nirK2

GO Term	Evidence	Action	Reason
GO:0005507 copper ion binding	IEA GO_REF:0000002	ACCEPT	Summary: ACCEPT. Copper binding is expected for a copper-containing nitrite reductase. Reason: nirK2 has the same conserved copper nitrite reductase architecture as bacterial NirK enzymes, including NO2-reductase_Cu/cupredoxin signatures and type 1 copper-site features. Falcon recovered RPA4145/nirK2 in comparative NirK literature but no purified nirK2 metal biochemistry. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt InterPro; IPR001287; NO2-reductase_Cu. file:RHOPA/nirK2/nirK2-deep-research-falcon.md Comparative NirK analyses include R. palustris CGA009 nirK2/RPA4145 with conserved copper-nitrite-reductase motifs.
GO:0016491 oxidoreductase activity	IEA GO_REF:0000118	KEEP AS NON CORE	Summary: KEEP_AS_NON_CORE. The annotation is correct but less informative than the specific nitrite reductase activity. Reason: Oxidoreductase activity is a true parent for the nitrite reductase reaction, but GO:0050421 captures the specific molecular function and should be treated as the core activity. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1.
GO:0042597 periplasmic space	IEA GO_REF:0000044	ACCEPT	Summary: ACCEPT. NirK-family nitrite reductases are periplasmic enzymes. Reason: UniProt predicts periplasmic localization and a signal peptide, consistent with exported bacterial copper nitrite reductase biology. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt SUBCELLULAR LOCATION: Periplasm. file:RHOPA/nirK2/nirK2-uniprot.txt SIGNAL 1..26
GO:0050421 nitrite reductase (NO-forming) activity	IEA GO_REF:0000120	ACCEPT	Summary: ACCEPT. This specific molecular function is consistent with the copper-containing nitrite reductase assignment. Reason: This is the precise EC-supported activity for the predicted enzyme. UniProt assigns EC 1.7.2.1 and both NCBIfam and PANTHER place the sequence in conserved multicopper/copper nitrite reductase families. The broad PTHR11709 family is functionally diverse, so the specific activity is justified by EC 1.7.2.1 plus TIGR02376/NO2-reductase_Cu rather than by multicopper oxidase membership alone. Falcon adds organism-level support: CGA009 cells grown with nitrite show detectable nitrite reductase activity and taxis toward nitrite, although those data are not a purified nirK2 assay. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1. file:RHOPA/nirK2/nirK2-uniprot.txt NCBIfam; TIGR02376; Cu_nitrite_red; 1. file:interpro/panther/PTHR11709/PTHR11709-deep-research-falcon.md PTHR11709 family research found multicopper oxidases are functionally diverse, so substrate-specific nitrite reductase activity requires specific EC/clade evidence. file:RHOPA/nirK2/nirK2-deep-research-falcon.md R. palustris CGA009 encodes nitrite reductase and NO-reductase genes, and nitrite-grown cells show detectable nitrite reductase activity, supporting physiological NO-forming nitrite reduction capacity.
GO:0019333 denitrification pathway	IEA GO_REF:0000041	ACCEPT	Summary: ACCEPT. UniPathway adds appropriate denitrification-pathway context for a NO-forming nitrite reductase. Reason: NO-forming nitrite reductase activity is the denitrification nitrite-to-NO step. The evidence is conserved EC/family inference plus UniProt pathway mapping. Falcon adds an important boundary: CGA009 encodes nitrite reductase and NO-reductase genes but lacked an obvious dissimilatory nitrate reductase in the cited genome survey, so this should be read as step-level denitrification/NOx pathway context rather than proof of a full nitrate-to-N2 route from nitrate. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4. file:RHOPA/nirK2/nirK2-deep-research-falcon.md CGA009 genome information indicates nitrite reductase and nitric oxide reductase capacity but no obvious dissimilatory nitrate reductase, supporting a nitrite/NOx segment rather than overclaiming complete nitrate respiration.

Deep Research

Falcon

(nirK2-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 37 citations 1 artifacts 2026-05-21T18:58:44.544062

Edison artifact artifact-00 (text/markdown)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional Annotation of nirK2 (UniProt Q6N2A5; locus RPA4145) in Rhodopseudomonas palustris CGA009

1. Target verification (gene/protein identity)

The research target is nirK2 / RPA4145 from Rhodopseudomonas palustris strain CGA009, corresponding to a copper-containing nitrite reductase (NirK; EC 1.7.2.1) as described in UniProt. Independent literature supports that R. palustris CGA009 encodes a nitrite reductase and that its NirK sequence is included in comparative NirK analyses with conserved copper-nitrite-reductase motifs, consistent with a multicopper oxidase-family CuNiR. (lee2002taxisresponseof pages 2-2, lee2002taxisresponseof pages 4-5, cantera2007moleculardiversityof pages 4-8)

2. Key concepts and definitions (current understanding)

2.1 Denitrification step catalyzed by NirK

Copper-containing nitrite reductase NirK (CuNiR/Cu-NIR) catalyzes the key denitrification transformation nitrite (NO2−) → nitric oxide (NO), a central NO-forming step in nitrogen-oxide respiration. (cua2010expressionofgenes pages 37-42)

