Bacterial assimilatory nitrate uptake and reduction

Bacterial nitrate utilization supplies ammonium for biosynthesis through successive nitrate-to-nitrite and nitrite-to-ammonium reductions. Four species-native implementations distinguish ferredoxin-dependent cyanobacterial enzymes, a multisubunit Bacillus nitrate reductase, and fused pyridine-nucleotide-linked nitrate reductases in Pseudomonas and Mycolicibacterium. Uptake assemblies are required when extracellular nitrate is the input; an intracellular-nitrate boundary permits omission of uptake. A separate E. coli comparison illustrates nitrate-fed assimilation during respiration and depends on an upstream respiratory nitrate reductase outside the represented protein panel. The module ends at ammonium, before its incorporation into glutamine or glutamate.

MODULE:bacterial_assimilatory_nitrate_reductionCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_assimilatory_nitrate_reduction.yaml

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

Of the four genes (nrtABCD) required for active transport of nitrate in the cyanobacterium Synechococcus sp. strain PCC 7942, nrtBCD encode membrane components of an ATP-binding cassette transporter involved in the transport of nitrite as well as of nitrate

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

Identities found at positions corresponding to those amino acids which in the above-mentioned proteins hold the Fe4S4-siroheme active center suggest that nitrite reductase from Synechococcus bears an active site much alike that present in those reductases.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

file:modules/bacterial_assimilatory_nitrate_reduction-source-analysis/nasN-identity-proof.json

nasN-identity-proof.json

Corrected DQ866862 encodes the 1351-residue protein A4ZHT3 exactly; this resolves the MSMEG_4206/NasN identity and overrides the ARBA-only sulfite label.

"translation_exactly_matches_uniprot": true

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC7152768/?report=xml

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

The main NasN reaction is NADPH-dependent, with a measured weaker NADH-supported reaction.

Among the physiological electron donors tested for the purified NasN, NADPH was preferred over NADH, as shown by a 26-fold greater activity with NADPH relative to NADH

DOI:10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

Native GlnR-linked expression supports NirBD recruitment in nitrogen limitation. Activity and paired assembly are inferred from target-specific NirB/NirD classifications, not a purified mc2 155 complex assay.

the nitrite reductase NirBD enzyme is up regulated by GlnR in nitrogen limitation

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

Under nitrate respiration, nitrate is converted to nitrite, which is subsequently converted to ammonium (NH4) by the cytosolic NADH-dependent nitrite reductase NirBD. Bacteria can then utilize NH4 as nitrogen source.

file:PSEPK/PP_1703/PP_1703-source-analysis/RESULTS.md

Modern PP_1703 CDS check

The continuous modern KT2440 CDS translates exactly to the complete Q88M71 fusion, supporting the single-CDS model despite historical split records; this is genomic-model evidence, not a full-length protein-expression or kinetic assay.

Bacterial-code translation gives 1,341 residues and a terminal TGA, no internal stop, and exact identity to both AAN67324.2 and Q88M71.

The 21 exact products preserve all 14 original exemplars and add seven native partners. PANTHER descriptors use the official OBO names and immutable target DR memberships solely as metadata; surprising family names do not overrule primary chemistry. No PTN ancestral placement is asserted. Native complexes require all named active units, without guessed stoichiometry. Evidence distinguishes direct experiments, source-analysis identity bridges, comparative mechanism inference and unresolved donor/assembly specificity. Scope stays CONCRETE because the module's rule is that a complete route uses both reductions from one native species, so each route is a species instance, and the four routes already span cyanobacteria, Firmicutes, Pseudomonadota and Actinomycetota with ferredoxin, multisubunit NADH and fused NAD(P)H enzyme architectures. Further routes, such as the Klebsiella oxytoca NasFEDCBA system, are not added until their members are reviewed. Complex subunits carry only a role, not a free-text function; the GO activity of each multisubunit step is asserted on the complex, and each subunit's own reviewed functions live in its gene review. PANTHER subfamilies are used where the member index places the target at subfamily level (B. subtilis NasA PTHR23515:SF2, E. coli NarU PTHR23515:SF6, NirA PTHR32439:SF0), matching the scopes in the curated family reviews. NasC and NasD have conflicting PANTHER placements between UniProt and PANTHER's per-organism files. NasD is pinned to PTHR43809:SF1 by a reasoned row in interpro/panther/panther-members-overrides.tsv, on its sirohaem-site and NasD-like InterPro signatures. NasC keeps its UniProt grounding PTHR43105:SF10, but no discriminator decides between that and PANTHER's PTHR43742:SF2 (ASSIMILATORY NITRATE REDUCTASE CATALYTIC SUBUNIT), so it is not pinned and the membership warning is left standing as the honest state.

19Nodes

14Parts

1Variant Sets

4Variants

13Annotons

7Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_assimilatory_nitrate_reduction deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

