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Information on EC 1.7.2.4 - nitrous-oxide reductase and Organism(s) Paracoccus denitrificans and UniProt Accession Q51705
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1.7.2.4 nitrous-oxide reductaseIUBMB Comments
The reaction is observed only in the direction of nitrous oxide reduction. Contains the mixed-valent dinuclear CuA species at the electron entry site of the enzyme, and the tetranuclear Cu-Z centre in the active site.
In Paracoccus pantotrophus, the electron donor is cytochrome c552.
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Word Map
- 1.7.2.4
-
denitrification
-
denitrify
- nitrite
-
greenhouse
- denitrificans
- paracoccus
- stutzeri
-
dinitrogen
-
wastewater
-
binuclear
-
tetranuclear
- cycloclastes
-
mixed-valence
-
multicopper
-
ammonia-oxidizing
-
n-cycle
- nautica
-
wolinella
-
arable
- nitrospirae
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stratospheric
- agriculture
-
t-rflp
- degradation
The taxonomic range for the selected organisms is: Paracoccus denitrificans
The expected taxonomic range for this enzyme is: Bacteria, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
nitrous oxide reductase, n2o reductase, n(2)or, nitrous-oxide reductase, cnosz, hdn2or, psn2or, z-type n2or, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
N(2)OR
-
-
-
-
N2O reductase
nitrous oxide reductase
N2O reductase
-
-
-
-
nitrous oxide reductase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
nitrogen:cytochrome c oxidoreductase (N2O-forming)
The reaction is observed only in the direction of nitrous oxide reduction. Contains the mixed-valent dinuclear CuA species at the electron entry site of the enzyme, and the tetranuclear Cu-Z centre in the active site.
In Paracoccus pantotrophus, the electron donor is cytochrome c552.
CAS REGISTRY NUMBER
COMMENTARY
55576-44-8
-
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
N2O + reduced cytochrome c550
N2 + H2O + cytochrome c550
-
-
-
?
nitrous oxide + 2 ferrocytochrome c + 2 H+
nitrogen + H2O + 2 ferricytochrome c
-
-
-
?
nitrogen + H2O + acceptor
nitrous oxide + reduced acceptor
-
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
nitrogen + H2O + 2 cytochrome c
-
-
-
-
?
nitrous oxide + reduced benzyl viologen + H+
nitrogen + H2O + oxidized benzyl viologen
-
-
-
-
r
nitrous oxide + reduced methyl viologen + H+
nitrogen + H2O + oxidized methyl viologen
-
-
-
-
r
additional information
?
-
-
determination of detailed gas kinetics and transcription patterns from batch culture experiments with Paracoccus denitrificans, allowing in vivo estimation of electron flow to O2 and N2O under various O2 regimes
-
-
?
nitrous oxide + reduced acceptor
nitrogen + H2O + acceptor
-
-
-
-
?
nitrous oxide + reduced acceptor
nitrogen + H2O + acceptor
-
methyl viologen as electron donor
-
-
?
nitrous oxide + reduced acceptor
nitrogen + H2O + acceptor
-
photochemically-reduced benzyl viologen as electron donor
-
-
?
nitrous oxide + reduced acceptor
nitrogen + H2O + acceptor
-
a mixture of N,N,N',N'-tetramethyl-p-phenylenediamine and ascorbate as electron donor
-
-
?
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
nitrous oxide + 2 ferrocytochrome c + 2 H+
nitrogen + H2O + 2 ferricytochrome c
-
-
-
?
