Rv0252 (nirB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: nitrite reductase [NAD(P)H] large subunit
- REFSEQ: nitrite reductase large subunit
- PATRIC: Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
- TUBERCULIST: Probable nitrite reductase [NAD(P)H] large subunit [FAD flavoprotein] NirB
- NCBI: Probable nitrite reductase [NAD(P)H] large subunit [FAD flavoprotein] NirB
- updated information (H37Rv4):
  - gene name: nirB
  - function:
  - reference:
Type: Not Target
Start: 302866
End: 305427
Operon:

Trans-membrane region:
Role: I.B.6.b - anaerobic
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0051539 - 4 iron, 4 sulfur cluster binding (Uniprot)
- GO:0051536 - iron-sulfur cluster binding (Uniprot)
- GO:0050661 - NADP binding (Uniprot)
- GO:0050660 - flavin adenine dinucleotide binding (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0042128 - nitrate assimilation (Uniprot)
- GO:0020037 - heme binding (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0008942 - nitrite reductase [NAD(P)H] activity (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005618 - cell wall (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- 3 NADH[c] + NO2[c] -> 3 NAD[c] + NH3[c]
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020): (none with >35% aa id)
Links to additional information on nirB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.106 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MPTAGSSRAPAAAREIVVVGHGMVGHRLVEAVRARDADGSLRITVLAEEGDAAYDRVGLTSYTESWDRALLALPGNDYAGDQRVRLLLNTRVTQIDRATK
SVVTAAGQRHRYDTLVLATGSYAFVPPVPGHDLPACHVYRTFDDLDAIRAGAQRTLDGGHTDGGVVIGGGLLGLEAANALRQFGLQTHVVEMMPRLMAQQ
IDEAGGALLARMIADLGIAVHVGTGTESIESVKHSDGSVWARVRLSDGEVIDAGVVIFAAGIRPRDELARAAGLAIGDRGGVLTDLSCRTSDPDIYAVGE
VAAIDGRCYGLVGPGYTSAEVVADRLLDGSAEFPEADLSTKLKLLGVDVASFGDAMGATENCLEVVINDAVKRTYAKLVLSDDATTLLGGVLVGDASSYG
VLRPMVGAELPGDPLALIAPAGSGAGAGALGVGALPDSAQICSCNNVTKGELKCAIADGCGDVPALKSCTAAGTSCGSCVPLLKQLLEAEGVEQSKALCE
HFSQSRAELFEIITATEVRTFSGLLDRFGRGKGCDICKPVVASILASTGSDHILDGEQASLQDSNDHFLANIQKNGSYSVVPRVPGGDIKPEHLILIGQI
AQDFGLYTKITGGQRIDLFGARVDQLPLIWQRLVDGGMESGHAYGKAVRTVKSCVGSDWCRYGQQDSVQLAIDLELRYRGLRAPHKIKLGVSGCARECAE
ARGKDVGVIATEKGWNLYVAGNGGMTPKHAQLLASDLDKETLIRYIDRFLIYYIRTADRLQRTAPWVESLGLDHVREVVCEDSLGLAEEFEAAMQRHVAN
YKCEWKGVLEDPDKLSRFVSFVNAPDAVDSTVTFTERAGRKVPVSIGIPRVRS

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000150; 6 non-insertions in a row out of 41 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 41 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.022150; 6 non-insertions in a row out of 41 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000700; 5 non-insertions in a row out of 41 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 41 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.21
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0353 (hspR) (Direct binding)
- Rv0757 (phoP) (Direct binding)
- Rv0818 (-) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv1990c (-) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv3246c (mtrA) (Direct binding)
- Rv3681c (whiB4) (Direct binding)

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Citation	A genomic view on nitrogen metabolism and nitrogen control in mycobacteria. authors,J. Amon,F. Titgemeyer,A. Burkovski J. Mol. Microbiol. Biotechnol. 2009	priti.priety	IPI	18824837	operon
Interaction	Operon Rv0253	priti.priety	IPI		operon authors,J. Amon,F. Titgemeyer,A. Burkovski A genomic view on nitrogen metabolism and nitrogen control in mycobacteria. J. Mol. Microbiol. Biotechnol. 2009
Citation	The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. S. Malm, Y. Tiffert et al. Microbiology (Reading, Engl.) 2009	ashwinigbhat	IPI	19332834	operon
Interaction	Operon Rv0253	ashwinigbhat	IPI		operon S. Malm, Y. Tiffert et al. The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Citation	A genomic view on nitrogen metabolism and nitrogen control in mycobacteria. authors,J. Amon,F. Titgemeyer,A. Burkovski J. Mol. Microbiol. Biotechnol. 2009	ashwinigbhat	IPI	18824837	operon
Interaction	Operon Rv0253	ashwinigbhat	IPI		operon authors,J. Amon,F. Titgemeyer,A. Burkovski A genomic view on nitrogen metabolism and nitrogen control in mycobacteria. J. Mol. Microbiol. Biotechnol. 2009
Interaction	Operon Rv0253	priti.priety	IPI		operon S. Malm, Y. Tiffert et al. The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Interaction	Operon Rv0253	ashwinigbhat	IPI		operon S. Malm, Y. Tiffert et al. The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Citation	The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. S. Malm, Y. Tiffert et al. Microbiology (Reading, Engl.) 2009	priti.priety	IPI	19332834	operon
Interaction	Operon Rv0253	priti.priety	IPI		operon S. Malm, Y. Tiffert et al. The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Interaction	RegulatedBy Rv3223c	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv1785c	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv1221	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv0353	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv1785c	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006

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