase reactivity products, only in the presence of oxidant peroxyacetic acid peroxidase reactivity products are obtained (1.6 equivalents per mol oxidant)
-
?
additional information
additional information
-
-
guaiacol is a diagnostic for peroxidase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant peroxidase reactivity products, only in the presence of oxidant peroxyacetic acid peroxidase reactivity products are obtained (1.6 equivalents per mol oxidant)
-
?
additional information
additional information
-
-
monochlorodimedone is a diagnostic for halogenation reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no halogenation is observed, not even when Cl-, Br-, or I- are added in excess (10 mM) under the same conditions or when oxidants such as peroxyacetic acid or H2O2 are added
-
?
additional information
additional information
-
-
peroxyacetic acid with chlorite
in excess of peroxyacetic acid the formation of two high-valent ferryl intermediates can be observed with stopped-flow UV-vis spectrophotometry in 0.1 M sodium phosphate buffer, pH 7.0, 10°C and with electron paramagnetic resonance in 20% ethylene glycol, 80% 0.010 M phosphate buffer, pH 7.14, addition of substrate and enzyme at 4°C, flash freezing in liquid N2 for analysis
-
-
additional information
additional information
-
-
thioanisole is a diagnostic for peroxygenase reactivity, 100 mM phosphate buffer (pH 6.8) and citrate phosphate buffer (pH 4.0)
no relevant sulfoxide products that would point to peroxygenase reactivity, only in the presence of oxidant peroxyacetic acid sulfoxide formation is observed (0.247 sulfoxide per mol oxidant)
-
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
chloride + O2
chlorite
-
chlorite dismutase catalyzes O2 release from chlorite with exquisite efficiency and specificity
-
-
r
chloride + O2
chlorite
B3U4H7
chlorite dismutase is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen
-
-
r
chlorite
chloride + O2
-
-
reaction provides oxygen for aerobic benzene biodegradation
-
?
chlorite
chloride + O2
-
-
reaction provides oxygen for aerobic benzene biodegradation
-
?
chlorite
chloride + O2
E2DI02
catalytic mechanism via ferryl species and ClO--anion
-
-
?
chlorite
chloride + O2
E2DI02
catalytic mechanism via ferryl species and ClO--anion
-
-
?
chlorite
chloride + O2
-
-
highly specific (no 18O from 18O-labeled water), no other side products with 18O-labeled ClO2- detectable
-
?
chlorite
chloride + O2
-
the heme enzyme rapidly converts chlorite to chloride and O2, suggesting a simple approach to overcoming both the technical difficulties in the systematic variation of the O2 concentration and its modest solubility
-
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
chlorite
chloride + O2
-
-
water is not involved in the O2-building reaction (no inclusion of 18O-isotope from labeled water)
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
chlorite
chloride + O2
-
-
water is not involved in the O2-building reaction (no inclusion of 18O-isotope from labeled water)
-
?
chlorite
chloride + O2
-
-
degradation of n-alkane or intermediates + chlorate
-
?
additional information
?
-
-
although its sequence is highly similar to functional chlorite dismutases, the HemQ protein has no steady state reactivity with chlorite, very modest reactivity with H2O2 or peracetic acid, and no observable transient intermediates
-
-
-
additional information
?