2.2 Enzyme class and redundancy with NirS

Two evolutionarily unrelated enzymes can perform NO-forming nitrite reduction: NirK (multicopper oxidase-family) and NirS (cytochrome cd1). They are often treated as functionally redundant for denitrification, and are rarely encoded together in the same genome. (pold2024phylogeneticsandenvironmental pages 1-2, cua2010expressionofgenes pages 37-42)

2.3 Structural organization, cofactors, and active site architecture

CuNiRs are homotrimeric enzymes; each monomer contains two copper centers: a type 1 copper (T1Cu) redox center that accepts electrons from a partner protein, and a type 2 copper (T2Cu) catalytic center where nitrite binds and is reduced to NO. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, cua2010expressionofgenes pages 37-42)

2.4 Mechanistic model: electron and proton transfer

High-resolution structural/spectroscopic work supports a mechanism in which nitrite binds at T2Cu (often described as a side-on binding mode), and reduction proceeds via proton-coupled electron transfer (PCET) from T1Cu to T2Cu through a Cys–His bridge, with catalytic residues (including conserved His/Asp) supporting proton delivery and gating. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, rose2023spectroscopicallyvalidatedmultiple pages 3-5, rose2023spectroscopicallyvalidatedmultiple pages 12-14)

2.5 Cellular localization

A widely cited property of Cu-NIR/NirK is periplasmic localization in Gram-negative bacteria (extracytoplasmic nitrite reduction coupled to periplasmic electron transfer chains). The most defensible localization for R. palustris CGA009 NirK2 is therefore periplasmic, although a strain-specific localization experiment for RPA4145 was not retrieved in the available sources. (cua2010expressionofgenes pages 37-42)

3. Organism-specific functional context in R. palustris CGA009

3.1 Evidence for nitrite-reductase activity and associated NOx metabolism potential

In a study explicitly using R. palustris CGA009, genome-sequencing information was reported to indicate that this strain encodes nitrite reductase and genes necessary for expression of nitric oxide reductase, but has no obvious ortholog of a dissimilatory nitrate reductase. (lee2002taxisresponseof pages 2-2)

Consistent with this genetic potential, R. palustris CGA009 cells grown microaerobically in the presence of nitrite showed detectable nitrite reductase activity and exhibited taxis toward nitrite (behavior interpreted as accumulation in regions permissive for nitrite respiration). (lee2002taxisresponseof pages 4-5, lee2002taxisresponseof pages 5-7)

Functional implication for nirK2/Q6N2A5: the strongest organism-specific evidence supports physiological nitrite reduction capacity in CGA009 and positions NirK-type nitrite reductase activity as a likely contributor to NO formation and NOx-responsive physiology under low-oxygen + nitrite conditions. (lee2002taxisresponseof pages 4-5, lee2002taxisresponseof pages 2-2)

3.2 Substrate specificity

The enzyme class definition and mechanistic evidence support nitrite (NO2−) as the substrate at the catalytic T2Cu site, with product NO. No evidence in the retrieved CGA009-specific literature suggested an alternative substrate specificity for NirK2 beyond canonical nitrite reduction. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, cua2010expressionofgenes pages 37-42, lee2002taxisresponseof pages 4-5)

4. Regulation and pathway integration (expert synthesis)

4.1 NO-responsive transcriptional control context

Comparative promoter analyses of nirK emphasize that Alphaproteobacterial nirK genes frequently show motifs associated with NnrR-family NO-responsive regulation, and note that in Rhodobacter sphaeroides NnrR requires NO as an effector to induce nirK expression. (cantera2007moleculardiversityof pages 9-10, cantera2007moleculardiversityof pages 4-8)

Interpretation for R. palustris nirK2: while direct promoter mapping/TF-binding experiments for RPA4145 were not retrieved here, the combination of (i) CGA009 encoding nitrite reductase and NO reductase genes and (ii) the broader Alphaproteobacterial association of nirK with NnrR-like NO-responsive control supports the working hypothesis that nirK2 participates in an NOx-responsive regulatory module (often centered around NnrR-like transcription factors) that couples nitrite reduction and downstream NO metabolism. (lee2002taxisresponseof pages 2-2, cantera2007moleculardiversityof pages 9-10)

4.2 Genomic neighborhood (limits of current evidence)

Across bacteria, nirK genes can occur in operonic contexts that include cytochrome c and c-type cytochrome biogenesis genes or other redox partners, consistent with periplasmic electron transfer requirements. However, a direct operon map for RPA4145 was not recoverable from the available excerpts; therefore, neighborhood statements for R. palustris nirK2 should be treated as inference from common NirK contexts rather than demonstrated facts for this locus. (cantera2007moleculardiversityof pages 8-9, starkenburg2008aninvestigationof pages 31-34)

