Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
, 43 (2), 676-706

Nitrate and Periplasmic Nitrate Reductases

Affiliations
Review

Nitrate and Periplasmic Nitrate Reductases

Courtney Sparacino-Watkins et al. Chem Soc Rev.

Abstract

The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.

Figures

Fig. 1
Fig. 1
A schematic representation of the bacterial nitrogen cycle.
Fig. 2
Fig. 2
Schematic representation of dissimilatory and assimilatory nitrate reduction.
Fig. 3
Fig. 3
Coordination about the molybdenumcenter of crystallographically characterized nitrate reductases with PDB codes. Ec: Escherichia coli, Dd: Desulfovibrio desulfuricans; Rs: Rhodobacter sphaeroides; Cn: Cupriavidus necator. Conformationally flexible Cys 152 in Cn-NapA structure is shown in two positions.
Fig. 4
Fig. 4
(A) The pyranopterin cofactor attached to the dinucleotide as found in bacterial nitrate reductases; (B) the basic pyranopterin cofactor found in all nitrate reductases; (C) the ring open form of the cofactor found in the structures of respiratory nitrate reductase, Nar.
Fig. 5
Fig. 5
Plot of two torsion angles (highlighted in bold lines) in molybdenum cofactors in SO, XO and NR. The linear line is represented by the equation [N = 49; R2 = 95; P < 0.0001). Note that values in NR exhibit a larger spread, those of XO and SO are tightly clustered, with the exception of four points, which are representing substrate or inhibitor bound form or eukNR.
Fig. 6
Fig. 6
Representative redox isomers of MPT. The Moco is viewed as a dihydropterin (see text for discussion).
Fig. 7
Fig. 7
Left: the structure of Rhodobacter sphaeroides NapAB (1OGY) highlighting the metal cofactors along with important amino acid residues. Right: a close up of the metal cofactors and select amino acid residues with distance suggesting a potential electron and or proton transfer path.
Fig. 8
Fig. 8
A sequence alignment, created using GeneDoc, of NapA from D. desulfuricans, Ralstonia eutropha, Rhodobacter sphaeroides, E. coli, and C. jejuni, representing δ, α, β, γ and ε proteobacteria, respectively. Sequence inserts (underlined in red), identical residues (black), [4Fe–4S] binding motif (red), the Mo-coordinated cysteine residue (orange); the lysine (green) and tyrosine (pink) are shown here, the latter two residues are predicted to be involved in electron transfer. The twin arginine translocase (TAT) signal peptide is underlined in blue. Also shown (bottom panel) is the homology models of C. jejuni NapA and NapAB. The insertion sequences, shown in red, are opposite to the NapB binding site. The homology models were created using Molecular Operating Environment (MOE) software heme is purple, [4Fe–4S] is orange, and the MPT is yellow.
Fig. 9
Fig. 9
Properties of NapA from representative organisms from each class of proteobacteria: alpha (α), beta (β), gamma (γ), delta (d), and epsilon (e). One representative organism from each proteobacteria is presented, though multiple organisms were evaluated from each class. C. jejuni NapA structure was generated from the 1OGY structure following standard homology modeling technique using MOE software. Pymol was used in aligning protein structures, calculate and graph electrostatic potential and rendered images.
Fig. 10
Fig. 10
Proposed catalytic mechanism of NapA of D. desulfuricans (A) and E. coli (B).
Fig. 11
Fig. 11
Proposed catalytic mechanism of respiratory nitrate reductase as suggested by Marangon et al.
Fig. 12
Fig. 12
A minimalistic mechanistic proposal for periplasmic nitrate reductase.
Fig. 13
Fig. 13
Proposed structures of the active sites of ‘high-g’, ‘very-high-g’ and ‘low-g’ species.
Fig. 14
Fig. 14
The proposed routes of electron transport to NapAB from quinone pool during nitrate reduction. Electrons can be transferred from menaquinone (MQH2) or ubiquinone (UQH2) with in the inner membrane by a quinone oxidase (i.e., NapC or NapH). Electrons are transported to NapAB via NapC, NapGH or NapCGH.
Fig. 15
Fig. 15
The protein structure of E. coli NapD in complex with the N-terminus of NapA. The protein backbone, of NapD (blue) and NapA (red), is displayed as a ribbon. The location of the two arginine residues (RR), for which the TAT leader sequence is named, is on the N-terminus of NapA. The figure the NMR solution structure (PDB ID: 2PQ4 was created using VMD (version 1.8.7) software.
Fig. 16
Fig. 16
Representative examples of the nap operon gene content and organization. Each nap gene (arrow) was identified by performing a blast search of the NCBI database, (*) indicates organisms that encode two nap operons.
Fig. 17
Fig. 17
Transcriptional regulation of the nap operon, and the pyranopterin and [4Fe–4S] cofactor biogenesis operons. Note that not all regulatory effects are present in the same organism. Proteins directly regulating the nap operon transcription are connected to “NapA” with a dashed line (–), and those that affect the cofactor biogenesis operons are connected to the specific operons by a double dashed line (==). The operons for pyranopterin and [4Fe–4S] cofactor biogenesis (blue) are moaABCDE and iscRSUA-hscBA-fdx, respectively. Lines with arrow (→) denote a positive regulatory effect, i.e., up-regulation, in the presence of the associated environmental signal; negative effects, i.e., down-regulation, is indicated with circle lines (−•). Concentration dependent regulation is indicated with brackets surrounding the chemical, for example [O2].
Fig. 18
Fig. 18
Phylogenic tree of NapA using 292 protein sequences. Positions containing gaps were eliminated, yielding a total of 600 amino acid positions in the final dataset. MEGA5 software was used for alignments and phylogenetic analyses. Formate dehydrogenase (FDH) was included in the analysis as an outlier. Three assimilatory nitrate reductases (Nas) were also included for reference. NapA sequences were collected from the NCBI database. Branches corresponding to similar species (sp.) or subspecies (ssp.) are collapsed. Branches are colored according to the phyla of proteobacteria: alpha (aqua); beta (navy blue); gamma (green); delta (orange); epsilon (red); non-proteobacteria (grey). Branch nodes are colored red (NapH); blue (NapC); red/blue (NapH + NapC); grey (no quinone oxidase). Diagrams at the four corners display the topology of the different Nap forms with respect to the periplasmic membrane and correspond to the node colors. Open circles represent NapA sequences from organisms where complete nap operon content is unknown.

Similar articles

See all similar articles

Cited by 39 PubMed Central articles

See all "Cited by" articles

Publication types

MeSH terms

Feedback