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Information on EC 1.7.2.1 - nitrite reductase (NO-forming) and Organism(s) Achromobacter cycloclastes and UniProt Accession P25006

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IUBMB Comments
The reaction is catalysed by two types of enzymes, found in the perimplasm of denitrifying bacteria. One type comprises proteins containing multiple copper centres, the other a heme protein, cytochrome cd1. Acceptors include c-type cytochromes such as cytochrome c-550 or cytochrome c-551 from Paracoccus denitrificans or Pseudomonas aeruginosa, and small blue copper proteins such as azurin and pseudoazurin. Cytochrome cd1 also has oxidase and hydroxylamine reductase activities. May also catalyse the reaction of hydroxylamine reductase (EC 1.7.99.1) since this is a well-known activity of cytochrome cd1.
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Achromobacter cycloclastes
UNIPROT: P25006
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The taxonomic range for the selected organisms is: Achromobacter cycloclastes
The enzyme appears in selected viruses and cellular organisms
Synonyms
hemoglobin, cunir, dissimilatory nitrite reductase, marc2, marc1, pseudomonas cytochrome oxidase, cytochrome cd1 nitrite reductase, cu-nir, axnir, cytochrome cd, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
copper-containing nitrite reductase
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dissimilatory nitrite reductase
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cytochrome c-551:O2, NO2- oxidoreductase
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cytochrome cd
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cytochrome oxidase
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oxidase, Pseudomonas cytochrome
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Pseudomonas cytochrome oxidase
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reductase, nitrite (cytochrome)
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-
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-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+
show the reaction diagram
reaction mechanism, overview. The transformation from the initial O-coordination of substrate to the final N-coordination of product is achieved by electron transfer from T1 copper to T2 copper, rather than by the previously reported side-on coordination of a NO intermediate, which only takes place in the reduced enzyme. Role of structural change in the critical residue Asp98, which affects the energetics of substrate attachment and product release at the T2 copper reaction center, while it does not significantly affect the activation energy and reaction pathways of the nitrite reduction process
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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oxidation
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reduction
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PATHWAY SOURCE
PATHWAYS
-
-, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
nitric-oxide:ferricytochrome-c oxidoreductase
The reaction is catalysed by two types of enzymes, found in the perimplasm of denitrifying bacteria. One type comprises proteins containing multiple copper centres, the other a heme protein, cytochrome cd1. Acceptors include c-type cytochromes such as cytochrome c-550 or cytochrome c-551 from Paracoccus denitrificans or Pseudomonas aeruginosa, and small blue copper proteins such as azurin and pseudoazurin. Cytochrome cd1 also has oxidase and hydroxylamine reductase activities. May also catalyse the reaction of hydroxylamine reductase (EC 1.7.99.1) since this is a well-known activity of cytochrome cd1.
CAS REGISTRY NUMBER
COMMENTARY hide
9027-00-3
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
nitrite + ferrocytochrome c
nitric oxide + H2O + ferricytochrome c
show the reaction diagram
-
-
?
nitrite + ferrocytochrome c + 2 H+
nitric oxide + H2O + ferricytochrome c
show the reaction diagram
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-
-
?
nitrite + reduced benzyl viologen
NO + H2O + oxidized benzyl viologen
show the reaction diagram
-
-
-
-
?