5. Recent developments (prioritizing 2023–2024)

5.1 Structural and mechanistic advances (2023)

A 2023 crystallography/spectroscopy study used MSOX serial crystallography with in-crystal optical spectroscopy (and referenced damage-reduced/XFEL models) to connect T1Cu redox changes to catalytic chemistry at T2Cu. Key recent mechanistic insights include:
- Explicit two-copper-site description (T1Cu electron-entry; T2Cu nitrite-binding/catalytic center). (rose2023spectroscopicallyvalidatedmultiple pages 1-3)
- pH dependence of activity via proton availability and PCET efficiency, including changes in proton-channel water ordering and catalytic Asp behavior. (rose2023spectroscopicallyvalidatedmultiple pages 3-5, rose2023spectroscopicallyvalidatedmultiple pages 12-14)
These results refine contemporary understanding of how CuNiRs couple electron transfer to proton delivery during nitrite-to-NO reduction. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, rose2023spectroscopicallyvalidatedmultiple pages 12-14)

Publication: Rose et al., 2023-08, Acta Crystallographica Section A, DOI/URL: https://doi.org/10.1107/S2053273323094627. (rose2023spectroscopicallyvalidatedmultiple pages 1-3)

5.2 Ecological/phylogenomic reframing of NirK vs NirS (2024)

A 2024 study built robust phylogenies of NirK and NirS from 6,973 isolate and metagenome-assembled genomes, identified 32 clades of structurally distinct lineages, and mapped relative abundances across 4,082 metagenomes from diverse biomes. This work shows that:
- Nir phylogeny can reflect ecology and functional gene associations differently from organismal phylogeny, suggesting convergent/independent niche associations for nitrite reduction capacity. (pold2024phylogeneticsandenvironmental pages 1-2)
- NirK lineages exhibit clade-specific associations and biome enrichments (e.g., some clades enriched in nitrate-rich oxygen-poor waters; others in sewage), supporting the idea that the “nirK gene” label hides substantial functional/ecological diversity. (pold2024phylogeneticsandenvironmental pages 5-8)

Publication: Pold et al., 2024-01, ISME Communications, DOI/URL: https://doi.org/10.1093/ismeco/ycae020. (pold2024phylogeneticsandenvironmental pages 1-2)

6. Current applications and real-world implementations (with data)

6.1 nirK as a biomarker in wastewater treatment plant (WWTP) monitoring

In activated sludge across four WWTPs, GeoChip 4.2 detected 2,055 nitrogen-cycling genes and specifically detected 184 nirK genes, with 62 nirK genes present in all samples. nirK abundance correlated positively with influent nitrogen variables (influent TN: r = 0.421, P < 0.01; ammonia: r = 0.358, P < 0.05), illustrating routine real-world use of nirK as a functional marker linking community potential to operational chemistry. (wang2014microbialcommunityfunctional pages 3-5)

Publication: Wang et al., 2014-03, PLoS ONE, DOI/URL: https://doi.org/10.1371/journal.pone.0093422. (wang2014microbialcommunityfunctional pages 3-5)

6.2 nirK detection and activity inference in stratified freshwater systems

In a subtropical deep reservoir oxygen-minimum zone study, nirK was assessed via clone libraries and qPCR/RT-qPCR approaches. The authors report 69 nirK clones forming 24 OTUs (97% similarity), and infer low activity via an RNA:DNA ratio for nirK of 0.0076 ± 0.001, with gene abundance/activity ranking narG > nirS > nirK > nosZ. This exemplifies common field implementation of nirK to track denitrifier/nitrite-reducer community structure and potential activity. (yu2014denitrifiercommunityin pages 3-4)

Publication: Yu et al., 2014-03, PLoS ONE, DOI/URL: https://doi.org/10.1371/journal.pone.0092055. (yu2014denitrifiercommunityin pages 3-4)

7. Expert synthesis for functional annotation of R. palustris CGA009 NirK2 (Q6N2A5)

Primary molecular function: copper-containing nitrite reductase (EC 1.7.2.1) that reduces NO2− to NO at a T2Cu catalytic site, receiving electrons via a T1Cu redox site and coupling electron transfer to proton delivery (PCET). (rose2023spectroscopicallyvalidatedmultiple pages 1-3, cua2010expressionofgenes pages 37-42)

Biological process / pathway: nitrogen-oxide respiration/denitrification segment centered on NO formation from nitrite; in CGA009, available evidence supports nitrite reduction capability and suggests downstream NO metabolism potential (NO reductase genes reported), even though a canonical dissimilatory nitrate reductase ortholog was not evident in the referenced genome survey. (lee2002taxisresponseof pages 2-2, lee2002taxisresponseof pages 4-5)

Cellular localization: most consistent with periplasmic CuNiR localization and periplasmic electron-transfer coupling; direct localization data for RPA4145 were not retrieved and should be treated as an evidence gap. (cua2010expressionofgenes pages 37-42)

Regulation: likely embedded in NO-responsive regulatory logic characteristic of Alphaproteobacterial nirK systems (NnrR-family associations), but experimental validation of RPA4145-specific regulation remains limited in the retrieved corpus. (cantera2007moleculardiversityof pages 9-10)

8. Evidence summary table

The following evidence map consolidates annotation-relevant statements and supporting sources (including publication dates and URLs).

