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Information on EC 1.7.2.1 - nitrite reductase (NO-forming) and Organism(s) Alcaligenes faecalis and UniProt Accession P38501
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1.7.2.1 nitrite reductase (NO-forming)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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- 1.7.2.1
- anemia
- mellitus
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glycated
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hematocrit
- erythrocyte
- hematological
- women
- arterial
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glycemic
- transfusion
- platelet
- children
- albumin
- cardiovascular
- cholesterol
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postoperative
- ferritin
- fetal
-
sickle
- creatinine
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preoperative
- bleeding
- cardiac
- erythropoietin
- hypertension
- heme
- triglyceride
- hemorrhage
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admission
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systolic
- venous
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demographic
-
january
-
hemolysis
-
c-reactive
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erythroid
- hypoglycemia
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comorbidities
- reticulocyte
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hemodialysis
- transferrin
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admitted
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hemodynamic
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placebo
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diastolic
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intraoperative
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outpatient
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anthropometric
- bilirubin
- waist
- medicine
- analysis
The taxonomic range for the selected organisms is: Alcaligenes faecalis
The enzyme appears in selected viruses and cellular organisms
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
cytochrome c-551:O2, NO2- oxidoreductase
-
-
-
-
cytochrome cd
-
-
-
-
cytochrome oxidase
-
-
-
-
oxidase, Pseudomonas cytochrome
-
-
-
-
Pseudomonas cytochrome oxidase
-
-
-
-
reductase, nitrite (cytochrome)
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
redox reaction
-
-
-
-
oxidation
-
-
-
-
reduction
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
-
-, -, -, -, -
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
9027-00-3
-
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
nitrite + H2O + reduced pseudoazurin
nitric oxide + H+ + pseudoazurin
reduction of pseudoazurin by ascorbate
-
-
?
nitrite + reduced pseudoazurin
NO + oxidized pseudoazurin
-
-
-
?
nitrite + reduced benzyl viologen
NO + oxidized benzyl viologen
-
random sequential mechanism
-
-
?
nitrite + reduced methyl viologen
NO + oxidized methyl viologen
-
random sequential mechanism
-
-
?
nitrite + reduced methyl viologen
NO + oxidized methyl viologen + H2O
-
-
-
-
?
nitrite + reduced pseudoazurin + H+
nitric oxide + oxidized pseudoazurin + H2O
-
-
-
-
r
nitrite + reduced pseudoazurin
NO + oxidized pseudoazurin
-
random sequential mechanism
-
-
?
additional information
?
-
density functional theory study of nitrite and nitric oxide adducts
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-
?
additional information
?
-
the active site residue is Ile257. The small molecules formate, acetate and nitrate mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom and interacting wit the oxidized catalytic metal ion, overview. Nitrite and the substrate mimic bind in the same asymmetric, bidentate manner
-
-
?
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
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Cu2+
copper-containing dissimilatory nitrite reductase, catalytic type 2 copper, binding site structure, analysis of binding structure and interaction with inhibitors, overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
steady-state kinetics
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TURNOVER NUMBER [1/s]
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
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.9 - 6.2
-
pH 4.9: about 55% of maximal ativity, pH 6.2: about 65% of maximal activity, reaction with 0.5 mM nitrite and pseudoazurin as electron donor
5.2 - 6.5
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pH 5.2: about 60% of maximal activity, pH 6.5: about 55% of maximal activity, reaction with 5 mM nitrite and pseudoazurin as electron donor
