Rv3846 (sodA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: superoxide dismutase [Fe]
- REFSEQ: superoxide dismutase [Fe] SODA
- PATRIC: Superoxide dismutase [Mn/Fe] (EC 1.15.1.1)
- TUBERCULIST: Superoxide dismutase [FE] SodA
- NCBI: Superoxide dismutase [FE] SodA
- updated information (H37Rv4):
  - gene name: sodA
  - function:
  - reference:
Type: Not Target
Start: 4320704
End: 4321327
Operon:

Trans-membrane region:
Role: III.F - Detoxification
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0052059 - evasion or tolerance by symbiont of host-produced reactive oxygen species (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0042597 - periplasmic space (Uniprot)
- GO:0019430 - removal of superoxide radicals (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0006979 - response to oxidative stress (Uniprot)
- GO:0006801 - superoxide metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0005506 - iron ion binding (Uniprot)
- GO:0004784 - superoxide dismutase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
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: 1ids, 1gn4, 1gn6, 1gn3, 1gn2
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
1IDS	99%	Mycobacterium tuberculosis	X-RAY STRUCTURE ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE DISMUTASE FROM MYCOBACTERIUM TUBERCULOSIS AT 2.0 ANGSTROMS RESOLUTIONS REVEALS NOVEL DIMER-DIMER INTERACTIONS
1GN6	99%	MYCOBACTERIUM TUBERCULOSIS	G152A mutant of Mycobacterium tuberculosis iron-superoxide dismutase.
1GN4	99%	MYCOBACTERIUM TUBERCULOSIS	H145E mutant of Mycobacterium tuberculosis iron-superoxide dismutase.
1GN3	99%	MYCOBACTERIUM TUBERCULOSIS	H145Q mutant of Mycobacterium tuberculosis iron-superoxide dismutase.
1GN2	99%	MYCOBACTERIUM TUBERCULOSIS	S123C mutant of the iron-superoxide dismutase from Mycobacterium tuberculosis.
1BT8	63%	Propionibacterium freudenreichii subsp. shermanii	P.SHERMANII SOD(FE+3) PH 10.0
1BSM	63%	Propionibacterium freudenreichii subsp. shermanii	P.SHERMANII SOD(FE+3) 140K PH8
1BS3	63%	Propionibacterium freudenreichii subsp. shermanii	P.SHERMANII SOD(FE+3) FLUORIDE
1AVM	63%	Propionibacterium freudenreichii subsp. shermanii	THE CAMBIALISTIC SUPEROXIDE DISMUTASE (FE-SOD) OF P. SHERMANII COORDINATED BY AZIDE
1AR5	63%	Propionibacterium freudenreichii subsp. shermanii	X-RAY STRUCTURE OF THE CAMBIALISTIC SUPEROXIDE DISMUTASE FROM PROPIONIBACTERIUM SHERMANII ACTIVE WITH FE OR MN

Links to additional information on sodA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -3.635 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VAEYTLPDLDWDYGALEPHISGQINELHHSKHHATYVKGANDAVAKLEEARAKEDHSAILLNEKNLAFNLAGHVNHTIWWKNLSPNGGDKPTGELAAAIA
DAFGSFDKFRAQFHAAATTVQGSGWAALGWDTLGNKLLIFQVYDHQTNFPLGIVPLLLLDMWEHAFYLQYKNVKVDFAKAFWNVVNWADVQSRYAAATSQ
TKGLIFG

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999500; 14 non-insertions in a row out of 14 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999900; 14 non-insertions in a row out of 14 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 14 non-insertions in a row out of 14 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 14 non-insertions in a row out of 14 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 14 non-insertions in a row out of 14 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv0260c (-)

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

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

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0260c (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): autocatalytic formation and effect on enzyme catalysis and spectroscopic properties. RA. Ghiladi, GM. Knudsen et al. J. Biol. Chem. 2005	njamshidi	ISS	15840564	KatG is a bifunctional enzyme . PMID 15840564
Term	EC:1.15.1.1 Superoxide dismutase. - ISS	njamshidi	ISS		KatG is a bifunctional enzyme . PMID 15840564 RA. Ghiladi, GM. Knudsen et al. The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): autocatalytic formation and effect on enzyme catalysis and spectroscopic properties. J. Biol. Chem. 2005
Term	TBRXN:SPODM superoxide dismutase - ISS	njamshidi	ISS		KatG is a bifunctional enzyme . PMID 15840564 RA. Ghiladi, GM. Knudsen et al. The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): autocatalytic formation and effect on enzyme catalysis and spectroscopic properties. J. Biol. Chem. 2005
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. R. Manganelli, MI. Voskuil et al. The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol. Microbiol. 2001
Interaction	RegulatedBy Rv2359	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 Rv1931c	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 Rv2359	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
Interaction	RegulatedBy Rv1931c	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
Interaction	RegulatedBy Rv0491	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003

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