Annotation aspect	Best-supported statement	Key evidence sources with year and DOI/URL
Identity	The target is the Rhodopseudomonas palustris CGA009 copper-containing nitrite reductase annotated as nirK2 / RPA4145 / UniProt Q6N2A5; literature on R. palustris explicitly refers to nirK2 (RPA4145), and comparative NirK analyses include the CGA009 sequence with conserved CuNIR motifs, supporting that this is the correct gene/protein rather than a different nirK homolog from another organism. (cantera2007moleculardiversityof pages 4-8)	Cantera & Stein 2007, Environ Microbiol; DOI: https://doi.org/10.1111/j.1462-2920.2006.01198.x
Enzyme class	NirK proteins are multicopper oxidase-family nitric-oxide-forming nitrite reductases (CuNiR/Cu-NIR) that are functionally equivalent to NirS in catalyzing nitrite-to-NO conversion, although NirK and NirS are evolutionarily unrelated and rarely coexist in the same genome. (cua2010expressionofgenes pages 37-42, pold2024phylogeneticsandenvironmental pages 1-2)	Cua 2010; Pold et al. 2024, ISME Commun. DOI: https://doi.org/10.1093/ismeco/ycae020
Reaction	The primary catalytic role is the one-electron reduction of nitrite (NO2−) to nitric oxide (NO), the central NO-forming step of denitrification/nitrogen-oxide metabolism. In R. palustris CGA009, genomic and physiological data indicate presence of nitrite reductase activity but no obvious dissimilatory nitrate reductase ortholog. (cua2010expressionofgenes pages 37-42, lee2002taxisresponseof pages 4-5, lee2002taxisresponseof pages 2-2)	Lee et al. 2002, Appl Environ Microbiol; DOI: https://doi.org/10.1128/AEM.68.5.2140-2147.2002; Cua 2010
Cofactors / active sites	Canonical CuNiRs are homotrimers; each monomer contains a type 1 Cu (T1Cu) electron-entry center and a type 2 Cu (T2Cu) catalytic nitrite-binding center. Comparative NirK analyses also highlight conserved Cu-binding motifs and catalytic residues in R. palustris-containing datasets. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, cua2010expressionofgenes pages 37-42, cantera2007moleculardiversityof pages 4-8)	Rose et al. 2023, Acta Cryst A; DOI: https://doi.org/10.1107/S2053273323094627; Cantera & Stein 2007, DOI above
Mechanism highlights	Nitrite binds at T2Cu, and reduction to NO proceeds by proton-coupled electron transfer (PCET) from T1Cu to T2Cu through a Cys-His bridge; catalytic His/Asp residues help proton delivery, and 2023 structural work resolved pH-dependent nitrite binding, proton channels, copper–nitrosyl intermediate formation, and NO release. (rose2023spectroscopicallyvalidatedmultiple pages 1-3, rose2023spectroscopicallyvalidatedmultiple pages 9-11, rose2023spectroscopicallyvalidatedmultiple pages 3-5, rose2023spectroscopicallyvalidatedmultiple pages 12-14)	Rose et al. 2023, Acta Cryst A; DOI: https://doi.org/10.1107/S2053273323094627
Localization	Cu-NIR/NirK enzymes are generally periplasmic trimeric enzymes. Thus, the best-supported localization for R. palustris nirK2 is periplasmic/extracytoplasmic, based on conserved CuNiR class properties rather than a CGA009-specific localization experiment. (cua2010expressionofgenes pages 37-42)	Cua 2010
Pathway context in CGA009	In R. palustris CGA009, genome-based statements in Lee et al. indicate the organism encodes nitrite reductase and genes necessary for nitric oxide reductase expression but lacks an obvious dissimilatory nitrate reductase ortholog; physiologically, nitrite-grown cells showed detectable nitrite reductase activity and taxis toward nitrite, consistent with nitrite respiration/NOx metabolism rather than full canonical nitrate-to-N2 denitrification. (lee2002taxisresponseof pages 4-5, lee2002taxisresponseof pages 2-2, lee2002taxisresponseof pages 5-7)	Lee et al. 2002, Appl Environ Microbiol; DOI: https://doi.org/10.1128/AEM.68.5.2140-2147.2002
Regulation	Direct CGA009 nirK2 regulation is not well resolved in the retrieved organism-specific evidence, but nirK promoters in Alphaproteobacteria commonly carry NnrR-related NO-responsive regulatory motifs, and comparative work notes NnrR/DNR/NsrR motif analysis for R. palustris-containing nirK datasets. This supports probable NO-responsive regulation by an NnrR-like system, but species-specific experimental confirmation for nirK2 remains limited here. (cantera2007moleculardiversityof pages 4-8, cantera2007moleculardiversityof pages 9-10)	Cantera & Stein 2007, Environ Microbiol; DOI: https://doi.org/10.1111/j.1462-2920.2006.01198.x
Gene neighborhood / inference	NirK genes can occur with cytochrome c and cytochrome-c-biogenesis genes or other redox partners in operons/clusters, supporting electron-transfer coupling in the periplasm. For CGA009 nirK2 specifically, strong direct neighborhood evidence was limited in the retrieved excerpts, so neighborhood assignment should be treated as bioinformatic inference from NirK contexts rather than direct proof for RPA4145. (cantera2007moleculardiversityof pages 8-9, starkenburg2008aninvestigationof pages 31-34)	Cantera & Stein 2007, Environ Microbiol; DOI: https://doi.org/10.1111/j.1462-2920.2006.01198.x; Starkenburg 2008
Recent (2023–2024) developments	Recent work substantially updated NirK interpretation: Rose 2023 provided damage-reduced structural/spectroscopic snapshots of CuNiR catalysis and pH dependence, while Pold 2024 reconstructed Nir phylogenies from 6,973 genomes, identified 32 clades, analyzed 6,422 full-length NirK sequences, and mapped distributions across 4,082 metagenomes, showing that NirK ecology/traits vary strongly by clade and biome. (pold2024phylogeneticsandenvironmental pages 1-2, pold2024phylogeneticsandenvironmental pages 5-8, rose2023spectroscopicallyvalidatedmultiple pages 1-3, rose2023spectroscopicallyvalidatedmultiple pages 12-14)	Rose et al. 2023, DOI above; Pold et al. 2024, ISME Commun. DOI: https://doi.org/10.1093/ismeco/ycae020
Applications / monitoring stats	nirK is widely used as a monitoring marker for denitrifying communities in engineered and natural systems. In activated sludge from four WWTPs, GeoChip detected 2,055 nitrogen-cycling genes, including 184 nirK genes, with 62 present in all samples; nirK abundance correlated with influent TN (r=0.421, P<0.01) and ammonia (r=0.358, P<0.05). In a reservoir oxygen-minimum zone, 69 nirK clones formed 24 OTUs, and nirK showed an RNA:DNA ratio of 0.0076 ± 0.001, with abundance/activity ranking narG > nirS > nirK > nosZ. (wang2014microbialcommunityfunctional pages 3-5, yu2014denitrifiercommunityin pages 3-4, yu2014denitrifiercommunityin pages 2-3)	Wang et al. 2014, PLoS ONE; DOI: https://doi.org/10.1371/journal.pone.0093422; Yu et al. 2014, PLoS ONE; DOI: https://doi.org/10.1371/journal.pone.0092055