7 gene-function check(s) reflected in core functions · 0 conflict(s) · 3 evidence or coverage gap(s) (20 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
ecoli_uptake_comparison_activity	narU (ECOLI) UniProtKB:P37758 Gene	nitrate transmembrane transporter activity GO:0015112	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ecoli_nitrite_reduction_comparison_activity	PROTEIN_COMPLEX Gene	nitrite reductase (NADH) activity GO:0106316	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
syne7_uptake_activity	PROTEIN_COMPLEX Gene	ABC-type nitrate transporter activity GO:0015414	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
syne7_nitrate_reduction_activity	narB (SYNE7) UniProtKB:P39458 Gene	ferredoxin-nitrate reductase activity GO:0047889	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
syne7_nitrite_reduction_activity	nirA (SYNE7) UniProtKB:P39661 Gene	ferredoxin-nitrite reductase activity GO:0048307	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacsu_uptake_activity	nasA (BACSU) UniProtKB:P42432 Gene	nitrate transmembrane transporter activity GO:0015112	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bacsu_nitrate_reduction_activity	PROTEIN_COMPLEX Gene	nitrate reductase activity GO:0008940	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
bacsu_nitrite_reduction_activity	PROTEIN_COMPLEX Gene	nitrite reductase (NADH) activity GO:0106316	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
psepk_uptake_activity	nasA (PSEPK) UniProtKB:Q88L43 Gene	nitrate transmembrane transporter activity GO:0015112	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_nitrate_reduction_activity	PP_1703 (PSEPK) UniProtKB:Q88M71 Gene	nitrate reductase [NAD(P)H] activity GO:0050463	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
psepk_nitrite_reduction_activity	PROTEIN_COMPLEX Gene	nitrite reductase [NAD(P)H] activity GO:0008942	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
mycs2_nitrate_reduction_activity	nasN (MYCS2) UniProtKB:A4ZHT3 Gene	nitrate reductase (NADPH) activity GO:0050464	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mycs2_nitrite_reduction_activity	PROTEIN_COMPLEX Gene	nitrite reductase [NAD(P)H] activity GO:0008942	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
ecoli_uptake_comparison_activity	Classification of ECOLI narU PANTHER:PTHR23515:SF6 Family	nitrate transmembrane transporter activity GO:0015112	Family Supported Family review supports GO:0015112 FAMILY_WIDE. The shared activity of the NNP family, placed at the root by PAINT and supported independently for respiratory NarU and for the assimilatory NasA porters of Bacillus and Pseudomonas. The fungal elsinochrome transporter ECT1 (B1A0U4) is a known outlier that has no gene review here.
syne7_nitrate_reduction_activity	Classification of SYNE7 narB PANTHER:PTHR43105:SF9 Family	ferredoxin-nitrate reductase activity GO:0047889	Family Function Unreviewed Family review leaves GO:0047889 UNRESOLVED. Not a subfamily property. SF9 mixes electron donors, so ferredoxin-dependent nitrate reduction has to be judged per member. It holds for the cyanobacterial NarB enzymes (Synechococcus elongatus PCC 7942 P39458, whose ferredoxin interaction is mapped; Synechocystis PCC 6803 P73448). It does not hold for the fused NAD(P)H-linked enzymes Mycolicibacterium NasN (A4ZHT3) and Pseudomonas PP_1703 (Q88M71), for Klebsiella oxytoca NasA (Q06457), the catalytic subunit of an NADH-linked assimilatory enzyme, or for Geobacter SfrA (Q74FU6, D7AF63). SfrA is an NADPH-dependent Fe(3+) reductase without a Mo cofactor, so it is not a nitrate reductase at all. The electron donor of Shewanella frigidimarina O33732 has not been established. Leaving this term UNRESOLVED rather than scoping it to SF9 is deliberate: the subfamily mixes donors and holds members of unknown donor, so a later curator should not tighten it to SUBFAMILY_ONLY without member-level evidence.
syne7_nitrite_reduction_activity	Classification of SYNE7 nirA PANTHER:PTHR32439:SF0 Family	ferredoxin-nitrite reductase activity GO:0048307	Family Supported Family review supports GO:0048307 for PANTHER:PTHR32439:SF0. Ferredoxin-nitrite reductase activity holds for the cyanobacterial NirA and plant NiR members of SF0, which retain the sirohaem/[4Fe-4S] centre. All five mycobacterial sulfite reductases in the same subfamily are listed as exceptions: M. tuberculosis SirA in two strain assemblies (P9WJ03, P9WJ02), M. bovis Sir (Q7TYP6) and M. paratuberculosis Sir1 and Sir2 (Q73YC1, Q73XV0). Substrate is a member property in this family, as for GO:0050311, so the scope holds only with every sulfite-reducing member excepted. SF9 (CobG, DsrA, CysI) is not covered.
bacsu_uptake_activity	Classification of BACSU nasA PANTHER:PTHR23515:SF2 Family	nitrate transmembrane transporter activity GO:0015112	Family Supported Family review supports GO:0015112 FAMILY_WIDE. The shared activity of the NNP family, placed at the root by PAINT and supported independently for respiratory NarU and for the assimilatory NasA porters of Bacillus and Pseudomonas. The fungal elsinochrome transporter ECT1 (B1A0U4) is a known outlier that has no gene review here.
psepk_uptake_activity	Classification of PSEPK nasA PANTHER:PTHR23515 Family	nitrate transmembrane transporter activity GO:0015112	Family Supported Family review supports GO:0015112 FAMILY_WIDE. The shared activity of the NNP family, placed at the root by PAINT and supported independently for respiratory NarU and for the assimilatory NasA porters of Bacillus and Pseudomonas. The fungal elsinochrome transporter ECT1 (B1A0U4) is a known outlier that has no gene review here.
psepk_nitrate_reduction_activity	Classification of PSEPK PP_1703 PANTHER:PTHR43105:SF9 Family	nitrate reductase [NAD(P)H] activity GO:0050463	Family Function Unreviewed Family review leaves GO:0050464 UNRESOLVED. Not a subfamily property. NADPH-preferring nitrate reduction is shown only for the fused Mycolicibacterium NasN (A4ZHT3) in SF9. It does not hold for the ferredoxin-dependent cyanobacterial NarB enzymes (P39458, P73448), or for the NADH-linked Klebsiella oxytoca NasA (Q06457). Geobacter SfrA (Q74FU6, D7AF63) uses NADPH but reduces Fe(3+), not nitrate, and lacks the Mo cofactor. The fused Pseudomonas ortholog PP_1703 (Q88M71) has no measured donor preference and is reviewed at the donor-generic nitrate reductase [NAD(P)H] parent. The electron donor of Shewanella frigidimarina O33732 has not been established. Leaving this term UNRESOLVED rather than scoping it to SF9 is deliberate, for the same reason as the ferredoxin-dependent term: the subfamily mixes donors and holds members of unknown donor.
mycs2_nitrate_reduction_activity	Classification of MYCS2 nasN PANTHER:PTHR43105:SF9 Family	nitrate reductase (NADPH) activity GO:0050464	Family Function Unreviewed Family review leaves GO:0050464 UNRESOLVED. Not a subfamily property. NADPH-preferring nitrate reduction is shown only for the fused Mycolicibacterium NasN (A4ZHT3) in SF9. It does not hold for the ferredoxin-dependent cyanobacterial NarB enzymes (P39458, P73448), or for the NADH-linked Klebsiella oxytoca NasA (Q06457). Geobacter SfrA (Q74FU6, D7AF63) uses NADPH but reduces Fe(3+), not nitrate, and lacks the Mo cofactor. The fused Pseudomonas ortholog PP_1703 (Q88M71) has no measured donor preference and is reviewed at the donor-generic nitrate reductase [NAD(P)H] parent. The electron donor of Shewanella frigidimarina O33732 has not been established. Leaving this term UNRESOLVED rather than scoping it to SF9 is deliberate, for the same reason as the ferredoxin-dependent term: the subfamily mixes donors and holds members of unknown donor.

Gene-review completeness (21/21 grounded genes reviewed)

21 complete review(s) · 2 with deep research · 0 missing review · 19 reviewed but lacking deep research

Gene	Review	Complete	Deep research
MSMEG_0428 A0QPK3	✓	✓	✗
narB P39458	✓	✓	✗
narU P37758	✓	✓	✗
nasA P42432	✓	✓	✗
nasA Q88L43	✓	✓	✓
nasB P42433	✓	✓	✗
nasC P42434	✓	✓	✗
nasD P42435	✓	✓	✗
nasE P42436	✓	✓	✗
nasN A4ZHT3	✓	✓	✗
nirA P39661	✓	✓	✗
nirB A0QPK2	✓	✓	✗
nirB P08201	✓	✓	✗
nirB Q88M69	✓	✓	✗
nirD P0A9I8	✓	✓	✗
nirD Q88M68	✓	✓	✗
nrtA P38043	✓	✓	✗
nrtB P38044	✓	✓	✗
nrtC P38045	✓	✓	✗
nrtD P38046	✓	✓	✗
PP_1703 Q88M71	✓	✓	✓

Tree

Species-native nitrate-to-ammonium routesMetabolic Pathwaybacterial_assimilatory_nitrate_reduction

Parts
1. physiological comparison optional
2. E. coli nitrate-fed respiratory assimilation comparisonMetabolic Pathwayecoli_respiratory_comparison
  
  Parts
  1. 1. uptake
  2. E. coli NarU nitrate uptake comparisonTransport Stepecoli_uptake_comparison
    
    Annotons
    
    E. coli NarU nitrate uptake comparison Gene Product: narU (ECOLI)
  3. 3. reduction
  4. E. coli NirBD NADH-dependent nitrite reduction comparisonReactionecoli_nitrite_reduction_comparison
    
    Annotons
    
    E. coli NirBD NADH-dependent nitrite reduction comparison Protein Complex: E. coli NirBD nitrite reductase
Variants
1. Complete species-native reduction route by organism and native enzyme architecture (Exactly One)
  1. PCC 7942 ferredoxin-dependent routeMetabolic Pathwaysyne7_route
    
    Parts
    
    1. uptake optional
    
    PCC 7942 NrtABCD nitrate uptakeTransport Stepsyne7_uptake
    
    Annotons
    
    PCC 7942 NrtABCD nitrate uptake Protein Complex: PCC 7942 NrtABCD nitrate/nitrite importer
    
    2. reduction
    
    PCC 7942 NarB ferredoxin-dependent nitrate reductionReactionsyne7_nitrate_reduction
    
    Annotons
    
    PCC 7942 NarB ferredoxin-dependent nitrate reduction Gene Product: narB (SYNE7)
    
    3. reduction
    
    PCC 7942 NirA ferredoxin-dependent nitrite reductionReactionsyne7_nitrite_reduction
    
    Annotons
    
    PCC 7942 NirA ferredoxin-dependent nitrite reduction Gene Product: nirA (SYNE7)
  2. Bacillus NasBC–NasDE routeMetabolic Pathwaybacsu_route
    
    Parts
    
    1. uptake optional
    
    Bacillus NasA nitrate uptakeTransport Stepbacsu_uptake
    
    Annotons
    
    Bacillus NasA nitrate uptake Gene Product: nasA (BACSU)
    
    2. reduction
    
    Bacillus NasBC nitrate reductionReactionbacsu_nitrate_reduction
    
    Annotons
    
    Bacillus NasBC nitrate reduction Protein Complex: Bacillus NasBC assimilatory nitrate reductase
    
    3. reduction
    
    Bacillus NasDE NADH-dependent nitrite reductionReactionbacsu_nitrite_reduction
    
    Annotons
    
    Bacillus NasDE NADH-dependent nitrite reduction Protein Complex: Bacillus NasDE nitrite reductase
  3. KT2440 PP_1703–NirBD routeMetabolic Pathwaypsepk_route
    
    Parts
    
    1. uptake optional
    
    KT2440 PP_2092 NasA nitrate uptakeTransport Steppsepk_uptake
    
    Annotons
    
    KT2440 PP_2092 NasA nitrate uptake Gene Product: nasA (PSEPK)
    
    2. reduction
    
    KT2440 PP_1703 NAD(P)H-linked nitrate reductionReactionpsepk_nitrate_reduction
    
    Annotons
    
    KT2440 PP_1703 NAD(P)H-linked nitrate reduction Gene Product: PP_1703 (PSEPK)
    
