Gene Ontology annotation through association of InterPro records with GO terms
UniProtKB entry for nirD (Q88M68)
PANTHER members for PTHR40562
Crystal structure of NirD, the small subunit of the nitrite reductase NirbD from Mycobacterium tuberculosis at 2.0 Å resolution.
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The Mycobacterium tuberculosis NirD structure lacks a cofactor despite its Rieske-related fold; this is comparative evidence for the accessory subunit, not a KT2440 structure.
"it does not contain any Fe-S cluster or other cofactors that might be involved in electron transfer"
A Nitrate-Blind P. putida Strain Boosts PHA Production in a Synthetic Mixed Culture.
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The introduction cites PP_1705 and PP_1706 as the assigned KT2440 assimilatory nitrite reductase.
"nirBD (PP_1705, PP_1706)"
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing.
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Native KT2440 pooled-mutant fitness supports nitrate uptake by PP_2092; the nitrate-condition fitness score is −2.6.
"We were also able to identify a distinct nitrate transporter PP_2092 (−2.6)."
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Absence of a significant nitrite-condition phenotype does not exclude redundant or conditional nitrite transport.
"However, no significant phenotype could be detected for this gene in the nitrite condition, suggesting that it may be specific to nitrate."
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The paper reports NarB and combined NirDB pathway phenotypes, without assigning the displayed combined NirDB score to each individual subunit.
"The enzymes associated with the initial steps of the assimilatory nitrogen system in P. putida are the reductases NarB and NirDB, for which we see significant growth phenotypes"
Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida.
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Native KT2440 experiments identify the nirBD operon and show NasT-dependent nirB transcription.
"the NalA-encoding sequence (nalA) is located upstream of the nirBD operon (PP_1705-PP_1706)."
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Loss of nasT prevents induction downstream of the leader terminator.
"the induction of nirB expression was abolished in ΔnasT, while the induction of nalA expression was not affected in ΔnasT"
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Nitrite-reductase activity was measured in cell lysate with an artificial electron donor; this does not identify the physiological pyridine nucleotide.
"3 mM methyl viologen, 1 mM KNO2, 17 mM Na2S2O4"
The nirB and nirD genes are essential for both assimilatory and dissimilatory reduction of nitrite in Pseudomonas putida Y-9 under aerobic conditions.
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In the distinct P. putida Y-9 strain, deletion of either nirB or nirD impairs nitrite reduction.
"Deletion of nirB or nirD severely impaired NO2- reduction."
file:PSEPK/nirD/nirD-source-analysis/README.md