Table: This table summarizes the best-supported functional annotation for Rhodopseudomonas palustris CGA009 nirK2/RPA4145/Q6N2A5, combining organism-specific evidence with authoritative CuNiR background and recent 2023–2024 advances. It is useful as a concise evidence map for function, pathway role, localization, regulation, and real-world monitoring relevance.

9. Key limitations of the current evidence set

Direct nirK2 (RPA4145) operon/neighborhood mapping and strain-specific subcellular localization experiments were not captured in the retrieved excerpts; statements on these points remain inference-based and should be verified by targeted genome-neighborhood inspection and signal peptide/periplasmic export prediction for Q6N2A5, or by experimental fractionation/proteomics. (starkenburg2008aninvestigationof pages 31-34, cua2010expressionofgenes pages 37-42)
The 2009 book chapter was retrieved in fragments that did not yield the referenced nirK2/nnrR discussion in extractable text; therefore it could not be used as primary evidence for gene adjacency in this report.

10. Core references (URLs and publication dates)

Rose SL et al. 2023-08. Acta Crystallographica Section A. “Spectroscopically validated multiple structures… for copper nitrite reductases.” https://doi.org/10.1107/S2053273323094627 (rose2023spectroscopicallyvalidatedmultiple pages 1-3)
Pold G et al. 2024-01. ISME Communications. “Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases…” https://doi.org/10.1093/ismeco/ycae020 (pold2024phylogeneticsandenvironmental pages 1-2)
Lee DY et al. 2002-05. Applied and Environmental Microbiology. “Taxis response of various denitrifying bacteria to nitrate and nitrite.” https://doi.org/10.1128/AEM.68.5.2140-2147.2002 (lee2002taxisresponseof pages 4-5)
Cantera JJL, Stein LY. 2007-03. Environmental Microbiology. “Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria.” https://doi.org/10.1111/j.1462-2920.2006.01198.x (cantera2007moleculardiversityof pages 4-8)
Wang X et al. 2014-03. PLoS ONE. “Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.” https://doi.org/10.1371/journal.pone.0093422 (wang2014microbialcommunityfunctional pages 3-5)
Yu Z et al. 2014-03. PLoS ONE. “Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir.” https://doi.org/10.1371/journal.pone.0092055 (yu2014denitrifiercommunityin pages 3-4)