    3. reduction
    
    KT2440 NirBD NAD(P)H-linked nitrite reductionReactionpsepk_nitrite_reduction
    
    Annotons
    
    KT2440 NirBD NAD(P)H-linked nitrite reduction Protein Complex: KT2440 NirBD nitrite reductase
  4. mc2 155 NasN–NirBD intracellular routeMetabolic Pathwaymycs2_route
    
    Parts
    
    1. reduction
    
    mc2 155 NasN NADPH-dependent nitrate reductionReactionmycs2_nitrate_reduction
    
    Annotons
    
    mc2 155 NasN NADPH-dependent nitrate reduction Gene Product: nasN (MYCS2)
    
    2. reduction
    
    mc2 155 inferred NAD(P)H-linked nitrite reductionReactionmycs2_nitrite_reduction
    
    Annotons
    
    mc2 155 inferred NAD(P)H-linked nitrite reduction Protein Complex: mc2 155 NirB–MSMEG_0428 nitrite reductase

Details

Species-native nitrate-to-ammonium routesMetabolic Pathwaybacterial_assimilatory_nitrate_reduction

A complete route requires both reductions from one native species implementation. Cross-species subunit substitutions and combining independently chosen upstream and downstream families are not allowed.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

Chemical continuity between reactions does not imply a stable reductase supercomplex or channeling. No ammonium incorporation, respiratory nitrate-reductase assembly, denitrification branch or Anabaena maturation protein is modeled.

Part: physiological comparison (optional)

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

Optional context only. These three E. coli products cannot satisfy the required native complete-route variant set.

E. coli nitrate-fed respiratory assimilation comparisonMetabolic Pathwayecoli_respiratory_comparison

NarU and NirBD represent uptake and nitrite reduction in a physiological comparison. The unrepresented respiratory nitrate reductase separates these reactions; nitrate uptake cannot directly feed the nitrite reductase. This is not a complete nitrate-to-ammonium variant.

Context

Escherichia coli K-12NCBITaxon:83333

Nitrate respiration supplies nitrite through an upstream respiratory nitrate reductase outside this panel

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

PMID:18691156

A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake.

Native NarU supports nitrate uptake and nitrite transport; the coupling mechanism is unresolved in this source.

NarK and NarU, catalyse nitrate uptake, nitrite export and nitrite uptake across the Escherichia coli cytoplasmic membrane by an unknown mechanism.

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

No material-flow edge bridges the missing nitrate-to-nitrite step. The upstream enzyme is known biology outside scope, not a new biological knowledge gap. Nitrate can be both sole electron acceptor and sole nitrogen source; detoxification/redox roles do not negate this assimilation context.

Part 1: uptake

PMID:18691156

A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake.

Native NarU supports nitrate uptake and nitrite transport; the coupling mechanism is unresolved in this source.

NarK and NarU, catalyse nitrate uptake, nitrite export and nitrite uptake across the Escherichia coli cytoplasmic membrane by an unknown mechanism.

Required within this species-native route.

E. coli NarU nitrate uptake comparisonTransport Stepecoli_uptake_comparison

NarU can also transport nitrite. Neither obligate nitrate/nitrite antiport nor a specific proton/sodium coupling mechanism is asserted.

PMID:18691156

A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake.

Native NarU supports nitrate uptake and nitrite transport; the coupling mechanism is unresolved in this source.

NarK and NarU, catalyse nitrate uptake, nitrite export and nitrite uptake across the Escherichia coli cytoplasmic membrane by an unknown mechanism.

NarU can also transport nitrite. Neither obligate nitrate/nitrite antiport nor a specific proton/sodium coupling mechanism is asserted.

Annotons

E. coli NarU nitrate uptake comparison

ecoli_uptake_comparison_activity

Participant: Gene Product: narU (ECOLI)

Gene Product:

narU (ECOLI)UniProtKB:P37758

Family:

Classification of ECOLI narUPANTHER:PTHR23515:SF6

Representative Members: narU (ECOLI)UniProtKB:P37758

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

nitrate transmembrane transporter activityGO:0015112

Substrates: nitrateCHEBI:17632

Products: nitrateCHEBI:17632

Cargo: nitrateCHEBI:17632

Source location: extracellular or periplasmic nitrate pool

Destination location: cytoplasmGO:0005737

Locations

plasma membraneGO:0005886

E. coli NarU nitrate uptake comparison

PMID:18691156

A single channel for nitrate uptake, nitrite export and nitrite uptake by Escherichia coli NarU and a role for NirC in nitrite export and uptake.

Native NarU supports nitrate uptake and nitrite transport; the coupling mechanism is unresolved in this source.

NarK and NarU, catalyse nitrate uptake, nitrite export and nitrite uptake across the Escherichia coli cytoplasmic membrane by an unknown mechanism.

Part 3: reduction

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

Required within this species-native route.

E. coli NirBD NADH-dependent nitrite reduction comparisonReactionecoli_nitrite_reduction_comparison

This can provide ammonium for biosynthesis during nitrate respiration. A respiratory nitrate reductase outside the 21-member panel must first produce nitrite.

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

This can provide ammonium for biosynthesis during nitrate respiration. A respiratory nitrate reductase outside the 21-member panel must first produce nitrite.

Annotons

E. coli NirBD NADH-dependent nitrite reduction comparison

ecoli_nitrite_reduction_comparison_activity

Participant: Protein Complex: E. coli NirBD nitrite reductase

Protein Complex:

E. coli NirBD nitrite reductase

Active units:

nirB

Participant: Gene Product: nirB (ECOLI)

Gene Product:

nirB (ECOLI)UniProtKB:P08201

Family:

Classification of ECOLI nirBPANTHER:PTHR43809

Representative Members: nirB (ECOLI)UniProtKB:P08201

Taxon:

Escherichia coli K-12NCBITaxon:83333

Role: Nitrite-reducing large component

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

file:ECOLI/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Curated database cross-reference places P08201 in PANTHER:PTHR43809; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR43809; NITRITE REDUCTASE (NADH) LARGE SUBUNIT; 1.

nirD

Participant: Gene Product: nirD (ECOLI)

Gene Product:

nirD (ECOLI)UniProtKB:P0A9I8

Family:

Classification of ECOLI nirDPANTHER:PTHR40562

Representative Members: nirD (ECOLI)UniProtKB:P0A9I8

Taxon:

Escherichia coli K-12NCBITaxon:83333

Role: Required small component of the native complex

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

file:ECOLI/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Curated database cross-reference places P0A9I8 in PANTHER:PTHR40562; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR40562; -; 1.

Taxon:

Escherichia coli K-12NCBITaxon:83333

Function

nitrite reductase (NADH) activityGO:0106316

Substrates: nitriteCHEBI:16301 NADH

Products: ammoniumCHEBI:28938 NAD+

Locations

cytoplasmGO:0005737

E. coli NirBD NADH-dependent nitrite reduction comparison

PMID:1435259

Transcriptional control, translation and function of the products of the five open reading frames of the Escherichia coli nir operon.

Both native E. coli NirB and NirD are required for NADH-dependent activity in this reconstitution; the small subunit is a complex contribution.

No NADH-dependent nitrite reductase activity was detected in extracts from bacteria lacking either NirB or NirD, but a mixture of the two was as active as an extract from wild-type bacteria.

PMID:34323689

NirD curtails the stringent response by inhibiting RelA activity in Escherichia coli.

Nitrate-fed E. coli can use nitrate as nitrogen source during nitrate respiration. Respiratory nitrate reduction supplies nitrite to NirBD; NarU plus NirBD is not a complete nitrate-reduction route.

Variant set: Complete species-native reduction route by organism and native enzyme architecture (Exactly One)

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC7152768/?report=xml

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

Purified recombinant M. smegmatis NasN is a diflavin-containing monomeric nitrate reductase; native genetics establishes nitrate assimilation.

NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN–FAD/NAD-binding, electron-receiving/transferring domain

Each variant fixes all concrete gene products and complex subunits. Uptake optionality applies only to an intracellular-nitrate input boundary; extracellular scenarios require the corresponding uptake node. MYCS2 has no extracellular implementation in this panel.

PCC 7942 ferredoxin-dependent routeMetabolic Pathwaysyne7_route

Complete native nitrate-to-ammonium reaction sequence. NrtABCD is required for the modeled extracellular uptake case; omission is allowed only for an intracellular nitrate boundary. The sequential reductases are not asserted to form a physical complex.