-
-
although its sequence is highly similar to functional chlorite dismutases, the HemQ protein has no steady state reactivity with chlorite, very modest reactivity with H2O2 or peracetic acid, and no observable transient intermediates
-
-
-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
heme
-
HemQ's equilibrium affinity for heme is in the low micromolar range. Holo-HemQ reconstituted with heme exhibits heme lysis after less than 50 turnovers with peroxide and less than 10 turnovers with chlorite. The heme-free apoprotein aggregates or unfolds over time. HemQ uses heme or porphyrin-like organic molecules as substrates. Heme in HemQ degrades in the presence of relatively small numbers of equivalents of H2O2, chlorite, or peracetic acid
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
(NH4)2SO4
-
activity increases with increasing salt concentration up to 2 M
Fe2+
Iron
Na2SO4
-
activity increases with increasing salt concentration up to 2 M
NaClO3
-
decreasing activity with increasing salt concentration
potassium phosphate
-
activity increases with increasing salt concentration up to 1 M salt, decrease beyond 1 M salt
Sodium phosphate
-
activity increases with increasing salt concentration up to 1 M salt, decrease beyond 1 M salt
additional information
-
kosmotropic salts such as sulfate and phosphate stabilize protein structures by water-structuring effects of the ions, chaotropic salts such as nitrate and chlorate reduce the activity, no effect of NaCl, NH4Cl, and NaHCO3 (up to 1.5 M) on enzyme activity
Iron
-
spectroscopic evidence is presented for a proximal histidine coordinating the heme iron center of the enzyme. The bond between the proximal histidine and the iron is weak and can be broken upon binding of NO. The midpoint potential, Em (Fe3+/2+) = -23 mV
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)
-
substrate inhibition at higher concentrations over 0.2 mM
azide
-
at 70 microM 44% inhibition, at 700 microM 89% inhibtion
Chlorite
-
irreversibly inactivates the enzyme after 17000 turnovers (per heme) and with a half-life of 0.39 min, resulting in bleaching of the heme chromophore. Guaiacol offers incomplete protection of the enzyme from inactivation
cyanide
-
at 70 microM 83% inhibition, at 700 microM 95% inhibtion
EDTA
-
at 70 microM 13% inhibition, at 700 microM 30% inhibtion
additional information
-
no product inhibition by O2 or chloride at millimolar concentrations
-
additional information
-
suicide inactivation by oxidative heme destruction
-
additional information
-
excess chlorite inactivates and bleaches the enzyme, 80% activity loss with 56 mM chlorite, 90% after second application of 56 mM chlorite; no inhibition by hydroxylamine or 3-amino-1,2,3-triazole
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
steady-state kinetics, and steady-state pH-rate profiles, overview
-
additional information
additional information
steady-state, pre-steady-state, and transient-state kinetics, overview
-
additional information
additional information
-
kinetic mechanism, overview
-
additional information
additional information
-
steady-state kinetics, overview
-
additional information
additional information
-
steady-state kinetics, overview
-
additional information
additional information
-
transient kinetic studies with wild-type and mutant enzymes, and steady-state kinetics, overview
-
additional information
additional information
-
Michaelis-Menten steady-state kinetics, overview
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
2.8
-
25°C, pH 6.0, 0.2 mM sodium chlorite, culture condition: n-decane/chlorate-grown cell, activity depends on chlorate concentration and amount of cell extract
5.7
7.7
-
25°C, pH 6.0, 0.2 mM sodium chlorite, culture condition: acetate/chlorate-grown cell, activity depends on chlorate concentration and amount of cell extract
22
443
-
Vmax, 100 mM sodium phosphate buffer, pH 6.0, 25°C, 0.2 mM chlorite
1500
100 mM K3PO4 (pH 7.0), 25°C, oxygen removal by bubbling with high-purity argon, measurement with modified Clarke electrode
additional information
5.7
-
benzene and chlorate, 30°C, oxygen production measured with Clark-type oxygen electrode
22
-
acetate and chlorate, 30°C, oxygen production measured with Clark-type oxygen electrode
additional information
Dechlorosoma sp.
-
measurement of chlorite dismutase activity by a chloride-specific electrode and ion chromatography via chloride production
additional information
-
the formation of O2 is influenced by the concentrations of enzyme and chlorite in 1 M phosphate buffer, pH 6.0, at 25°C, undiluted chlorite dismutase (0.64 mg/l) produces 98 microM O2 with 100 microM ClO2-, 205 microM O2 with 200 microM ClO2-, 300 microM O2 with 300 microM ClO2-, 10 times diluted chlorite dismutase (0.064 mg/l) produces 34 microM O2 with 100 microM ClO2-, 69 microM O2 with 200 microM ClO2-, 96 microM O2 with 300 microM ClO2-
additional information
-
activity the range 29.8-36.4 U/mg dry weight sludge
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.8
additional information
-
no pH dependencies in the presence of guaiacol, thioanisole, and monochlorodimedone
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 10.5
-
activity range, pH-rate profiles and pH-dependent ligand binding constants, active and inactive enzyme forms dependent on the protonation status, steady-state pH-rate profiles, overview
4.7 - 7
Dechlorosoma sp.
