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Overview for MACiE Entry M0276

Version history

General Information

EC Number: 1.7.99.4 (A member of the Oxidoreductases, Acting on other nitrogenous compounds as donors, With other acceptors)

Enzyme Name: nitrate reductase

Biological Species: Rhodobacter sphaeroides (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • Q53176 - Periplasmic nitrate reductase

Representative PDB Code: 1ogy - CRYSTAL STRUCTURE OF THE HETERODIMERIC NITRATE REDUCTASEFROM RHODOBACTER SPHAEROIDES (Resolution = 3.2 Å).

Catalytic CATH Codes:

  • 3.40.228.10 - Dimethylsulfoxide Reductase, domain 2
  • Unassigned Domain

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of electron donor

Image of nitrate

Image of proton

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Image of water

Image of nitrite

Image of electron acceptor

electron donor
C00030
CHEBI:15022
nitrate
C00244
CHEBI:17632
2 proton
C00080
CHEBI:24636
water
C00001
CHEBI:15377
nitrite
C00088
CHEBI:16301
electron acceptor
C00028
CHEBI:17654

Overall Comment: Recent research has identified the previously assigned oxygen ligand within the Mo coordination sphere as a sulfur atom. Some of the cited references use mechanisms which require an oxygen, rather than sulfur to occupy this coordination site [2].


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Stepwise Description of the Reaction

Step 1The nitrate oxyanion attacks the molybdenum coordination in a displacement reaction, eliminating the Cys152 sulfur which results in the formation of a disulfide bridge within the coordination sphere.
Step 2The nitrate ligand undergoes heterolytic dissociation from molybdenum to form the nitrite product. The oxygen ligand is left behind at the metal centre.
Step 3The close proximity iron sulfur cluster provides an electron to the molybdenum centre via a bridging lysine residue.
Step 4A solvent molecule acts as a proton donor to the dianionic molybdenum centre.
Step 5The close proximity iron sulfur cluster provides an electron to the molybdenum centre via a bridging lysine residue.
Step 6A solvent molecule acts as a proton donor, forming a water ligand within the metal coordination sphere.
Step 7The Cys152 sulfur atom substitutes the water molecule coordinated to the molybdenum centre.

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Catalytic Residues Involved

Type Number Chain Location of Function
Lys 56 A Side Chain
Gly 383 A Main Chain Amide
Glu 384 A Side Chain
Met 153 A Side Chain
Met 346 A Side Chain
Cys 152 A Side Chain

Organic Cofactors for M0276

Type Identity Chain
Molybdopterin guanosine dinucleotide MGD 1803 A Overview
Molybdopterin guanosine dinucleotide MGD 1804 A Overview

Metal Cofactors for M0276

Type Het group Number Chain
iron SF4 1801 A Overview
molybdenum MO 1802 A Overview
iron HEC 1128 B Overview
iron HEC 1129 B Overview

References

  1. J. M. Dias et al. (1999), Structure, 7, 65-79. Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.
    Medline: 10368307
  2. M. J. Romao (2009), Dalton Trans., 21, 4053-4068. Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
    Medline: 19452052
  3. N. M. F. S. A. Cerqueira et al. (2009), J. Comput. Chem., 30, 2466-2484. The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase.
    Medline: 19360810

Homologue information for M0276 (1ogy)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0144 arsenite oxidase
1.20.98.1
1g8k 3.40.228.10
0.0.0.0
2.40.40.20
3.40.50.740
0.250.0526Compare

Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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binding (molecular function)
transport (biological process)
nitrate reductase activity (molecular function)
electron carrier activity (molecular function)
oxidoreductase activity (molecular function)
oxidoreductase activity, acting on other nitrogenous compounds as donors (molecular function)
electron transport chain (biological process)
molybdenum ion binding (molecular function)
nitrate assimilation (biological process)
periplasmic space (cellular component)
metal ion binding (molecular function)
iron-sulfur cluster binding (molecular function)
4 iron, 4 sulfur cluster binding (molecular function)
oxidation-reduction process (biological process)
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