Context

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Intracellular nitrate input; extracellular input additionally requires the modeled native uptake step

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

url:https://idus.us.es/bitstream/handle/11441/129668/Involvement%20of%20the%20C-terminal%20Domain.pdf?sequence=1

Involvement of the C-terminal Domain of an ATP-binding Subunit in the Regulation of the ABC-type Nitrate/Nitrite Transporter of the Cyanobacterium Synechococcus sp. Strain PCC 7942*

Native PCC 7942 derivative experiments measure both reductases using an artificial donor. This supports reaction continuity but does not establish exclusive native ferredoxin specificity.

NR and NiR activities were determined at 30 °C

Connections

syne7_uptake -> syne7_nitrate_reduction Provides Input For

The upstream step supplies nitrate consumed by the downstream step in the same organism.

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:9341163

Involvement of the C-terminal domain of an ATP-binding subunit in the regulation of the ABC-type nitrate/nitrite transporter of the Cyanobacterium synechococcus sp. strain PCC 7942.

The C-terminal domain of NrtC participates in ammonium-promoted inhibition of native nitrate/nitrite uptake. NrtC is also an essential transport component; regulation is not its only role.

the C-terminal domain of NrtC is involved in the ammonium-promoted inhibition of the nitrate/nitrite transporter.

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:14871493

Complex formation between ferredoxin and Synechococcus ferredoxin: nitrate oxidoreductase.

NarB catalyzes nitrate-to-nitrite reduction with ferredoxin. Donor experiments include heterologous Anabaena ferredoxin, not an exclusive native ferredoxin assignment.

When reduced ferredoxin served as the electron donor for the reduction of nitrate to nitrite, the activity of the enzyme declined markedly as the ionic strength increased.

PMID:15166246

Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.

NarB contains molybdenum and an iron-sulfur center; source biochemistry supports the molybdoenzyme architecture.

Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

The electron-transfer study used PCC 7942 NarB with Synechocystis PCC 6803 ferredoxin, so it does not establish the exclusive native donor accession.

Both recombinant wild-type Fd from the cyanobacterium Synechocystis sp. PCC 6803 and recombinant, C-terminally Histagged Synechococcus sp. PCC 7942 NR were expressed in Escherichia coli

url:https://idus.us.es/bitstream/handle/11441/129668/Involvement%20of%20the%20C-terminal%20Domain.pdf?sequence=1

Involvement of the C-terminal Domain of an ATP-binding Subunit in the Regulation of the ABC-type Nitrate/Nitrite Transporter of the Cyanobacterium Synechococcus sp. Strain PCC 7942*

Native PCC 7942 derivative experiments measure both reductases using an artificial donor. This supports reaction continuity but does not establish exclusive native ferredoxin specificity.

NR and NiR activities were determined at 30 °C

syne7_nitrate_reduction -> syne7_nitrite_reduction Provides Input For

The upstream step supplies nitrite consumed by the downstream step in the same organism.

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:14871493

Complex formation between ferredoxin and Synechococcus ferredoxin: nitrate oxidoreductase.

NarB catalyzes nitrate-to-nitrite reduction with ferredoxin. Donor experiments include heterologous Anabaena ferredoxin, not an exclusive native ferredoxin assignment.

When reduced ferredoxin served as the electron donor for the reduction of nitrate to nitrite, the activity of the enzyme declined markedly as the ionic strength increased.

PMID:15166246

Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.

NarB contains molybdenum and an iron-sulfur center; source biochemistry supports the molybdoenzyme architecture.

Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

The electron-transfer study used PCC 7942 NarB with Synechocystis PCC 6803 ferredoxin, so it does not establish the exclusive native donor accession.

Both recombinant wild-type Fd from the cyanobacterium Synechocystis sp. PCC 6803 and recombinant, C-terminally Histagged Synechococcus sp. PCC 7942 NR were expressed in Escherichia coli

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

file:SYNE7/nirA/nirA-uniprot.txt

nirA-uniprot.txt

Curated database cross-reference places P39661 in PANTHER:PTHR32439; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR32439; FERREDOXIN--NITRITE REDUCTASE, CHLOROPLASTIC; 1.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

url:https://idus.us.es/bitstream/handle/11441/129668/Involvement%20of%20the%20C-terminal%20Domain.pdf?sequence=1

Involvement of the C-terminal Domain of an ATP-binding Subunit in the Regulation of the ABC-type Nitrate/Nitrite Transporter of the Cyanobacterium Synechococcus sp. Strain PCC 7942*

Native PCC 7942 derivative experiments measure both reductases using an artificial donor. This supports reaction continuity but does not establish exclusive native ferredoxin specificity.

NR and NiR activities were determined at 30 °C

Part 1: uptake (optional)

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:9341163

Involvement of the C-terminal domain of an ATP-binding subunit in the regulation of the ABC-type nitrate/nitrite transporter of the Cyanobacterium synechococcus sp. strain PCC 7942.

The C-terminal domain of NrtC participates in ammonium-promoted inhibition of native nitrate/nitrite uptake. NrtC is also an essential transport component; regulation is not its only role.

the C-terminal domain of NrtC is involved in the ammonium-promoted inhibition of the nitrate/nitrite transporter.

Optional only when nitrate is supplied at the intracellular module boundary. This exact native uptake assembly is required for the modeled extracellular-nitrate whole-cell realization; optional does not mean transport is physiologically dispensable.

PCC 7942 NrtABCD nitrate uptakeTransport Stepsyne7_uptake

The native system also transports nitrite. NrtC regulation was studied in a plasmid-cured PCC 7942 derivative; no separate regulatory protein is added to the route.

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:9341163

Involvement of the C-terminal domain of an ATP-binding subunit in the regulation of the ABC-type nitrate/nitrite transporter of the Cyanobacterium synechococcus sp. strain PCC 7942.

The C-terminal domain of NrtC participates in ammonium-promoted inhibition of native nitrate/nitrite uptake. NrtC is also an essential transport component; regulation is not its only role.

the C-terminal domain of NrtC is involved in the ammonium-promoted inhibition of the nitrate/nitrite transporter.

The native system also transports nitrite. NrtC regulation was studied in a plasmid-cured PCC 7942 derivative; no separate regulatory protein is added to the route.

Annotons

PCC 7942 NrtABCD nitrate uptake

syne7_uptake_activity

Participant: Protein Complex: PCC 7942 NrtABCD nitrate/nitrite importer

Protein Complex:

PCC 7942 NrtABCD nitrate/nitrite importer

Active units:

nrtA

Participant: Gene Product: nrtA (SYNE7)

Gene Product:

nrtA (SYNE7)UniProtKB:P38043

Family:

Classification of SYNE7 nrtAPANTHER:PTHR30024

Representative Members: nrtA (SYNE7)UniProtKB:P38043

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Role: Nitrate/nitrite binding lipoprotein

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

NrtA is required for transporter function; recombinant truncated NrtA binds nitrate and nitrite. Binding affinity is not a whole-cell transport Km.

Characterization of the nrtA deletional mutants showed that the 45-kDa protein is essential for the functioning of the nitrate/nitrite transporter.

file:SYNE7/nrtA/nrtA-uniprot.txt

nrtA-uniprot.txt

Curated database cross-reference places P38043 in PANTHER:PTHR30024; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR30024; ALIPHATIC SULFONATES-BINDING PROTEIN-RELATED; 1.

nrtB

Participant: Gene Product: nrtB (SYNE7)

Gene Product:

nrtB (SYNE7)UniProtKB:P38044

Family:

Classification of SYNE7 nrtBPANTHER:PTHR30151

Representative Members: nrtB (SYNE7)UniProtKB:P38044

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Role: Membrane translocation component

PMID:8437564

Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synechococcus sp. PCC7942.

Native sequence and mutant analysis assign NrtB to the membrane component.

NrtB is a hydrophobic protein having structural similarity to the integral membrane components of bacterial transport systems that are dependent on periplasmic substrate-binding proteins.

file:SYNE7/nrtB/nrtB-uniprot.txt

nrtB-uniprot.txt

Curated database cross-reference places P38044 in PANTHER:PTHR30151; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR30151; ALKANE SULFONATE ABC TRANSPORTER-RELATED, MEMBRANE SUBUNIT; 1.

nrtC

Participant: Gene Product: nrtC (SYNE7)

Gene Product:

nrtC (SYNE7)UniProtKB:P38045

Family:

Classification of SYNE7 nrtCPANTHER:PTHR42788:SF7

Representative Members: nrtC (SYNE7)UniProtKB:P38045

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Role: ATP-binding component with a C-terminal regulatory domain

PMID:8437564

Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synechococcus sp. PCC7942.

