Gene Description

nirK1 encodes a predicted periplasmic copper-containing nitrite reductase in Rhodopseudomonas palustris CGA009. The UniProt record names the protein as a copper-containing nitrite reductase with EC 1.7.2.1, supporting its role in the nitrite-to-nitric-oxide step of nitrogen oxide respiration.

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005507 copper ion binding	IEA GO_REF:0000002	ACCEPT	Summary: ACCEPT. Copper binding is consistent with the annotated copper-containing nitrite reductase family and catalytic activity. Reason: nirK1 is annotated as a copper-containing nitrite reductase and has cupredoxin/NO2-reductase_Cu family signatures plus conserved copper-site features. The inference is family/domain based, not direct biochemical evidence in this strain. Falcon found no primary paper characterizing Q6N4N1/RPA3306 directly. Supporting Evidence: file:RHOPA/nirK1/nirK1-uniprot.txt InterPro; IPR001287; NO2-reductase_Cu. file:RHOPA/nirK1/nirK1-deep-research-falcon.md The report supports T1Cu/T2Cu CuNIR architecture from family evidence and did not recover nirK1/RPA3306-specific metal biochemistry.
GO:0042597 periplasmic space	IEA GO_REF:0000044	ACCEPT	Summary: ACCEPT. Bacterial NirK enzymes are periplasmic nitrite reductases, and the UniProt record identifies this protein as a precursor. Reason: The UniProt record predicts periplasmic localization and an N-terminal signal peptide. This matches the expected compartment for bacterial copper nitrite reductases. Supporting Evidence: file:RHOPA/nirK1/nirK1-uniprot.txt SUBCELLULAR LOCATION: Periplasm. file:RHOPA/nirK1/nirK1-uniprot.txt SIGNAL 1..26
GO:0050421 nitrite reductase (NO-forming) activity	IEA GO_REF:0000120	ACCEPT	Summary: ACCEPT. This is the specific molecular function expected for copper nitrite reductase EC 1.7.2.1. Reason: This is the precise EC-supported activity for a NirK copper nitrite reductase. UniProt assigns EC 1.7.2.1 and the NO2-reductase_Cu/TIGR02376 family model supports conserved NO-forming nitrite reductase function. Falcon adds that no direct RPA3306 enzyme assay was recovered, so the support remains conserved-function inference. Supporting Evidence: file:RHOPA/nirK1/nirK1-uniprot.txt RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1. file:RHOPA/nirK1/nirK1-uniprot.txt NCBIfam; TIGR02376; Cu_nitrite_red; 1. file:RHOPA/nirK1/nirK1-deep-research-falcon.md NirK/CuNIR family evidence supports nitrite-to-NO reduction with electron transfer from T1Cu to the T2Cu catalytic site.
GO:0019333 denitrification pathway	IEA GO_REF:0000041	ACCEPT	Summary: ACCEPT. UniPathway provides useful pathway context: nirK1 catalyzes the NO-forming nitrite-reduction step within bacterial denitrification. Reason: The pathway annotation follows directly from the enzyme assignment: NO-forming nitrite reduction is step 2/4 in nitrate reduction (denitrification). This is a conserved-function inference from EC/family evidence and UniProt pathway mapping rather than a strain-specific experiment. Falcon found genome-context evidence for nirK with norB/nosZ in CGA009, but not direct nirK1-specific physiology. Supporting Evidence: file:RHOPA/nirK1/nirK1-uniprot.txt PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4. file:RHOPA/nirK1/nirK1-deep-research-falcon.md Comparative denitrification-genome analysis includes R. palustris CGA009 among nirK-harboring genomes and maps nirK relative to norB and nosZ, supporting pathway context without direct nirK1 biochemistry.

Core Functions

Catalyzes NO-forming nitrite reduction as a copper-containing periplasmic enzyme in the denitrification pathway.

Molecular Function:

nitrite reductase (NO-forming) activity

Directly Involved In:

denitrification pathway

Supporting Evidence:

file:RHOPA/nirK1/nirK1-uniprot.txt
RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1.
file:RHOPA/nirK1/nirK1-deep-research-falcon.md
Falcon deep research supports that nirK1 should be accepted for NO-forming nitrite reductase activity and denitrification pathway, with evidence coming from conserved EC/domain/family inference plus CGA009 genome context rather than direct RPA3306-specific biochemistry.

References

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Deep Research

Falcon

(nirK1-deep-research-falcon.md)

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📚 Additional Documentation

Notes

(nirK1-notes.md)

nirK1 notes

UniProt Q6N4N1 names nirK1 as a copper-containing nitrite reductase, EC 1.7.2.1 [file:RHOPA/nirK1/nirK1-uniprot.txt "RecName: Full=Copper-containing nitrite reductase"; "EC=1.7.2.1"].
The UniPathway annotation to denitrification pathway is accepted because NO-forming nitrite reduction is a canonical denitrification step [GO_REF:0000041; file:RHOPA/nirK1/nirK1-goa.tsv].

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