nitrous oxide + 2 reduced cytochrome c
nitrogen + H2O + 2 cytochrome c
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
cupredoxin
a copper enzyme with cupredoxin containing blue T1 copper and red T2 copper. Blue and red copper centers form initially before they are pH-dependently transformed into purple CuA center, lower pH resulting in fewer trapped T1 and T2 coppers and faster transition. Structure overview
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
copper
N2OR contains two copper centers, CuA, a binuclear mixed-valence center and CuZ, a tetranuclear sulfide-bridged copper cluster
Cu2+
Cu
Cu2+
-
bound in a Cu centre, dependent on. The state of Cuz in extracted N2OR depends on the conditions during purification. Anoxic purification yields the purple, active form of the enzyme, whereas oxic conditions results in a blue form of N2OR with a redox inert Cuz centre, Cuz*. The blue form of N2OR is catalytically inactive, but may be reactivated in vitro by a strong reductant such as reduced methyl viologen
Cu2+
a copper enzyme with cupredoxin containing blue T1 copper and red T2 copper. Blue and red copper centers form initially before they are pH-dependently transformed into purple CuA center, lower pH resulting in fewer trapped T1 and T2 coppers and faster transition
Cu2+
the enzyme contains a tetranuclear copper-sulfide center consisting of the binuclear mixed-valent CuA center that acts as the electron transferring center, and the catalytic center, CuZ
Cu2+
the multicopper enzyme contains a CuA and a tetranuclear copper sulfide-bridged CuZ center
Cu
-
one dinuclear centre CuA and a copper cluster CuZ in which four copper ions are litigated by seven histidine imidazoles and a bridging inorganic sufide
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
O2
-
50% inactivation after 30 min, 80% regained activity after incubation with reduced benzyl viologen
O2
-
inactivation with O2 is largely reversible by exposure to benzyl viologen cation radical at room temperature for several hours
O2
-
N2OR being more sensitive to O2 than the other N-oxide reductases. The enzyme's apparent inactivation by O2 may be due to changes in the redox state of the unique Cuz-centre found in N2OR
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8
-
in presence of N,N,N',N'-tetramethyl-p-phenylenediamine and ascorbate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
-
gene nosZ, transcription of nosZ takes place concomitantly with that of narG under suboxic conditions. Catalytically functional N2OR is synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2O reduction rates are 10 times higher when anaerobic precultures are subjected to the same conditions. Upon oxygen exposure, there is an incomplete and transient inactivation of N2OR that can be ascribed to its lower ability to compete for electrons compared with terminal oxidases
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
the enzyme catalyses the last step of denitrification
physiological function
-
transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions
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). NOSZ_PARDE
652
1
71414
Swiss-Prot
Chloroplast (Reliability: 3)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
homodimer
-
2 * ?, each monomer is composed of two domains, a C-terminal cupredoxin domain carrying a dinuclear electron entry site CuA, an N-terminal seven-bladed propeller domain with the active center CuZ
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
building of two models of the active site reveals two distinct mechanisms. In the first model, N2O binds to the fully reduced tetranuclear Cu4S core in a bent my-(1,3)-O,N bridging fashion between the CuI and CuIV centres and subsequently extrudes N2 while generating the corresponding bridged my-oxo species. In the second model, substrate N2O binds loosely to one of the coppers of the tetranuclear Cu4S core in a terminal fashion, i.e., using only the oxygen atom. Loss of N2 generates the same my-oxo copper core. The free energies of activation predicted for these two alternative pathways are close to one another and do not provide decisive support for one over the other
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
strains with a nosXnirX double mutation or nirX single mutation show loss of N2O respiration
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
turnover dependent activation, nitrite and fluoride accelerate this process
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
N2OR being more sensitive to O2 than the other N-oxide reductases. The enzyme's apparent inactivation by O2 may be due to changes in the redox state of the unique Cuz-centre found in N2OR
-
742384
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene nosZ, transcription of nosZ takes place concomitantly with that of narG under suboxic conditions. Catalytically functional N2OR is synthesized and active in aerobically raised cells transferred to vials with 7 vol% O2 in headspace, but N2O reduction rates are 10 times higher when anaerobic precultures are subjected to the same conditions. Upon oxygen exposure, there is an incomplete and transient inactivation of N2OR that can be ascribed to its lower ability to compete for electrons compared with terminal oxidases, quantitative real-time PCR enzyme expression analysis
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
aerobically raised cells of Paracoccus denitrificans induce transcription of nosZ immediately after being transferred to intermediate O2 concentration (7 vol% O2 in headspace) in the presence of NO3- resulting in increased catalytically active enzyme levels
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Haltia, T.; Brown, K.; Tegoni, M.; Gambillau, C.; Saraste, M.; Mattila, K.; Djinovic-Carugo, K.
The crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 A resolution
Biochem. J.
369
77-88
2003
Paracoccus denitrificans
Snyder, S.W.; Hollocher, T.G.
Purification and some characteristics of nitrous oxide reductase from Paracoccus denitrificans
J. Biol. Chem.
262
6515-6525
1987
Paracoccus denitrificans
Kucera, I.; Boublikova, P.; Dadak, V.
Amperometric assay of activity and pH-optimum of N2O-reductase of Paracoccus denitrificans
Collect. Czech. Chem. Commun.
49
2709-2712
1984
Paracoccus denitrificans
-
Snyder, S.W.; Hollocher, T.C.
Nitrous oxide reductase and the 120,000 MW copper protein of N2-producing denitrifying bacteria are different entities
Biochem. Biophys. Res. Commun.
119
588-592
1984
Paracoccus denitrificans, Pseudomonas denitrificans (nom. rej.), Pseudomonas stutzeri
Kristjansson, J.K.; Hollocher, T.C.
Partial purification and characterization of nitrous oxide reductase from Paracoccus denitrificans
Curr. Microbiol.
6
247-251
1981
Paracoccus denitrificans
-
Kristjansson, J.K.; Hollocher, T.C.
First practical assay for soluble nitrous oxide reductase of denitrifying bacteria and a partial kinetic characterization
J. Biol. Chem.
255
704-707
1980
Paracoccus denitrificans
Mattila, K.; Haltia, T.
How does nitrous oxide reductase interact with its electron donors?--A docking study
Proteins
59
708-722
2005
Cereibacter sphaeroides, Paracoccus denitrificans (Q51705)
Wunsch, P.; Koerner, H.; Neese, F.; van Spanning, R.J.; Kroneck, P.M.; Zumft, W.G.
NosX function connects to nitrous oxide (N2O) reduction by affecting the Cu(Z) center of NosZ and its activity in vivo
FEBS Lett.
579
4605-4609
2005
Paracoccus denitrificans
Savelieff, M.G.; Wilson, T.D.; Elias, Y.; Nilges, M.J.; Garner, D.K.; Lu, Y.
Experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase
Proc. Natl. Acad. Sci. USA
105
7919-7924
2008
Paracoccus denitrificans (Q51705), Paracoccus denitrificans
Ertem, M.Z.; Cramer, C.J.; Himo, F.; Siegbahn, P.E.
N-O bond cleavage mechanism(s) in nitrous oxide reductase
J. Biol. Inorg. Chem.
17
687-698
2012
Paracoccus denitrificans (Q51705)
Qu, Z.; Bakken, L.R.; Molstad, L.; Frostegard, A.; Bergaust, L.L.
Transcriptional and metabolic regulation of denitrification in Paracoccus denitrificans allows low but significant activity of nitrous oxide reductase under oxic conditions
Environ. Microbiol.
18
2951-2963
2016
Paracoccus denitrificans
Carreira, C.; Pauleta, S.R.; Moura, I.
The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification
J. Inorg. Biochem.
177
423-434
2017
Stutzerimonas stutzeri (P19573), Paracoccus denitrificans (Q51705)
Pauleta, S.R.; Carepo, M.S.P.; Moura, I.
The tetranuclear copper-sulfide center of nitrous oxide reductase
Met. Ions Life Sci.
20
139-164
2020
Wolinella succinogenes, Stutzerimonas stutzeri (P19573), Paracoccus denitrificans (Q51705), Wolinella succinogenes DSM 1740, Paracoccus denitrificans Pd1222 (Q51705)
EXTERNAL LINKS (specific for EC-Number 1.7.2.4)
Transporter Classification Database (TCDB): 3.D.4.2.2
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