NrtC and NrtD are the two ATP-binding components; this assignment is supported by sequence architecture and native transporter genetics.

The N-terminal portion of NrtC (amino acid residues 1-254) and NrtD are 58% identical to each other in their amino acid sequences, and resemble the ATP-binding components of binding protein-dependent transport systems.

PMID:9341163

Involvement of the C-terminal domain of an ATP-binding subunit in the regulation of the ABC-type nitrate/nitrite transporter of the Cyanobacterium synechococcus sp. strain PCC 7942.

The C-terminal domain of NrtC participates in ammonium-promoted inhibition of native nitrate/nitrite uptake. NrtC is also an essential transport component; regulation is not its only role.

the C-terminal domain of NrtC is involved in the ammonium-promoted inhibition of the nitrate/nitrite transporter.

file:SYNE7/nrtC/nrtC-uniprot.txt

nrtC-uniprot.txt

Curated database cross-reference places P38045 in PANTHER:PTHR42788:SF7; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR42788:SF7; NITRATE ABC TRANSPORTER ATP-BINDING PROTEIN; 1.

nrtD

Participant: Gene Product: nrtD (SYNE7)

Gene Product:

nrtD (SYNE7)UniProtKB:P38046

Family:

Classification of SYNE7 nrtDPANTHER:PTHR42788:SF7

Representative Members: nrtD (SYNE7)UniProtKB:P38046

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Role: ATP-binding component

PMID:8437564

Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synechococcus sp. PCC7942.

NrtC and NrtD are the two ATP-binding components; this assignment is supported by sequence architecture and native transporter genetics.

file:SYNE7/nrtD/nrtD-uniprot.txt

nrtD-uniprot.txt

Curated database cross-reference places P38046 in PANTHER:PTHR42788:SF7; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR42788:SF7; NITRATE ABC TRANSPORTER ATP-BINDING PROTEIN; 1.

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Function

ABC-type nitrate transporter activityGO:0015414

Substrates: nitrateCHEBI:17632 ATP water

Products: nitrateCHEBI:17632 ADP phosphate

Cargo: nitrateCHEBI:17632

Source location: extracellular or periplasmic nitrate pool

Destination location: cytoplasmGO:0005737

Locations

plasma membraneGO:0005886

PCC 7942 NrtABCD nitrate uptake

PMID:9006953

Substrate-binding lipoprotein of the cyanobacterium Synechococcus sp. strain PCC 7942 involved in the transport of nitrate and nitrite.

Native PCC 7942 NrtABCD is required for the high-affinity nitrate/nitrite uptake system; NrtA is its substrate-binding lipoprotein.

PMID:9341163

Involvement of the C-terminal domain of an ATP-binding subunit in the regulation of the ABC-type nitrate/nitrite transporter of the Cyanobacterium synechococcus sp. strain PCC 7942.

The C-terminal domain of NrtC participates in ammonium-promoted inhibition of native nitrate/nitrite uptake. NrtC is also an essential transport component; regulation is not its only role.

the C-terminal domain of NrtC is involved in the ammonium-promoted inhibition of the nitrate/nitrite transporter.

Part 2: reduction

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:14871493

Complex formation between ferredoxin and Synechococcus ferredoxin: nitrate oxidoreductase.

NarB catalyzes nitrate-to-nitrite reduction with ferredoxin. Donor experiments include heterologous Anabaena ferredoxin, not an exclusive native ferredoxin assignment.

When reduced ferredoxin served as the electron donor for the reduction of nitrate to nitrite, the activity of the enzyme declined markedly as the ionic strength increased.

PMID:15166246

Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.

NarB contains molybdenum and an iron-sulfur center; source biochemistry supports the molybdoenzyme architecture.

Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

The electron-transfer study used PCC 7942 NarB with Synechocystis PCC 6803 ferredoxin, so it does not establish the exclusive native donor accession.

Both recombinant wild-type Fd from the cyanobacterium Synechocystis sp. PCC 6803 and recombinant, C-terminally Histagged Synechococcus sp. PCC 7942 NR were expressed in Escherichia coli

Required within this species-native route.

PCC 7942 NarB ferredoxin-dependent nitrate reductionReactionsyne7_nitrate_reduction

Reduced ferredoxin is the supported donor class. Heterologous donor experiments do not establish an exclusive native ferredoxin accession or interchangeable partner specificity.

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:14871493

Complex formation between ferredoxin and Synechococcus ferredoxin: nitrate oxidoreductase.

NarB catalyzes nitrate-to-nitrite reduction with ferredoxin. Donor experiments include heterologous Anabaena ferredoxin, not an exclusive native ferredoxin assignment.

When reduced ferredoxin served as the electron donor for the reduction of nitrate to nitrite, the activity of the enzyme declined markedly as the ionic strength increased.

PMID:15166246

Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.

NarB contains molybdenum and an iron-sulfur center; source biochemistry supports the molybdoenzyme architecture.

Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

The electron-transfer study used PCC 7942 NarB with Synechocystis PCC 6803 ferredoxin, so it does not establish the exclusive native donor accession.

Both recombinant wild-type Fd from the cyanobacterium Synechocystis sp. PCC 6803 and recombinant, C-terminally Histagged Synechococcus sp. PCC 7942 NR were expressed in Escherichia coli

Reduced ferredoxin is the supported donor class. Heterologous donor experiments do not establish an exclusive native ferredoxin accession or interchangeable partner specificity.

Annotons

PCC 7942 NarB ferredoxin-dependent nitrate reduction

syne7_nitrate_reduction_activity

Participant: Gene Product: narB (SYNE7)

Gene Product:

narB (SYNE7)UniProtKB:P39458

Family:

Classification of SYNE7 narBPANTHER:PTHR43105:SF9

Representative Members: narB (SYNE7)UniProtKB:P39458

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Function

ferredoxin-nitrate reductase activityGO:0047889

Substrates: nitrateCHEBI:17632 reduced ferredoxin

Products: nitriteCHEBI:16301 oxidized ferredoxin

Cofactors: molybdenum-bis-molybdopterin guanine dinucleotide [4Fe-4S] cluster

PCC 7942 NarB ferredoxin-dependent nitrate reduction

PMID:8624415

A cyanobacterial narB gene encodes a ferredoxin-dependent nitrate reductase.

Purified PCC 7942 NarB reduces nitrate with reduced ferredoxin; methyl viologen can bypass the physiological electron-input interaction.

either reduced methyl viologen or reduced ferredoxin could be used as an electron donor for the reduction of nitrate

PMID:14871493

Complex formation between ferredoxin and Synechococcus ferredoxin: nitrate oxidoreductase.

NarB catalyzes nitrate-to-nitrite reduction with ferredoxin. Donor experiments include heterologous Anabaena ferredoxin, not an exclusive native ferredoxin assignment.

When reduced ferredoxin served as the electron donor for the reduction of nitrate to nitrite, the activity of the enzyme declined markedly as the ionic strength increased.

PMID:15166246

Tuning a nitrate reductase for function. The first spectropotentiometric characterization of a bacterial assimilatory nitrate reductase reveals novel redox properties.

NarB contains molybdenum and an iron-sulfur center; source biochemistry supports the molybdoenzyme architecture.

Metal and acid-labile sulfide analysis revealed nearest integer values of 4:4:1 (iron/sulfur/molybdenum)/molecule of NarB.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

The electron-transfer study used PCC 7942 NarB with Synechocystis PCC 6803 ferredoxin, so it does not establish the exclusive native donor accession.

Both recombinant wild-type Fd from the cyanobacterium Synechocystis sp. PCC 6803 and recombinant, C-terminally Histagged Synechococcus sp. PCC 7942 NR were expressed in Escherichia coli

Part 3: reduction

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

file:SYNE7/nirA/nirA-uniprot.txt

nirA-uniprot.txt

Curated database cross-reference places P39661 in PANTHER:PTHR32439; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR32439; FERREDOXIN--NITRITE REDUCTASE, CHLOROPLASTIC; 1.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

Required within this species-native route.

PCC 7942 NirA ferredoxin-dependent nitrite reductionReactionsyne7_nitrite_reduction

Native nirA sequence, conserved catalytic residues and curated ferredoxin-nitrite-reductase classification support the activity. Native-cell NiR assays used artificial methyl viologen; no purified target/native-ferredoxin specificity assay is claimed. This NirA is not the heterotrophic NirBD complex; Anabaena maturation-associated NirB is not included.