References

(lee2002taxisresponseof pages 2-2): Dong Yun Lee, Adela Ramos, Lee Macomber, and James P. Shapleigh. Taxis response of various denitrifying bacteria to nitrate and nitrite. Applied and Environmental Microbiology, 68:2140-2147, May 2002. URL: https://doi.org/10.1128/aem.68.5.2140-2147.2002, doi:10.1128/aem.68.5.2140-2147.2002. This article has 63 citations and is from a peer-reviewed journal.
(lee2002taxisresponseof pages 4-5): Dong Yun Lee, Adela Ramos, Lee Macomber, and James P. Shapleigh. Taxis response of various denitrifying bacteria to nitrate and nitrite. Applied and Environmental Microbiology, 68:2140-2147, May 2002. URL: https://doi.org/10.1128/aem.68.5.2140-2147.2002, doi:10.1128/aem.68.5.2140-2147.2002. This article has 63 citations and is from a peer-reviewed journal.
(cantera2007moleculardiversityof pages 4-8): J. Jason L. Cantera and Lisa Y. Stein. Molecular diversity of nitrite reductase genes (nirk) in nitrifying bacteria. Environmental microbiology, 9 3:765-76, Mar 2007. URL: https://doi.org/10.1111/j.1462-2920.2006.01198.x, doi:10.1111/j.1462-2920.2006.01198.x. This article has 170 citations and is from a domain leading peer-reviewed journal.
(cua2010expressionofgenes pages 37-42): L Cua. Expression of genes linked to nox detoxification in aerobic bacteria. Unknown journal, 2010.
(pold2024phylogeneticsandenvironmental pages 1-2): Grace Pold, Germán Bonilla-Rosso, Aurélien Saghaï, Marc Strous, Christopher M Jones, and Sara Hallin. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME Communications, Jan 2024. URL: https://doi.org/10.1093/ismeco/ycae020, doi:10.1093/ismeco/ycae020. This article has 26 citations and is from a peer-reviewed journal.
(rose2023spectroscopicallyvalidatedmultiple pages 1-3): Samuel L. Rose, Svetlana V. Antonyuk, Robert R. Eady, Felix Ferroni, Takehiko Tosha, Masaki Yamamoto, Samuel Horrell, Robin Owen, and S. Samar Hasnain. Spectroscopically validated multiple structures from one crystal (msox) and damage-free atomic structures using xfel for copper nitrite reductases. Acta Crystallographica Section A Foundations and Advances, 79:C147-C147, Aug 2023. URL: https://doi.org/10.1107/s2053273323094627, doi:10.1107/s2053273323094627. This article has 0 citations.
(rose2023spectroscopicallyvalidatedmultiple pages 3-5): Samuel L. Rose, Svetlana V. Antonyuk, Robert R. Eady, Felix Ferroni, Takehiko Tosha, Masaki Yamamoto, Samuel Horrell, Robin Owen, and S. Samar Hasnain. Spectroscopically validated multiple structures from one crystal (msox) and damage-free atomic structures using xfel for copper nitrite reductases. Acta Crystallographica Section A Foundations and Advances, 79:C147-C147, Aug 2023. URL: https://doi.org/10.1107/s2053273323094627, doi:10.1107/s2053273323094627. This article has 0 citations.
(rose2023spectroscopicallyvalidatedmultiple pages 12-14): Samuel L. Rose, Svetlana V. Antonyuk, Robert R. Eady, Felix Ferroni, Takehiko Tosha, Masaki Yamamoto, Samuel Horrell, Robin Owen, and S. Samar Hasnain. Spectroscopically validated multiple structures from one crystal (msox) and damage-free atomic structures using xfel for copper nitrite reductases. Acta Crystallographica Section A Foundations and Advances, 79:C147-C147, Aug 2023. URL: https://doi.org/10.1107/s2053273323094627, doi:10.1107/s2053273323094627. This article has 0 citations.
(lee2002taxisresponseof pages 5-7): Dong Yun Lee, Adela Ramos, Lee Macomber, and James P. Shapleigh. Taxis response of various denitrifying bacteria to nitrate and nitrite. Applied and Environmental Microbiology, 68:2140-2147, May 2002. URL: https://doi.org/10.1128/aem.68.5.2140-2147.2002, doi:10.1128/aem.68.5.2140-2147.2002. This article has 63 citations and is from a peer-reviewed journal.
(cantera2007moleculardiversityof pages 9-10): J. Jason L. Cantera and Lisa Y. Stein. Molecular diversity of nitrite reductase genes (nirk) in nitrifying bacteria. Environmental microbiology, 9 3:765-76, Mar 2007. URL: https://doi.org/10.1111/j.1462-2920.2006.01198.x, doi:10.1111/j.1462-2920.2006.01198.x. This article has 170 citations and is from a domain leading peer-reviewed journal.
(cantera2007moleculardiversityof pages 8-9): J. Jason L. Cantera and Lisa Y. Stein. Molecular diversity of nitrite reductase genes (nirk) in nitrifying bacteria. Environmental microbiology, 9 3:765-76, Mar 2007. URL: https://doi.org/10.1111/j.1462-2920.2006.01198.x, doi:10.1111/j.1462-2920.2006.01198.x. This article has 170 citations and is from a domain leading peer-reviewed journal.
(starkenburg2008aninvestigationof pages 31-34): SR Starkenburg. An investigation of carbon and nitrogen metabolism through a genomic analysis of the genus nitrobacter. Unknown journal, 2008.
(pold2024phylogeneticsandenvironmental pages 5-8): Grace Pold, Germán Bonilla-Rosso, Aurélien Saghaï, Marc Strous, Christopher M Jones, and Sara Hallin. Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles. ISME Communications, Jan 2024. URL: https://doi.org/10.1093/ismeco/ycae020, doi:10.1093/ismeco/ycae020. This article has 26 citations and is from a peer-reviewed journal.
(wang2014microbialcommunityfunctional pages 3-5): Xiaohui Wang, Yu Xia, Xianghua Wen, Yunfeng Yang, and Jizhong Zhou. Microbial community functional structures in wastewater treatment plants as characterized by geochip. PLoS ONE, 9:e93422, Mar 2014. URL: https://doi.org/10.1371/journal.pone.0093422, doi:10.1371/journal.pone.0093422. This article has 83 citations and is from a peer-reviewed journal.
(yu2014denitrifiercommunityin pages 3-4): Zheng Yu, Jun Yang, and Lemian Liu. Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir. PLoS ONE, 9:e92055, Mar 2014. URL: https://doi.org/10.1371/journal.pone.0092055, doi:10.1371/journal.pone.0092055. This article has 51 citations and is from a peer-reviewed journal.
(rose2023spectroscopicallyvalidatedmultiple pages 9-11): Samuel L. Rose, Svetlana V. Antonyuk, Robert R. Eady, Felix Ferroni, Takehiko Tosha, Masaki Yamamoto, Samuel Horrell, Robin Owen, and S. Samar Hasnain. Spectroscopically validated multiple structures from one crystal (msox) and damage-free atomic structures using xfel for copper nitrite reductases. Acta Crystallographica Section A Foundations and Advances, 79:C147-C147, Aug 2023. URL: https://doi.org/10.1107/s2053273323094627, doi:10.1107/s2053273323094627. This article has 0 citations.
(yu2014denitrifiercommunityin pages 2-3): Zheng Yu, Jun Yang, and Lemian Liu. Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir. PLoS ONE, 9:e92055, Mar 2014. URL: https://doi.org/10.1371/journal.pone.0092055, doi:10.1371/journal.pone.0092055. This article has 51 citations and is from a peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