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
the driving force for electron transfer from type 1 copper to type 2 copper comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the type 2 copper site
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, free or in complex with small molecule inhibitors, hanging drop vapor diffusion method, room temperature, 25 mg/ml protein in 20 mM Tris-HCl, pH 7.0, is mixed with an equal volume of reservoir containing 6-10% PEG 4000, 100 mM sodium acetate, pH 4.0, addition of 20 mM of ligands 20 mM of azide, formate, or nitrate, X-ray diffraction structure determination and analysis at 1.5-1.8 A resolution
crystals are grown at 19°C by hanging drop vapour diffusion using a reservoir of 100 mM sodium acetate, pH 4.7, 6%-10% polyethylene glycol 4000 and 1-5 mM cupric chloride, each drop is made from an equal volume of reservoir and a 15 mg/ml protein stock solution buffered in 10 mM Tris pH 7.0, crystals of mutants diffract to 1.8 A, nitrite-soaked oxidized crystals are obtained by placing crystals in reservoir solution supplemented with 5 mM sodium nitrite
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M150G crystals are grown at room temperature by hanging drop vapor diffusion method
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
M150G
mutant enzyme shows lower catalytic activity than the wild-type enzyme. The type-1 site optical spectrum differs significantly from that of the native enzyme. The midpoint potential of the type-1 site of nitrite reductase M150G is higher than that of the native enzyme
M150T
mutant enzyme shows lower catalytic activity than the wild-type enzyme
M150G
-
mutation increases the reorganization energy by 0.3 eV (30 kJ/mol), binding of the nearby Met62 to the type-1 Cu site lowers the reorganization energy back to approximately the wild-type value
M150T
M150T
-
mutant enzyme has a type-1 site with a 125-mV higher midpoint potential and a 0.3-eV higher reorganization energy leading to an about 50-fold slower intramolecular electrontransfer to the type-2 site
M150T
-
mutation increases the reorganization energy by 0.3 eV (30 kJ/mol)
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type enzyme from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography, the tag is removed by thrombin, followed by anion exchange chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of the wild-type enzyme in Escherichia coli strain BL21 (DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Silvestrini, M.C.; Falcinelli, S.; Ciabatti, I.; Cutruzzola, F.; Brunori, M.
Pseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview
Biochimie
76
641-654
1994
Alcaligenes faecalis, Paracoccus denitrificans, Halomonas halodenitrificans, Paracoccus pantotrophus, Pseudomonas aeruginosa, Pseudomonas stutzeri, Thiobacillus denitrificans
Wijma, H.J.; Canters, G.W.; de Vries, S.; Verbeet, M.P.
Bidirectional catalysis by copper-containing nitrite reductase
Biochemistry
43
10467-10474
2004
Alcaligenes faecalis, Alcaligenes faecalis S-6
Boulanger, M.J.; Murphy, M.E.
Directing the mode of nitrite binding to a copper-containing nitrite reductase from Alcaligenes faecalis S-6: characterization of an active site isoleucine
Protein Sci.
12
248-256
2003
Alcaligenes faecalis, Alcaligenes faecalis S-6
Wijma, H.J.; MacPherson, I.; Farver, O.; Tocheva, E.I.; Pecht, I.; Verbeet, M.P.; Murphy, M.E.; Canters, G.W.
Effect of the methionine ligand on the reorganization energy of the type-1 copper site of nitrite reductase
J. Am. Chem. Soc.
129
519-525
2007
Alcaligenes faecalis, Alcaligenes faecalis S-6
Wijma, H.J.; Jeuken, L.J.; Verbeet, M.P.; Armstrong, F.A.; Canters, G.W.
A random-sequential mechanism for nitrite binding and active site reduction in copper-containing nitrite reductase
J. Biol. Chem.
281
16340-16346
2006
Alcaligenes faecalis
Silaghi-Dumitrescu, R.
Copper-containing nitrite reductase: a DFT study of nitrite and nitric oxide adducts
J. Inorg. Biochem.
100
396-402
2006
Alcaligenes faecalis (P38501)
Wijma, H.J.; Macpherson, I.; Alexandre, M.; Diederix, R.E.; Canters, G.W.; Murphy, M.E.; Verbeet, M.P.
A rearranging ligand enables allosteric control of catalytic activity in copper-containing nitrite reductase
J. Mol. Biol.
358
1081-1093
2006
Alcaligenes faecalis (P38501), Alcaligenes faecalis S-6 (P38501)
Tocheva, E.I.; Eltis, L.D.; Murphy, M.E.
Conserved active site residues limit inhibition of a copper-containing nitrite reductase by small molecules
Biochemistry
47
4452-4460
2008
Alcaligenes faecalis (P38501), Alcaligenes faecalis S-6 (P38501), Alcaligenes faecalis S-6
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