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

file:SYNE7/nirA/nirA-uniprot.txt

nirA-uniprot.txt

Curated database cross-reference places P39661 in PANTHER:PTHR32439; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR32439; FERREDOXIN--NITRITE REDUCTASE, CHLOROPLASTIC; 1.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

url:https://idus.us.es/bitstream/handle/11441/129668/Involvement%20of%20the%20C-terminal%20Domain.pdf?sequence=1

Involvement of the C-terminal Domain of an ATP-binding Subunit in the Regulation of the ABC-type Nitrate/Nitrite Transporter of the Cyanobacterium Synechococcus sp. Strain PCC 7942*

Native PCC 7942 derivative experiments measure both reductases using an artificial donor. This supports reaction continuity but does not establish exclusive native ferredoxin specificity.

NR and NiR activities were determined at 30 °C

Annotons

PCC 7942 NirA ferredoxin-dependent nitrite reduction

syne7_nitrite_reduction_activity

Participant: Gene Product: nirA (SYNE7)

Gene Product:

nirA (SYNE7)UniProtKB:P39661

Family:

Classification of SYNE7 nirAPANTHER:PTHR32439:SF0

Representative Members: nirA (SYNE7)UniProtKB:P39661

Taxon:

Synechococcus elongatus PCC 7942 = FACHB-805NCBITaxon:1140

Function

ferredoxin-nitrite reductase activityGO:0048307

Substrates: nitriteCHEBI:16301 reduced ferredoxin

Products: ammoniumCHEBI:28938 oxidized ferredoxin

Cofactors: siroheme [4Fe-4S] cluster

PCC 7942 NirA ferredoxin-dependent nitrite reduction

PMID:8490140

Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases.

The native PCC 7942 nirA product is a nitrite reductase with conserved siroheme/[4Fe-4S] active-center residues; ferredoxin-class assignment combines this homology with curated target classification.

file:SYNE7/nirA/nirA-uniprot.txt

nirA-uniprot.txt

Curated database cross-reference places P39661 in PANTHER:PTHR32439; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR32439; FERREDOXIN--NITRITE REDUCTASE, CHLOROPLASTIC; 1.

PMID:28520412

Identification of the Ferredoxin-Binding Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase.

Nitrate assimilation proceeds through nitrate-to-nitrite reduction followed by nitrite-to-ammonia reduction. This is reaction continuity, not evidence for a physical complex between the enzymes.

The first step is catalyzed by nitrate reductase (NR) and involves the initial two-electron reduction of nitrate to nitrite.

url:https://idus.us.es/bitstream/handle/11441/129668/Involvement%20of%20the%20C-terminal%20Domain.pdf?sequence=1

Involvement of the C-terminal Domain of an ATP-binding Subunit in the Regulation of the ABC-type Nitrate/Nitrite Transporter of the Cyanobacterium Synechococcus sp. Strain PCC 7942*

Native PCC 7942 derivative experiments measure both reductases using an artificial donor. This supports reaction continuity but does not establish exclusive native ferredoxin specificity.

NR and NiR activities were determined at 30 °C

Bacillus NasBC–NasDE routeMetabolic Pathwaybacsu_route

Native 168-lineage route grounded by JH642-derived experiments. NasBC and NasDE each require their own native subunits; donor specificity is modeled at the supported granularity.

Context

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Intracellular nitrate input; extracellular input additionally requires the modeled native uptake step

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

PMID:7868621

The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.

Primary native genetics establishes the nasABCDEF nitrate/nitrite-assimilation system. Detailed polarity controls and artificial-donor limits are recorded separately from the cached abstract.

The isolation of the nasABCDEF genes of B. subtilis, which are required for nitrate/nitrite assimilation, is reported.

Native 168-lineage route grounded by JH642-derived experiments. NasBC and NasDE each require their own native subunits; donor specificity is modeled at the supported granularity.

Connections

bacsu_uptake -> bacsu_nitrate_reduction Provides Input For

The upstream step supplies nitrate consumed by the downstream step in the same organism.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

bacsu_nitrate_reduction -> bacsu_nitrite_reduction Provides Input For

The upstream step supplies nitrite consumed by the downstream step in the same organism.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Native NasDE activity is cytosolic. These assays concern JH642-derived strains in the 168 lineage.

No nitrite reductase activity was detected in the membrane fraction, whereas nearly all activity was present in the cytosolic fraction, indicating that the NasDE enzyme is a cytoplasmic protein.

Part 1: uptake (optional)

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

Bacillus NasA nitrate uptakeTransport Stepbacsu_uptake

Native JH642-derived genetics supports nitrate uptake. Nitrite transport, affinity and energy coupling are not established here.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

PMID:7868621

The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.

Primary native genetics establishes the nasABCDEF nitrate/nitrite-assimilation system. Detailed polarity controls and artificial-donor limits are recorded separately from the cached abstract.

The isolation of the nasABCDEF genes of B. subtilis, which are required for nitrate/nitrite assimilation, is reported.

Native JH642-derived genetics supports nitrate uptake. Nitrite transport, affinity and energy coupling are not established here.

Annotons

Bacillus NasA nitrate uptake

bacsu_uptake_activity

Participant: Gene Product: nasA (BACSU)

Gene Product:

nasA (BACSU)UniProtKB:P42432

Family:

Classification of BACSU nasAPANTHER:PTHR23515:SF2

Representative Members: nasA (BACSU)UniProtKB:P42432

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Function

nitrate transmembrane transporter activityGO:0015112

Substrates: nitrateCHEBI:17632

Products: nitrateCHEBI:17632

Cargo: nitrateCHEBI:17632

Source location: extracellular or periplasmic nitrate pool

Destination location: cytoplasmGO:0005737

Locations

plasma membraneGO:0005886

Bacillus NasA nitrate uptake

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

Native JH642-derived NasA loss supports nitrate uptake; it does not demonstrate a particular transport coupling mechanism or exclude incidental nitrite uptake.

NasA loss abolished nitrate growth despite retained nitrate reductase activity, supporting uptake.

PMID:7868621

The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.

Primary native genetics establishes the nasABCDEF nitrate/nitrite-assimilation system. Detailed polarity controls and artificial-donor limits are recorded separately from the cached abstract.

The isolation of the nasABCDEF genes of B. subtilis, which are required for nitrate/nitrite assimilation, is reported.

Part 2: reduction

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

Required within this species-native route.

Bacillus NasBC nitrate reductionReactionbacsu_nitrate_reduction

Use donor-generic GO:0008940 because the primary native nitrate assay used methyl viologen. Physiological NADH input is supported by the review and domain architecture, not a retrieved direct native donor-preference experiment.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

PMID:7868621

The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.

Primary native genetics establishes the nasABCDEF nitrate/nitrite-assimilation system. Detailed polarity controls and artificial-donor limits are recorded separately from the cached abstract.

The isolation of the nasABCDEF genes of B. subtilis, which are required for nitrate/nitrite assimilation, is reported.

Annotons

Bacillus NasBC nitrate reduction

bacsu_nitrate_reduction_activity

Participant: Protein Complex: Bacillus NasBC assimilatory nitrate reductase

Protein Complex:

Bacillus NasBC assimilatory nitrate reductase

Active units:

nasB

Participant: Gene Product: nasB (BACSU)

Gene Product:

nasB (BACSU)UniProtKB:P42433

Family:

Classification of BACSU nasBPANTHER:PTHR43429:SF3

Representative Members: nasB (BACSU)UniProtKB:P42433

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Role: Diaphorase electron-input component

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

file:BACSU/nasB/nasB-uniprot.txt

nasB-uniprot.txt

Curated database cross-reference places P42433 in PANTHER:PTHR43429:SF3; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR43429:SF3; NITRITE REDUCTASE [NAD(P)H]; 1.

nasC

Participant: Gene Product: nasC (BACSU)

Gene Product:

nasC (BACSU)UniProtKB:P42434

Family:

Classification of BACSU nasCPANTHER:PTHR43105:SF10

Representative Members: nasC (BACSU)UniProtKB:P42434

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Role: Molybdenum nitrate-reducing catalytic component

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

file:BACSU/nasC/nasC-uniprot.txt

nasC-uniprot.txt

Curated database cross-reference places P42434 in PANTHER:PTHR43105:SF10; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR43105:SF10; NADH-QUINONE OXIDOREDUCTASE SUBUNIT G; 1.

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Function

nitrate reductase activityGO:0008940

Substrates: nitrateCHEBI:17632 reduced electron donor; physiological NADH inferred

Products: nitriteCHEBI:16301 oxidized electron donor

Bacillus NasBC nitrate reduction

file:BACSU/nasB/nasB-source-analysis/native-nas-system.md

native-nas-system.md

NasB and NasC are both required for native assimilatory nitrate reduction after polarity controls. Primary assay donor was methyl viologen, not direct NADH kinetics.