nitrite + reduced pseudoazurin
NO + oxidized pseudoazurin
show the reaction diagram
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the rate-determining step in the enzyme reaction sequence is not the intermolecular electron transfer process between pseudoazurin and AcNIR, but the reduction of substrate by AcNIR in the steady-state assay system
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
nitrite + ferrocytochrome c + 2 H+
nitric oxide + H2O + ferricytochrome c
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
copper
green copper enzyme
Cu2+
each monomer of the trimeric enzyme contains two copper sites: type I (T1) and type II (T2), which are connected via a cysteine (Cys)-histidine (His) bridge for rapid electron transfer. T1 and T2 copper sites structure, PDB ID 2BWD
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
the enzyme is involved in the denitrification anoxic process, which occurs in four reduction steps: initial conversion of nitrate to nitrite, followed by transformation of nitrite to nitric oxide, subsequent reduction of nitric oxide to nitrous oxide, and the final conversion of nitrous oxide to dinitrogen gas. All stages are catalyzed by complex metalloenzymes with different transition metal cofactors. Dissimilatory nitrite reductases (NiRs) catalyze the reduction of nitrite to nitric oxide, the committed step in denitrification. There are two main types: one containing iron (cd1NiRs) and the other copper (CuNiRs)
additional information
determination of the activation energies, transition states, and minimum energy pathways of CuNiR for reaction mechanism analysis. Structure modelling of the CuNiR active site involving residues His100, His135, His306, Asp98, His255, Ile257 and four water molecules. Structure-function analysis, detailed overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NIR_ACHCY
378
0
40771
Swiss-Prot
-
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
105000
sedimentation equlibrium
37000
3 * 37000, calculated from sequence, crystal structure
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotrimer
CuNiRs are organized as homotrimers with three identical monomers tightly associated together
trimer
3 * 37000, calculated from sequence, crystal structure
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
atomic resolution structures of four forms of the green Cu-nitrite reductase: structure of the resting state of the enzyme at 0.9 A, structure of then nitrite-soaked complex at 1.10 A resolution, structure of the endogenously bound NO complex at 1.12-A resolution, structure of endogenously bound nitrite and NO in the same crystal at 1.15-A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
W144L
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visible absorption and EPR spectrum is similar to that of wild-type AcNIR. The redox potentials of the mutant is also nearly equal to that of wild-type. Although the enzymatic activities of the mutants are also the same as that of wild-type enzyme, the intermolecular electron transfer rate constants from pseudoazurin to mutant AcNIRs is 3-4fold less than that from pseudoazurin to wild-type AcNIR using electrochemical methods
W144L/Y203L
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visible absorption and EPR spectrum is similar to that of wild-type AcNIR. The redox potentials of the mutant is also nearly equal to that of wild-type. Although the enzymatic activities of the mutants are also the same as that of wild-type enzyme, the intermolecular electron transfer rate constants from pseudoazurin to mutant AcNIRs is 3-4fold less than that from pseudoazurin to wild-type AcNIR using electrochemical methods
Y203L
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visible absorption and EPR spectrum is similar to that of wild-type AcNIR. The redox potentials of the mutant is also nearly equal to that of wild-type. Although the enzymatic activities of the mutants are also the same as that of wild-type enzyme, the intermolecular electron transfer rate constants from pseudoazurin to mutant AcNIRs is 3-4fold less than that from pseudoazurin to wild-type AcNIR using electrochemical methods
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Ichiki, H.; Tanaka, Y.; Mochizuki, K.; Yoshimatsu, K.; Sakurai, T.; Fujiwara, T.
Purification, characterization, and genetic analysis of Cu-containing dissimilatory nitrite reductase from a denitrifying halophilic archaeon, Haloarcula marismortui
J. Bacteriol.
183
4149-4156
2001
Achromobacter xylosoxidans, Fusarium oxysporum, Haloarcula marismortui, Haloferax denitrificans, Achromobacter cycloclastes (P25006)
Manually annotated by BRENDA team
Yamaguchi, K.; Shuta, K.; Suzuki, S.
Roles of Trp144 and Tyr203 in copper-containing nitrite reductase from Achromobacter cycloclastes IAM1013
Biochem. Biophys. Res. Commun.
336
210-214
2005
Achromobacter cycloclastes, Achromobacter cycloclastes IAM1013
Manually annotated by BRENDA team
Antonyuk, S.V.; Strange, R.W.; Sawers, G.; Eady, R.R.; Hasnain, S.S.
Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism
Proc. Natl. Acad. Sci. USA
102
12041-12046
2005
Achromobacter cycloclastes (P25006)
Manually annotated by BRENDA team
Li, Y.; Hodak, M.; Bernholc, J.
Enzymatic mechanism of copper-containing nitrite reductase
Biochemistry
54
1233-1242
2015
Achromobacter cycloclastes (P25006)
Manually annotated by BRENDA team