cua2010expressionofgenes pages 37-42
lee2002taxisresponseof pages 2-2
rose2023spectroscopicallyvalidatedmultiple pages 1-3
pold2024phylogeneticsandenvironmental pages 1-2
pold2024phylogeneticsandenvironmental pages 5-8
wang2014microbialcommunityfunctional pages 3-5
yu2014denitrifiercommunityin pages 3-4
cantera2007moleculardiversityof pages 9-10
cantera2007moleculardiversityof pages 4-8
lee2002taxisresponseof pages 4-5
rose2023spectroscopicallyvalidatedmultiple pages 3-5
rose2023spectroscopicallyvalidatedmultiple pages 12-14
lee2002taxisresponseof pages 5-7
cantera2007moleculardiversityof pages 8-9
starkenburg2008aninvestigationof pages 31-34
rose2023spectroscopicallyvalidatedmultiple pages 9-11
yu2014denitrifiercommunityin pages 2-3
https://doi.org/10.1107/S2053273323094627.
https://doi.org/10.1093/ismeco/ycae020.
https://doi.org/10.1371/journal.pone.0093422.
https://doi.org/10.1371/journal.pone.0092055.
https://doi.org/10.1111/j.1462-2920.2006.01198.x
https://doi.org/10.1093/ismeco/ycae020
https://doi.org/10.1128/AEM.68.5.2140-2147.2002;
https://doi.org/10.1107/S2053273323094627;
https://doi.org/10.1107/S2053273323094627
https://doi.org/10.1128/AEM.68.5.2140-2147.2002
https://doi.org/10.1111/j.1462-2920.2006.01198.x;
https://doi.org/10.1371/journal.pone.0093422;
https://doi.org/10.1371/journal.pone.0092055
https://doi.org/10.1371/journal.pone.0093422
https://doi.org/10.1128/aem.68.5.2140-2147.2002,
https://doi.org/10.1111/j.1462-2920.2006.01198.x,
https://doi.org/10.1093/ismeco/ycae020,
https://doi.org/10.1107/s2053273323094627,
https://doi.org/10.1371/journal.pone.0093422,
https://doi.org/10.1371/journal.pone.0092055,