-
pH 4.8: 45% of maximal activity, pH 7.0: 45% of maximal activity, strain KJ
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
-
the enzyme does not contain a signal peptide for protein translocation into the periplasm and that the cleaving of a signal peptide at the N terminus would severely disturb the structure of the N-terminal domain
-
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28400
30000
4 * 30000 Da, elution position on a gel-filtration column using Stokes radius to determine molecular weight points to globular tetramer, collisional activation of the ions ejects one monomer of the pentamer, so that low-charged tetramer counter complex ions are also observed with native mass spectrometry; 5 * 30000 Da, tandem mass spectrometry, native mass spectrometry, active state in solution; 6 * 30000, multiple anomalous dispersion crystal structure, one heme per monomer (histidine 170 axial heme ligand), arginine 183 probably with essential role in substrate positioning and activation, activity of the hexamer not measurable because of the presence of the thiocyanate inhibitor, each monomer appears to be acting on its own, therefore, different quaternary states may be biologically relevant depending on protein concentration, pH, or other factors
30420
monomer without heme, native mass spectrometry, enzyme buffer-exchanged to 50 mM ammonium acetate, pH 6.8, with centrifugal filter units with 30 kDa cutoff
31000
-
4 * 31000, heme content 1.5 mol Fe2+/mol enzyme (calculated from Soret peak shift measurement), 2.2 mol Fe2+/mol enzyme (metal analysis by ICP-MS)
31030
monomer with heme, native mass spectrometry, enzyme buffer-exchanged to 50 mM ammonium acetate, pH 6.8, with centrifugal filter units with 30 kDa cutoff
110000
-
SDS-PAGE, native enzyme with Superdex 200 column with 50 mM potassium phosphate buffer, pH 7.0 and 100 mM NaCl
155000
pentamer, native mass spectrometry, native mass spectrometry, enzyme buffer-exchanged to 50 mM ammonium acetate, pH 6.8, with centrifugal filter units with 30 kDa cutoff
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
-
conformational and thermal stability of recombinant dimeric Cld from Nitrobacter winogradskyi, overview
hexamer
homodimer
homopentamer
homotetramer
monomer
pentamer
tetramer
additional information
-
the Cld-like protein from the chemolithoautotrophic nitrite oxidizer Nitrobacter winogradskyi is significantly smaller than all previously known chlorite dismutases
?
Bacteria GR-1
-
x * 32000, SDS-PAGE
-
hexamer
6 * 30000, multiple anomalous dispersion crystal structure, one heme per monomer (histidine 170 axial heme ligand), arginine 183 probably with essential role in substrate positioning and activation, activity of the hexamer not measurable because of the presence of the thiocyanate inhibitor, each monomer appears to be acting on its own, therefore, different quaternary states may be biologically relevant depending on protein concentration, pH, or other factors
hexamer
-
6 * 30000, multiple anomalous dispersion crystal structure, one heme per monomer (histidine 170 axial heme ligand), arginine 183 probably with essential role in substrate positioning and activation, activity of the hexamer not measurable because of the presence of the thiocyanate inhibitor, each monomer appears to be acting on its own, therefore, different quaternary states may be biologically relevant depending on protein concentration, pH, or other factors
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homodimer
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subunit interface and active site structures, structure modeling, overview
homopentamer
each monomer of NdCld is characterized by two topologically equivalent four-stranded antiparallel beta-sheets forming a beta-barrel, flanked on both sides by six alpha-helices, overview
homotetramer
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4 * 31000, heme content 1.5 mol Fe2+/mol enzyme (calculated from Soret peak shift measurement), 2.2 mol Fe2+/mol enzyme (metal analysis by ICP-MS)
homotetramer
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4 * 31000, heme content 1.5 mol Fe2+/mol enzyme (calculated from Soret peak shift measurement), 2.2 mol Fe2+/mol enzyme (metal analysis by ICP-MS)
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pentamer
5 * 30000 Da, tandem mass spectrometry, native mass spectrometry, active state in solution
pentamer
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5 * 30000 Da, tandem mass spectrometry, native mass spectrometry, active state in solution
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pentamer
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conformational and thermal stability of recombinant pentameric Cld from Nitrospira defluvii, overview
tetramer
4 * 30000 Da, elution position on a gel-filtration column using Stokes radius to determine molecular weight points to globular tetramer, collisional activation of the ions ejects one monomer of the pentamer, so that low-charged tetramer counter complex ions are also observed with native mass spectrometry
tetramer
