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Catalytic Site Atlas

CSA LITERATURE entry for 1nid

E.C. namenitrite reductase (NO-forming)
SpeciesAchromobacter cycloclastes (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1nidThere are 95 Homologs
CSA Entries With UniProtID P25006
CSA Entries With EC Number
PDBe Entry 1nid
PDBSum Entry 1nid
MACiE Entry M0004

Literature Report

IntroductionDenitrification, the reduction of dissolved nitrate and nitrite to gaseous NO, N20 and N2 is an important process in the recycling of nitrogen in the biosphere. It is chiefly carried out by denitrifying bacteria, which contain nitrate and nitrite reductases. Many species use a haem cd1 based nitrite reductase, but another group of denitrifying bacteria use this copper-containing enzyme. The enzymes in question catalyse the reduction of nitrite (NO2-) to NO + H2O. They contain two copper centres, a Type I centre which receives electrons from pseudoazurin (a copper containing protein), and a type II centre which is the site of nitrite reduction.
MechansimElectrons are transferred from pseudoazurin to the type I copper centre and then to the type II copper centre where nitrite reduction occurs.
The resting oxidised state of the enzyme contains a water molecule coordinated to a Cu2+ ion at the type II copper centre. Nitrite then binds to the type II copper ion and and displaces the water molecule. The type II copper now receives an electron from the type I copper and transfers it to the nitrite, which together with protonation of the nitrite leads to reduction of nitrite to NO + H2O.
Two protons are needed for the reduction of NO2- to NO + H2O, but the details of proton transfer have still not been firmly established. Proposed sources for the protons include His 255 (although it has also been proposed that this residue is not positioned appropriately for this role); the water molecule that bridges His 255 and Asp 98; the water molecule initially bound to copper (which is suggested to be deprotonated by Asp 98 prior to its displacement by NO2-, with Asp 98 later supplying the proton to the nitrite); and the nitrite entering as HNO2 with one proton already present.

Catalytic Sites for 1nid

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA98136macie:sideChainMay be involved in supplying proton(s) for the reduction of NO2- to NO + H2O.
HisA255293macie:sideChainHas been variously proposed to have roles in providing a positive charge to assist the pushing of an electron onto the nitrite during the reduction, protonating the substrate during the reduction, and modifying the properties of Asp 98 via the intervening water molecule.

Literature References

Notes:Copper containing nitrite reductase seems to be highly unique, despite the close similarity between many metal binding sites. In particular, this CATH number contains a large number of other metalloproteins, with different catalytic residue configurations. Clarification is needed of the details of proton transfer and on the roles of His 255, Asp 98, and the bridging water molecule.
Boulanger MJ
Catalytic roles for two water bridged residues (Asp-98 and His-255) in the active site of copper-containing nitrite reductase.
J Biol Chem 2000 275 23957-23964
PubMed: 10811642
Murphy ME
Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.
J Biol Chem 1997 272 28455-28460
PubMed: 9353305
Adman ET
The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.
J Biol Chem 1995 270 27458-27474
PubMed: 7499203
Kukimoto M
X-ray structure and site-directed mutagenesis of a nitrite reductase from Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction.
Biochemistry 1994 33 5246-5252
PubMed: 8172899
Kataoka K
Structure-based engineering of Alcaligenes xylosoxidans copper-containing nitrite reductase enhances intermolecular electron transfer reaction with pseudoazurin.
J Biol Chem 2004 279 53374-53378
PubMed: 15475344
Suzuki S
Metal coordination and mechanism of multicopper nitrite reductase.
Acc Chem Res 2000 33 728-735
PubMed: 11041837
Pinho D
Copper-containing nitrite reductase from Pseudomonas chlororaphis DSM 50135.
Eur J Biochem 2004 271 2361-2369
PubMed: 15182351