Nitrite dismutase

 

This enzyme is one of the nitrophorins originating from the blood feeding insect Rhodnius prolixus. Heme protein nitrophorins can catalyse the conversion of nitrite to nitric oxide (NO) with concomitant nitrate production at neutral pH. NO induces vasodilation and reduces platelet aggregation, increasing the insect's blood supply.

 

Reference Protein and Structure

Sequence
Q94734 UniProt (1.7.6.1) IPR023613 (Sequence Homologues) (PDB Homologues)
Biological species
Rhodnius prolixus (Triatomid bug) Uniprot
PDB
3mvf - Crystal Structure of Nitrophorin 4 from Rhodnius prolixus Complexed with Nitrite at pH 7.4 (1.4 Å) PDBe PDBsum 3mvf
Catalytic CATH Domains
2.40.128.20 CATHdb (see all for 3mvf)
Cofactors
Heme b (1)
Click To Show Structure

Enzyme Reaction (EC:1.7.6.1)

hydron
CHEBI:15378ChEBI
+
nitrite
CHEBI:16301ChEBI
→
water
CHEBI:15377ChEBI
+
nitrate
CHEBI:17632ChEBI
+
nitric oxide
CHEBI:16480ChEBI
Alternative enzyme names: Prolixin S, Nitrophorin 7,

Enzyme Mechanism

Introduction

The mechanism for nitrite disproportionation at neutral pH uses a heme b cofactor. The heme iron is coordinated to the first substrate nitrite, which undergoes an oxygen atom transfer (OAT) to a second nitrite molecule in the protein pocket. This forms a FeNO intermediate, which reduces a third nitrite substrate yielding two NO molecules. The side-chain of Asp30 transiently stores protons required for the reaction. The exact ordering of intermediates and reactions remains ambiguous and the precise mechanism is largely inferred by the curator.

Catalytic Residues Roles

UniProt PDB* (3mvf)
His80 His59A Coordinated to heme cofactor. metal ligand
Leu151 Leu130A L130R mutation reduces enzymatic activity. hydrogen bond donor
Asp51 Asp30A Side-chain transiently stores protons required for the reaction. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
*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

intermediate formation, charge delocalisation, coordination to a metal ion, radical formation, redox reaction, proton transfer, rate-determining step, bimolecular nucleophilic addition, dehydration, electron transfer, substitution (not covered by the Ingold mechanisms)

References

  1. He C et al. (2015), J Am Chem Soc, 137, 4141-4150. Nitrite dismutase reaction mechanism: kinetic and spectroscopic investigation of the interaction between nitrophorin and nitrite. DOI:10.1021/ja512938u. PMID:25751738.
  2. Di Russo NV et al. (2012), PLoS Comput Biol, 8, e1002761-. pH-Dependent conformational changes in proteins and their effect on experimental pK(a)s: the case of Nitrophorin 4. DOI:10.1371/journal.pcbi.1002761. PMID:23133364.
  3. Knipp M et al. (2011), IUBMB Life, 63, 304-312. Nitrophorins: nitrite disproportionation reaction and other novel functionalities of insect heme-based nitric oxide transport proteins. DOI:10.1002/iub.451. PMID:21491557.
  4. Benabbas A et al. (2010), J Am Chem Soc, 132, 2811-2820. Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. DOI:10.1021/ja910005b. PMID:20121274.

Step 1. Oxygen atom transfer (OAT) from the coordinated NO2- to a second NO2- ion in the protein pocket, forming an FeNO intermediate and an NO3- ion. Proton transfer to Asp30 from solvent.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp30A proton acceptor
His59A metal ligand
Asp30A hydrogen bond acceptor
Leu130A hydrogen bond donor

Chemical Components

intermediate formation, charge delocalisation, coordination to a metal ion, radical formation, redox reaction, proton transfer, rate-determining step

Step 2. Proton-coupled electron transfer (PCET). The FeNO intermediate reacts with a third NO2- in the protein pocket, forming a radical. Oxidation of this intermediate forms a second NO and water. The exact mechanism of this step remains uncertain and is here largely inferred by the curator.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His59A metal ligand
Asp30A proton donor, hydrogen bond donor

Chemical Components

ingold: bimolecular nucleophilic addition, charge delocalisation, coordination to a metal ion, dehydration, electron transfer, proton transfer, redox reaction, radical formation

Step 3. NO of complex replaced by H2O to close the reaction cycle.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles

Chemical Components

substitution (not covered by the Ingold mechanisms)
Download: Image, Marvin File

Step 1. Oxygen atom transfer (OAT) from the coordinated NO2- to a second NO2- ion in the protein pocket, forming an FeNO intermediate and an NO3- ion. Proton transfer to Asp30 from solvent.

Step 2. Proton-coupled electron transfer (PCET). The FeNO intermediate reacts with a third NO2- in the protein pocket, forming a radical. Oxidation of this intermediate forms a second NO and water. The exact mechanism of this step remains uncertain and is here largely inferred by the curator.

Step 3. NO of complex replaced by H2O to close the reaction cycle.

Products.

Contributors

Noa Marson, Antonio Ribeiro