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4 * 30000 Da, elution position on a gel-filtration column using Stokes radius to determine molecular weight points to globular tetramer, collisional activation of the ions ejects one monomer of the pentamer, so that low-charged tetramer counter complex ions are also observed with native mass spectrometry
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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the enzyme in the natural host contains a covalent modification, probably an intrachain cross-link involving a residue in the 52-55 region and a residue in the 215-223 region. A tyrosine-histidine cross-link appears possible, and can account for EPR differences between the native and recombinant enzymes as well as the spectrophotometric titration of the native enzyme
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
thiocyanate inhibited enzyme with incorporated heme, crystals grown from well solution containing 100 mM Mes buffer (pH 5.5), 25% polyethylene glycol monomethyl ether 2000, 0.3 M KSCN, 5% glycerol, 160-260 mM (NH4)2SO4, before data collection crystals are soaked in a solution of the mother liquor including 16% glycerol, crystal is flash-frozen and kept at -173°C (100 K) for multiple anomalous dispersion (MAD) with synchrotron radiation
recombinant protein, buffer-exchanged into 20 mM HEPES, pH 7.0, hanging-drop vapor diffusion, 16% PEG 8000, 0.2 M calcium acetate, 90 mM MES, pH 6.5, 293 K, chrystals appear after 2 h, co-crystals with substrate analogues sodium nitrite and sodium cyanide under same conditions
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purified recombinant His-tagged enzyme, sitting-drop vapor diffusion technique and a nanodropdispensing robot, from 1.0 M Na2HPO4-NaH2PO4, pH 8.2, at 22°C, 1 week, X-ray diffraction structure determination and analysis at 2.10 A resolution
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purified recombinant His-tagged wild-type and mutant enzymes with bound cyanide, 22°C, sitting drop vapour diffusion method, X-ray diffraction structure determination and analysis at 1.85-2.70 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
3 - 10
-
the pentameric enzyme is very stable between pH 3 and 10 with Tm=92°C at pH 7.0
724448
4 - 12
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the activity decreases dramatically below pH 5 and above pH 10, loss of activity is irreversible and accompanied by dramatic and rapid changes in the heme UV/vis chromophore, overview
712251
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40
50
additional information
additional information
-
conformational and thermal stability of recombinant dimeric Cld from Nitrobacter winogradskyi, overview
additional information
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conformational and thermal stability of recombinant pentameric Cld from Nitrospira defluvii, overview
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is capable of approximately 17000 turnovers per heme before undergoing irreversible inactivation due to oxidative damage to the heme
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
the enzyme is capable of approximately 17000 turnovers per heme before undergoing irreversible inactivation due to oxidative damage to the heme
-
724334
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cell pellet suspended in 0.05 M Tris-HCl buffer, pH 9.5 and 0.05 EDTA for 30 min at room temperature, centrifuged, supernatant ultracentrifuged, red supernatant containing periplasmic fraction separated from pellet, diluted with 10 mM Tris-HCl buffer, pH 7.2, purification with ÄKTAfplc, diluted supernatant loaded onto hydroxyapatite column with 10 mM Tris-HCl, pH 7.2, enzyme elutes at the start of a linear gradient of 10 mM Tris-Hcl, pH 7.2 to 450 mM potassium phosphate, pH 7.2, storage at -20°C
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cell-free extracts are prepared from strain AW-1 cells grown in anaerobic medium with n-decane as sole carbon and energy source and chlorate as electron acceptor, centrifugation, storage of extracts under N2 gas at 4°C
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centrifuged cell extract, cells grown in AW-1-sulfate medium with benzene and chlorate or benzene and oxygen
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HiLoad 16/60 Superdex 200 prep-grade column, equilibrated with 20 mM Tris-HCl (pH 7.5) and 135 mM NaCl to determin molecular Stokes radius
recombinant enzyme from Escherichia coli by anion exchange chromatography and gel filtration
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recombinant His-tagged enzyme from Escherichia coli strain Tuner (DE3) by affinity chromatography
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recombinant His-tagged enzyme from Escherichia coli strain Tuner (DE3) by nickel affinity chromatography and gel filtration
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recombinant mature Cld from Tuner(DE3) Escherichia coli cells by anion exchange chromatography and gel filtration
