Nitric-oxide reductase (FMN)

 

Moorella thermoacetica is a strictly anaerobic bacterium that utilises dissimilatory nitrate reduction for growth. It contains an A-type flavoprotein (FprA) that catalyses the reduction of nitric oxide to nitrogen dioxide, using FMN and a non-heme, non-sulphur diiron site.

 

Reference Protein and Structure

Sequence
Q9FDN7 UniProt (1.-.-.-) IPR016440 (Sequence Homologues) (PDB Homologues)
Biological species
Moorella thermoacetica ATCC 39073 (Bacteria) Uniprot
PDB
1ycf - Oxidized (di-ferric) FprA from Moorella thermoacetica (3.0 Å) PDBe PDBsum 1ycf
Catalytic CATH Domains
3.60.15.10 CATHdb (see all for 1ycf)
Cofactors
Mu-oxo-diiron (1)
Click To Show Structure

Enzyme Reaction (EC:1.7.-.-)

nitric oxide
CHEBI:16480ChEBI
+
FMNH2
CHEBI:16048ChEBI
→
water
CHEBI:15377ChEBI
+
dinitrogen oxide
CHEBI:17045ChEBI
+
FMN
CHEBI:17621ChEBI

Enzyme Mechanism

Introduction

The resting enzyme has an Fe(II)Fe(II) (diferrous) centre. Coordination of two molecules of NO (one for each Fe(II)) occurs. A diferrous dinitrosyl complex is produced. The FMNH2 reduces the diferrous dinitrosyl. The diiron centre is now Fe(II)Fe(II), but the nitrosyl ligands have an extra electron each. Tyr 195 and His 25 protonate the oxygen atoms of the nitrosyl ligand and finally, the ligands react to give N2O and H2O, leaving the enzyme with the diferrous centre again.

Catalytic Residues Roles

UniProt PDB* (1ycf)
His25 His25(24)A His 25 is proposed to act as a proton donor to the nitrosyl ligands. proton shuttle (general acid/base)
His228, Asp85 His228(227)A, Asp85(84)A Forms part of the iron 2 binding site. metal ligand
His81, Glu83, His148 His81(80)A, Glu83(82)A, His148(147)A Forms part of the iron 1 binding site. metal ligand
Asp167 Asp167(166)A Acts as a bridging ligand between iron 1 and iron 2 metal ligand
Tyr195 Tyr195(194)A Tyr 195 is proposed to act as a proton donor to the nitrosyl ligands. proton shuttle (general acid/base)
*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. Silaghi-Dumitrescu R et al. (2005), Biochemistry, 44, 6492-6501. X-ray Crystal Structures ofMoorella thermoaceticaFprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase†,‡. DOI:10.1021/bi0473049. PMID:15850383.
  2. Khatua S et al. (2015), J Inorg Biochem, 142, 145-153. Flavodiiron nitric oxide reductases: Recent developments in the mechanistic study and model chemistry for the catalytic reduction of NO. DOI:10.1016/j.jinorgbio.2014.09.018. PMID:25458587.
  3. Caranto JD et al. (2014), J Am Chem Soc, 136, 7981-7992. The Nitric Oxide Reductase Mechanism of a Flavo-Diiron Protein: Identification of Active-Site Intermediates and Products. DOI:10.1021/ja5022443. PMID:24828196.
  4. Blomberg LM et al. (2007), J Biol Inorg Chem, 12, 79-89. Theoretical study of the reduction of nitric oxide in an A-type flavoprotein. DOI:10.1007/s00775-006-0166-x. PMID:16957917.
  5. Silaghi-Dumitrescu R et al. (2003), Biochemistry, 42, 2806-2815. A Flavodiiron Protein and High Molecular Weight Rubredoxin fromMoorella thermoaceticawith Nitric Oxide Reductase Activity†. DOI:10.1021/bi027253k. PMID:12627946.

Step 1.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His81(80)A metal ligand
Glu83(82)A metal ligand
Asp85(84)A metal ligand
His148(147)A metal ligand
Asp167(166)A metal ligand
His228(227)A metal ligand
Tyr195(194)A proton shuttle (general acid/base)
His25(24)A proton shuttle (general acid/base)

Chemical Components

Step 1.

Contributors

Jonathan T. W. Ng, Gemma L. Holliday