NasB and NasC were independently required for nitrate utilization after downstream expression was restored.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC94119/

Prokaryotic Nitrate Reduction: Molecular Properties and Functional Distinction among Bacterial Nitrate Reductases

NasB supplies the diaphorase region and NasC the catalytic region. NADH is the review-level physiological interpretation; the module uses donor-generic GO:0008940 for this native complex.

In B. subtilis, the nasBC genes code for the NADH-nitrate reductase: NasB is a diaphorase with NADH- and FAD-binding domains, and NasC is the catalytic subunit.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

NasBC supplies the assimilatory upstream reaction during aerobic growth. Anaerobic respiratory NarGHJI is a different upstream input outside this route.

Our previous results showed that nitrate reductase encoded by nasB and nasC located upstream of the nasD gene functions only in nitrate assimilation during aerobic growth

PMID:7868621

The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis.

Primary native genetics establishes the nasABCDEF nitrate/nitrite-assimilation system. Detailed polarity controls and artificial-donor limits are recorded separately from the cached abstract.

The isolation of the nasABCDEF genes of B. subtilis, which are required for nitrate/nitrite assimilation, is reported.

Part 3: reduction

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Native NasDE activity is cytosolic. These assays concern JH642-derived strains in the 168 lineage.

No nitrite reductase activity was detected in the membrane fraction, whereas nearly all activity was present in the cytosolic fraction, indicating that the NasDE enzyme is a cytoplasmic protein.

Required within this species-native route.

Bacillus NasDE NADH-dependent nitrite reductionReactionbacsu_nitrite_reduction

Native lysate activity is predominantly NADH-dependent. The less-than-10% NADPH-supported signal cannot be assigned specifically to NasDE from this crude-extract assay. NasDE can also act downstream of respiratory NarGHJI anaerobically, outside this assimilatory NasBC route.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Native NasDE activity is cytosolic. These assays concern JH642-derived strains in the 168 lineage.

No nitrite reductase activity was detected in the membrane fraction, whereas nearly all activity was present in the cytosolic fraction, indicating that the NasDE enzyme is a cytoplasmic protein.

Annotons

Bacillus NasDE NADH-dependent nitrite reduction

bacsu_nitrite_reduction_activity

Participant: Protein Complex: Bacillus NasDE nitrite reductase

Protein Complex:

Bacillus NasDE nitrite reductase

Active units:

nasD

Participant: Gene Product: nasD (BACSU)

Gene Product:

nasD (BACSU)UniProtKB:P42435

Family:

Classification of BACSU nasDPANTHER:PTHR43809

Representative Members: nasD (BACSU)UniProtKB:P42435

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Role: Nitrite-reducing large component

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

file:BACSU/nasD/nasD-uniprot.txt

nasD-uniprot.txt

Curated database cross-reference places P42435 in PANTHER:PTHR43809; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR43809; NITRITE REDUCTASE (NADH) LARGE SUBUNIT; 1.

nasE

Participant: Gene Product: nasE (BACSU)

Gene Product:

nasE (BACSU)UniProtKB:P42436

Family:

Classification of BACSU nasEPANTHER:PTHR21496:SF23

Representative Members: nasE (BACSU)UniProtKB:P42436

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Role: Required small component of the native nitrite reductase

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

file:BACSU/nasE/nasE-uniprot.txt

nasE-uniprot.txt

Curated database cross-reference places P42436 in PANTHER:PTHR21496:SF23; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR21496:SF23; 3-PHENYLPROPIONATE_CINNAMIC ACID DIOXYGENASE FERREDOXIN SUBUNIT; 1.

Taxon:

Bacillus subtilis subsp. subtilis str. 168NCBITaxon:224308

Function

nitrite reductase (NADH) activityGO:0106316

Substrates: nitriteCHEBI:16301 NADH

Products: ammoniumCHEBI:28938 NAD+

Cofactors: siroheme iron-sulfur cluster

Locations

cytoplasmGO:0005737

Bacillus NasDE NADH-dependent nitrite reduction

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Both NasD and NasE are needed for native nitrite reductase activity, with downstream-expression controls. No exact oligomeric stoichiometry is established.

both nasD and nasE genes are required for enzyme activity.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Bacillus lysate nitrite-reductase activity is predominantly NADH-dependent. The minor NADPH-supported signal does not establish a NasDE-specific NADPH reaction.

Activity with NADPH was less than 10% of that with NADH.

PMID:9765565

Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE.

Native NasDE activity is cytosolic. These assays concern JH642-derived strains in the 168 lineage.

No nitrite reductase activity was detected in the membrane fraction, whereas nearly all activity was present in the cytosolic fraction, indicating that the NasDE enzyme is a cytoplasmic protein.

KT2440 PP_1703–NirBD routeMetabolic Pathwaypsepk_route

Native genetic/physiological support plus explicit fused-enzyme and NirBD-assembly inferences. No direct full-fusion donor preference, purified native NirBD assembly requirement or Y-9-to-KT2440 assay substitution is claimed.

Context

Pseudomonas putida KT2440NCBITaxon:160488

Intracellular nitrate input; extracellular input additionally requires the modeled native uptake step

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

Connections

psepk_uptake -> psepk_nitrate_reduction Provides Input For

The upstream step supplies nitrate consumed by the downstream step in the same organism.

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

No significant nitrite phenotype was detected for PP_2092; the source leaves redundant nitrite transport possible. The modeled uptake reaction is nitrate.

However, no significant phenotype could be detected for this gene in the nitrite condition, suggesting that it may be specific to nitrate.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00384; Molybdopterin; 1.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00175; NAD_binding_1; 1.

psepk_nitrate_reduction -> psepk_nitrite_reduction Provides Input For

The upstream step supplies nitrite consumed by the downstream step in the same organism.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00384; Molybdopterin; 1.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00175; NAD_binding_1; 1.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

The native lysate assay uses reduced methyl viologen; it does not discriminate NADH from NADPH as physiological input.

3 mM methyl viologen, 1 mM KNO2, 17 mM Na2S2O4

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02374; nitri_red_nirB; 1.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02378; nirD_assim_sml; 1.

Part 1: uptake (optional)

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

No significant nitrite phenotype was detected for PP_2092; the source leaves redundant nitrite transport possible. The modeled uptake reaction is nitrate.

However, no significant phenotype could be detected for this gene in the nitrite condition, suggesting that it may be specific to nitrate.

KT2440 PP_2092 NasA nitrate uptakeTransport Steppsepk_uptake

Fitness supports the uptake assignment, not a universal clean-knockout necessity or high-affinity kinetic claim. It is the uptake implementation required by this extracellular model, while alternative native transporters are not ruled out.

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

No significant nitrite phenotype was detected for PP_2092; the source leaves redundant nitrite transport possible. The modeled uptake reaction is nitrate.

However, no significant phenotype could be detected for this gene in the nitrite condition, suggesting that it may be specific to nitrate.

Annotons

KT2440 PP_2092 NasA nitrate uptake

psepk_uptake_activity

Participant: Gene Product: nasA (PSEPK)

Gene Product:

nasA (PSEPK)UniProtKB:Q88L43

Family:

Classification of PSEPK nasAPANTHER:PTHR23515

Representative Members: nasA (PSEPK)UniProtKB:Q88L43

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

nitrate transmembrane transporter activityGO:0015112

Substrates: nitrateCHEBI:17632

Products: nitrateCHEBI:17632

Cargo: nitrateCHEBI:17632

Source location: extracellular or periplasmic nitrate pool

Destination location: cytoplasmGO:0005737

Locations

plasma membraneGO:0005886

KT2440 PP_2092 NasA nitrate uptake

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

Native KT2440 pooled-mutant fitness supports PP_2092 nitrate uptake. This is not a clean deletion proving absolute transport necessity.

We were also able to identify a distinct nitrate transporter PP_2092 (−2.6).

PMID:35285712

Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.

No significant nitrite phenotype was detected for PP_2092; the source leaves redundant nitrite transport possible. The modeled uptake reaction is nitrate.

However, no significant phenotype could be detected for this gene in the nitrite condition, suggesting that it may be specific to nitrate.

Part 2: reduction

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00384; Molybdopterin; 1.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00175; NAD_binding_1; 1.

Required within this species-native route.

KT2440 PP_1703 NAD(P)H-linked nitrate reductionReactionpsepk_nitrate_reduction

The pyridine-nucleotide donor class is inferred from the fused reductase architecture and comparative biochemistry. The historical KT2442 fragment maps to the catalytic region only; native KT2440 NADPH preference, monomeric state and purified full-fusion kinetics are not established.