📄 View Raw YAML

id: Q6N2A5
gene_symbol: nirK2
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:258594
  label: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
description: >-
  nirK2 encodes a second predicted copper-containing nitrite reductase in
  Rhodopseudomonas palustris CGA009. The UniProt/GOA profile supports
  NO-forming nitrite reductase activity; organism-level evidence supports
  nitrite reduction and NOx metabolism in CGA009, even though a dissimilatory
  nitrate reductase was not evident in the cited genome survey.
existing_annotations:
- term:
    id: GO:0005507
    label: copper ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      ACCEPT. Copper binding is expected for a copper-containing nitrite
      reductase.
    action: ACCEPT
    reason: >-
      nirK2 has the same conserved copper nitrite reductase architecture as
      bacterial NirK enzymes, including NO2-reductase_Cu/cupredoxin signatures
      and type 1 copper-site features. Falcon recovered RPA4145/nirK2 in
      comparative NirK literature but no purified nirK2 metal biochemistry.
    supported_by:
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: InterPro; IPR001287; NO2-reductase_Cu.
    - reference_id: file:RHOPA/nirK2/nirK2-deep-research-falcon.md
      supporting_text: >-
        Comparative NirK analyses include R. palustris CGA009 nirK2/RPA4145
        with conserved copper-nitrite-reductase motifs.
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: >-
      KEEP_AS_NON_CORE. The annotation is correct but less informative than the
      specific nitrite reductase activity.
    action: KEEP_AS_NON_CORE
    reason: >-
      Oxidoreductase activity is a true parent for the nitrite reductase
      reaction, but GO:0050421 captures the specific molecular function and
      should be treated as the core activity.
    supported_by:
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: 'RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1.'
- term:
    id: GO:0042597
    label: periplasmic space
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      ACCEPT. NirK-family nitrite reductases are periplasmic enzymes.
    action: ACCEPT
    reason: >-
      UniProt predicts periplasmic localization and a signal peptide, consistent
      with exported bacterial copper nitrite reductase biology.
    supported_by:
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Periplasm.'
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: SIGNAL          1..26
- term:
    id: GO:0050421
    label: nitrite reductase (NO-forming) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      ACCEPT. This specific molecular function is consistent with the
      copper-containing nitrite reductase assignment.
    action: ACCEPT
    reason: >-
      This is the precise EC-supported activity for the predicted enzyme.
      UniProt assigns EC 1.7.2.1 and both NCBIfam and PANTHER place the sequence
      in conserved multicopper/copper nitrite reductase families. The broad
      PTHR11709 family is functionally diverse, so the specific activity is
      justified by EC 1.7.2.1 plus TIGR02376/NO2-reductase_Cu rather than by
      multicopper oxidase membership alone. Falcon adds organism-level support:
      CGA009 cells grown with nitrite show detectable nitrite reductase activity
      and taxis toward nitrite, although those data are not a purified nirK2
      assay.
    supported_by:
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: 'RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1.'
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: NCBIfam; TIGR02376; Cu_nitrite_red; 1.
    - reference_id: file:interpro/panther/PTHR11709/PTHR11709-deep-research-falcon.md
      supporting_text: >-
        PTHR11709 family research found multicopper oxidases are functionally
        diverse, so substrate-specific nitrite reductase activity requires
        specific EC/clade evidence.
    - reference_id: file:RHOPA/nirK2/nirK2-deep-research-falcon.md
      supporting_text: >-
        R. palustris CGA009 encodes nitrite reductase and NO-reductase genes,
        and nitrite-grown cells show detectable nitrite reductase activity,
        supporting physiological NO-forming nitrite reduction capacity.
- term:
    id: GO:0019333
    label: denitrification pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: >-
      ACCEPT. UniPathway adds appropriate denitrification-pathway context for a
      NO-forming nitrite reductase.
    action: ACCEPT
    reason: >-
      NO-forming nitrite reductase activity is the denitrification nitrite-to-NO
      step. The evidence is conserved EC/family inference plus UniProt pathway
      mapping. Falcon adds an important boundary: CGA009 encodes nitrite
      reductase and NO-reductase genes but lacked an obvious dissimilatory
      nitrate reductase in the cited genome survey, so this should be read as
      step-level denitrification/NOx pathway context rather than proof of a full
      nitrate-to-N2 route from nitrate.
    supported_by:
    - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
      supporting_text: 'PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4.'
    - reference_id: file:RHOPA/nirK2/nirK2-deep-research-falcon.md
      supporting_text: >-
        CGA009 genome information indicates nitrite reductase and nitric oxide
        reductase capacity but no obvious dissimilatory nitrate reductase,
        supporting a nitrite/NOx segment rather than overclaiming complete
        nitrate respiration.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB Subcellular Location vocabulary mapping
  findings: []
- id: GO_REF:0000118
  title: Manual transfer of experimentally verified manual GO annotation data to orthologs by Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:RHOPA/nirK2/nirK2-uniprot.txt
  title: UniProt record for nirK2
  findings:
  - statement: >-
      UniProt/GOA support a copper nitrite reductase assignment for Q6N2A5.
- id: file:interpro/panther/PTHR11709/PTHR11709-deep-research-falcon.md
  title: Falcon family deep research for PTHR11709 multicopper oxidases
  findings:
  - statement: >-
      Family research supports a cautious evolutionary interpretation: the
      multicopper oxidase family is broad, but nirK2 has additional
      NO2-reductase_Cu, TIGR02376, and EC evidence for NO-forming nitrite
      reductase activity.
- id: file:RHOPA/nirK2/nirK2-deep-research-falcon.md
  title: Falcon deep research for nirK2
  findings:
  - statement: >-
      Falcon deep research for nirK2 verifies RPA4145/nirK2 in R. palustris
      CGA009 NirK literature and supports NO-forming CuNIR activity. It also
      found organism-level nitrite reductase activity and nitrite taxis in
      CGA009, while noting the cited genome survey found no obvious
      dissimilatory nitrate reductase.
core_functions:
- description: >-
    Catalyzes NO-forming nitrite reduction as part of bacterial denitrification.
  molecular_function:
    id: GO:0050421
    label: nitrite reductase (NO-forming) activity
  directly_involved_in:
  - id: GO:0019333
    label: denitrification pathway
  supported_by:
  - reference_id: file:RHOPA/nirK2/nirK2-uniprot.txt
    supporting_text: >-
      UniProt/GOA identify Q6N2A5 as a nitrite reductase family protein with
      nitrite reductase (NO-forming) activity.
  - reference_id: file:RHOPA/nirK2/nirK2-deep-research-falcon.md
    supporting_text: >-
      Falcon deep research supports nitrite reductase (NO-forming) activity and
      step-level denitrification/NOx pathway context for nirK2, while avoiding
      an overclaim that CGA009 necessarily carries a complete nitrate-to-N2
      denitrification chain.

Gene Description

Existing Annotations Review

Core Functions

Catalyzes NO-forming nitrite reduction as part of bacterial denitrification.