Nitrite reductase (cytochrome cd1 type)

 

Cytochrome cd1 (cyt cd1) nitrite reductase is a dimeric enzyme of the bacterial periplasm that plays a key role in denitrification, the respiratory reduction of nitrite to nitric oxide in the nitrogen cycle. Each subunit of the cyt cd1 dimer contains one cytochrome c and one d1 haem group [PMID:12556530]. The active site contains a specialised d1 haem, where the nitrite substrate is bound and reduced. This d1 haem is bound in an 8-bladed beta-propeller, which is also found in some members of the WD40 repeat-containing proteins (IPR001680).

 

Reference Protein and Structure

Sequence
P24474 UniProt (1.7.2.1, 1.7.99.1) IPR011048 (Sequence Homologues) (PDB Homologues)
Biological species
Pseudomonas aeruginosa PAO1 (Bacteria) Uniprot
PDB
1nir - OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA (2.15 Å) PDBe PDBsum 1nir
Catalytic CATH Domains
2.140.10.20 CATHdb 1.10.760.10 CATHdb (see all for 1nir)
Cofactors
Ferroheme c(2-) (1), Heme b (1)
Click To Show Structure

Enzyme Reaction (EC:1.7.2.1)

iron(2+)
CHEBI:29033ChEBI
+
hydron
CHEBI:15378ChEBI
+
nitrous acid
CHEBI:25567ChEBI
→
iron(3+)
CHEBI:29034ChEBI
+
nitric oxide
CHEBI:16480ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: cd-cytochrome nitrite reductase, (Nitrite reductase (cytochrome)), Cytochrome c-551:O(2), NO(2)(+) oxidoreductase, Cytochrome cd, Cytochrome cd1, Hydroxylamine (acceptor) reductase, Methyl viologen-nitrite reductase, Nitrite reductase (cytochrome; NO-forming), Pseudomonas cytochrome oxidase, Nitrite reductase, Nitrite reductase (cytochrome),

Enzyme Mechanism

Introduction

This enzyme catalyses the reduction of nitrite to NO (nitric oxide) in the bacterial energy conversion denitrification process. It contain two distinct redox centres: one covalently bound c-haem, which is reduced by external electron donors, and another peculiar porphyrin, the d1-haem (3,8-dioxo-17-acrylate-porphyrindione), where nitrite is reduced to NO. During the catalytic cycle the substrate (i.e. nitrite) binds to the ferrous enzyme and is then reduced to yield NO and oxidised d1-haem. Reduction of the d1-haem occurs (by intramolecular electron transfer) from the c-haem, which in turn is reduced by external electron donors

Catalytic Residues Roles

UniProt PDB* (1nir)
Cys75, Cys72 Cys50A, Cys47A Covalently attached to the porphyrin ring of the heme cofactor. covalently attached
Met113, His76 Met88A, His51A Form the axial ligands to the heme cofactor. metal ligand
His352, His394 His327A, His369A Acts to stabilise the the enzyme–substrate complex. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Cutruzzola F et al. (2001), Proc Natl Acad Sci U S A, 98, 2232-2237. The nitrite reductase from Pseudomonas aeruginosa: Essential role of two active-site histidines in the catalytic and structural properties. DOI:10.1073/pnas.041365298. PMID:11226222.
  2. Rinaldo S et al. (2011), Biochem Soc Trans, 39, 195-200. The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase. DOI:10.1042/BST0390195. PMID:21265772.
  3. Rinaldo S et al. (2011), Biochem J, 435, 217-225. Observation of fast release of NO from ferrous d₁ haem allows formulation of a unified reaction mechanism for cytochrome cd₁ nitrite reductases. DOI:10.1042/BJ20101615. PMID:21244362.
  4. Farver O et al. (2009), Biophys J, 96, 2849-2856. Intramolecular electron transfer in Pseudomonas aeruginosa cd(1) nitrite reductase: thermodynamics and kinetics. DOI:10.1016/j.bpj.2008.12.3937. PMID:19348767.
  5. Rinaldo S et al. (2008), Biochem Soc Trans, 36, 1155-1159. New insights into the activity of Pseudomonas aeruginosa cd1 nitrite reductase. DOI:10.1042/BST0361155. PMID:19021515.
  6. Gordon EH et al. (2003), J Biol Chem, 278, 11773-11781. Structure and kinetic properties of Paracoccus pantotrophus cytochrome cd1 nitrite reductase with the d1 heme active site ligand tyrosine 25 replaced by serine. DOI:10.1074/jbc.M211886200. PMID:12556530.
  7. Sun W et al. (2002), Biochem Biophys Res Commun, 291, 1-7. Cyanide binding to cd(1) nitrite reductase from Pseudomonas aeruginosa: role of the active-site His369 in ligand stabilization. DOI:10.1006/bbrc.2002.6391. PMID:11829453.
  8. Nurizzo D et al. (1998), Biochemistry, 37, 13987-13996. Conformational changes occurring upon reduction and NO binding in nitrite reductase from Pseudomonas aeruginosa. DOI:10.1021/bi981348y. PMID:9760233.

Step 1.

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Catalytic Residues Roles

Residue Roles
Cys47A covalently attached
Cys50A covalently attached
His51A metal ligand
Met88A metal ligand
His327A electrostatic stabiliser
His369A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Gemma L. Holliday