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00384; Molybdopterin; 1.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00175; NAD_binding_1; 1.

Annotons

KT2440 PP_1703 NAD(P)H-linked nitrate reduction

psepk_nitrate_reduction_activity

Participant: Gene Product: PP_1703 (PSEPK)

Gene Product:

PP_1703 (PSEPK)UniProtKB:Q88M71

Family:

Classification of PSEPK PP_1703PANTHER:PTHR43105:SF9

Representative Members: PP_1703 (PSEPK)UniProtKB:Q88M71

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

nitrate reductase [NAD(P)H] activityGO:0050463

Substrates: nitrateCHEBI:17632 NADH or NADPH

Products: nitriteCHEBI:16301 NAD+ or NADP+ (matching the input donor)

Cofactors: molybdenum-bis-molybdopterin guanine dinucleotide FMN FAD [4Fe-4S] cluster

KT2440 PP_1703 NAD(P)H-linked nitrate reduction

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC101894/?report=xml

Inactivation of gltB Abolishes Expression of the Assimilatory Nitrate Reductase Gene (nasB) in Pseudomonas putida KT2442

Historical KT2442 disruption/complementation supports an assimilatory nitrate-reductase catalytic region; the clone was not the full modern fusion.

In conclusion, these results clearly demonstrate that P. putida N25 bears the mini-Tn5 luxAB transposon within the assimilatory nitrate reductase.

file:PSEPK/PP_1703/PP_1703-source-analysis/README.md

README.md

The historic catalytic region maps exactly to Q88M71 residues 1–724, supporting target identity at that region without claiming a full-fusion biochemical assay.

AF203789 encodes 724 residues identical to Q88M71 residues 1–724.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00384; Molybdopterin; 1.

file:PSEPK/PP_1703/PP_1703-uniprot.txt

PP_1703-uniprot.txt

Q88M71 domain classification supports the fused molybdenum catalytic and pyridine-nucleotide electron-input architecture; NADPH preference is not established.

DR Pfam; PF00175; NAD_binding_1; 1.

file:PSEPK/PP_1703/PP_1703-source-analysis/RESULTS.md

Modern PP_1703 CDS check

Bacterial-code translation gives 1,341 residues and a terminal TGA, no internal stop, and exact identity to both AAN67324.2 and Q88M71.

Part 3: reduction

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

The native lysate assay uses reduced methyl viologen; it does not discriminate NADH from NADPH as physiological input.

3 mM methyl viologen, 1 mM KNO2, 17 mM Na2S2O4

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02374; nitri_red_nirB; 1.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02378; nirD_assim_sml; 1.

Required within this species-native route.

KT2440 NirBD NAD(P)H-linked nitrite reductionReactionpsepk_nitrite_reduction

Native expression/protein and lysate activity support the reaction. The reduced-methyl-viologen assay does not determine physiological NADH versus NADPH preference. Assembly and donor class are conserved-mechanism inferences; Y-9 experiments are not substituted for KT2440 assays.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

The native lysate assay uses reduced methyl viologen; it does not discriminate NADH from NADPH as physiological input.

3 mM methyl viologen, 1 mM KNO2, 17 mM Na2S2O4

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02374; nitri_red_nirB; 1.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02378; nirD_assim_sml; 1.

Annotons

KT2440 NirBD NAD(P)H-linked nitrite reduction

psepk_nitrite_reduction_activity

Participant: Protein Complex: KT2440 NirBD nitrite reductase

Protein Complex:

KT2440 NirBD nitrite reductase

Active units:

nirB

Participant: Gene Product: nirB (PSEPK)

Gene Product:

nirB (PSEPK)UniProtKB:Q88M69

Family:

Classification of PSEPK nirBPANTHER:PTHR43809

Representative Members: nirB (PSEPK)UniProtKB:Q88M69

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Role: Nitrite-reducing large component

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02374; nitri_red_nirB; 1.

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Curated database cross-reference places Q88M69 in PANTHER:PTHR43809; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR43809; NITRITE REDUCTASE (NADH) LARGE SUBUNIT; 1.

nirD

Participant: Gene Product: nirD (PSEPK)

Gene Product:

nirD (PSEPK)UniProtKB:Q88M68

Family:

Classification of PSEPK nirDPANTHER:PTHR40562

Representative Members: nirD (PSEPK)UniProtKB:Q88M68

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Role: Small component contributing to nitrite reduction

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02378; nirD_assim_sml; 1.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Curated database cross-reference places Q88M68 in PANTHER:PTHR40562; this is membership metadata for this exact target, not a family-wide functional claim.

DR PANTHER; PTHR40562; -; 1.

Taxon:

Pseudomonas putida KT2440NCBITaxon:160488

Function

nitrite reductase [NAD(P)H] activityGO:0008942

Substrates: nitriteCHEBI:16301 NADH or NADPH

Products: ammoniumCHEBI:28938 NAD+ or NADP+ (matching the input donor)

Cofactors: siroheme FAD [4Fe-4S] cluster

KT2440 NirBD NAD(P)H-linked nitrite reduction

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

Native KT2440 experiments support nirBD expression during nitrate assimilation and lysate nitrite reductase activity. They perturb NasT/c-di-GMP rather than individually reconstituting both subunits.

NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation.

PMID:38000372

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.

The native lysate assay uses reduced methyl viologen; it does not discriminate NADH from NADPH as physiological input.

3 mM methyl viologen, 1 mM KNO2, 17 mM Na2S2O4

file:PSEPK/nirB/nirB-uniprot.txt

nirB-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02374; nitri_red_nirB; 1.

file:PSEPK/nirD/nirD-uniprot.txt

nirD-uniprot.txt

Target-specific NirB/NirD classification supports its inferred role in the native nitrite reductase assembly.

DR NCBIfam; TIGR02378; nirD_assim_sml; 1.

mc2 155 NasN–NirBD intracellular routeMetabolic Pathwaymycs2_route

Intracellular nitrate input only. NasN is experimentally established; the downstream native NirB/MSMEG_0428 assembly is inferred from classification and nitrogen-limitation expression. This panel cannot satisfy an extracellular-nitrate uptake scenario.

Context

Mycolicibacterium smegmatis MC2 155NCBITaxon:246196

Intracellular nitrate input only; no nitrate uptake protein is included

file:modules/bacterial_assimilatory_nitrate_reduction-source-analysis/nasN-identity-proof.json

nasN-identity-proof.json

Corrected DQ866862 encodes the 1351-residue protein A4ZHT3 exactly; this resolves the MSMEG_4206/NasN identity and overrides the ARBA-only sulfite label.

"translation_exactly_matches_uniprot": true

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC7152768/?report=xml

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

Purified recombinant M. smegmatis NasN is a diflavin-containing monomeric nitrate reductase; native genetics establishes nitrate assimilation.

DOI:10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

the nitrite reductase NirBD enzyme is up regulated by GlnR in nitrogen limitation

file:modules/bacterial_assimilatory_nitrate_reduction-source-analysis/nasN-identity-proof.json

nasN-identity-proof.json

Corrected DQ866862 encodes the 1351-residue protein A4ZHT3 exactly; this resolves the MSMEG_4206/NasN identity and overrides the ARBA-only sulfite label.

"translation_exactly_matches_uniprot": true

url:https://pmc.ncbi.nlm.nih.gov/articles/PMC7152768/?report=xml

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

Purified recombinant M. smegmatis NasN is a diflavin-containing monomeric nitrate reductase; native genetics establishes nitrate assimilation.

DOI:10.1186/1471-2164-14-301

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

the nitrite reductase NirBD enzyme is up regulated by GlnR in nitrogen limitation

Connections

mycs2_nitrate_reduction -> mycs2_nitrite_reduction Provides Input For

The upstream step supplies nitrite consumed by the downstream step in the same organism.

file:modules/bacterial_assimilatory_nitrate_reduction-source-analysis/nasN-identity-proof.json

nasN-identity-proof.json

Corrected DQ866862 encodes the 1351-residue protein A4ZHT3 exactly; this resolves the MSMEG_4206/NasN identity and overrides the ARBA-only sulfite label.

"translation_exactly_matches_uniprot": true

PMID:33471823

Mycobacterium smegmatis does not display functional redundancy in nitrate reductase enzymes.

Independent native work reconciles the newer MSMEI_4108 locus with MSMEG_4206.

A BLAST search revealed that MSMEI_4108 corresponds to MSMEG_4206