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recombinant N-terminally His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant Strep-tagged enzyme from Escherichia coli strain Tuner (DE3) by affinity chromatography, the Strep-II-tag is fully cleaved off using TEV-protease, followed by gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, phylogenetic analysis, expression of His-tagged enzyme in Escherichia coli strain Tuner (DE3)
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enzyme gene chemically synthesized without signal sequence, cloned into vector pET28a with histidine tag and thrombin cleavage site (removed before crystallization), and overexpressed
expression in Escherichia coli results in an active enzyme with similar spectral properties as the native enzyme
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expression in Escherichia coli, EPR differences between the native and recombinant enzymes as well as the spectrophotometric titration of the native enzyme
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expression of C-terminally His-tagged enzyme in Escherichia coli strain Tuner (DE3)
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gene hemQ, overexpression in Escherichia coli, complementation of the hemQ-defective Staphylococcus aureus mutant
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phylogenetic analysis, expression of N-terminally His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
recombinant expression of the enzyme without the N-terminal signal, but with N-terminal TEV-cleavable Strep-II tag in Escherichia coli strain Tuner (DE3)
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the gene encoding mature Cld, secretion peptide removed and replaced with an N-terminal Met residue, is expressed in untagged form from the pET41a vector in Tuner(DE3) Escherichia coli cells
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
W155F
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site-directed mutagenesis, mutation of a conserved residue on the proximal side of the heme causes a loss of the characteristic pentameric oligomerization state, secondary structure, and heme binding properties of the wild-type protein. Conversion to an inactive, heme-free form is accelerated by dilution
W156F
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site-directed mutagenesis, mutation of a conserved residue on the proximal side of the heme causes a loss of the characteristic pentameric oligomerization state, secondary structure, and heme binding properties of the wild-type protein. Conversion to an inactive, heme-free form is accelerated by dilution
W227F
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site-directed mutagenesis, mutation of a conserved residue on the proximal side of the heme, but W227F retains many properties of the wild-type protein, the mutant reacts with peracetic acid at pH 6.0-8.0, overview
R173A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme, structure determination and comparison to the wild-type enzyme
R173K
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme, structure determination and comparison to the wild-type enzyme
additional information
additional information
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a Staphylococcus aureus strain with an inactivated hemQ gene is generated and shown to be a slow growing small colony variant under aerobic but not anaerobic conditions
additional information
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a Staphylococcus aureus strain with an inactivated hemQ gene is generated and shown to be a slow growing small colony variant under aerobic but not anaerobic conditions
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
environmental protection
molecular biology
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use of the heme enzyme for the rapid, in situ generation of O2 at concentrations far exceeding 2 mM in coupled enzyme reaction systems to study O consumption or O2 involving reaction steps. Catalytic concentrations of chlorite O2-lyase can be used to initiate the reaction of an O2-utilizing (metallo)enzyme by rapid mixing with the highly soluble, non-volatile ClO2, rather than with the sparingly soluble, gaseous O2, e.g. activation of the beta2 subunit of class Ic ribonucleotide reductase from Chlamydia trachomatis by mixing its MnII/FeII complex with ClO2- in the presence of chlorite O2-lyase, overview
biotechnology
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degradation of benzene from anoxic polluted soil with chlorate
biotechnology
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degradation of benzene from anoxic polluted soil with chlorate
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environmental protection
bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment
environmental protection
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the enzyme from Nitrospira defluvii is an interesting candidate for bioremediation of chlorite
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LINKS TO OTHER DATABASES (specific for EC-Number 1.13.11.49)
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