Rv2007c (fdxA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ferredoxin
- REFSEQ: ferredoxin FDXA
- PATRIC: 4Fe-4S ferredoxin iron-sulfur binding
- TUBERCULIST: Ferredoxin FdxA
- NCBI: Ferredoxin FdxA
- updated information (H37Rv4):
  - gene name: fdxA
  - function:
  - reference:
Type: Not Target
Start: 2256084
End: 2256428
Operon:

Trans-membrane region:
Role: I.B.6.c - Electron transport
GO terms:
- GO:0075136 - response to host (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0052572 - response to host immune response (Uniprot)
- GO:0051539 - 4 iron, 4 sulfur cluster binding (Uniprot)
- GO:0051538 - 3 iron, 4 sulfur cluster binding (Uniprot)
- GO:0051536 - iron-sulfur cluster binding (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0022900 - electron transport chain (Uniprot)
- GO:0009055 - electron transfer activity (Uniprot)
- GO:0006535 - cysteine biosynthetic process from serine (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0001666 - response to hypoxia (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:
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
2V2K	57%	MYCOBACTERIUM SMEGMATIS	THE CRYSTAL STRUCTURE OF FDXA, A 7FE FERREDOXIN FROM MYCOBACTERIUM SMEGMATIS
1H98	51%	THERMUS AQUATICUS	New Insights into Thermostability of Bacterial Ferredoxins: High Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus thermophilus
1BD6	48%	Bacillus schlegelii	7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, MINIMIZED AVERAGE STRUCTURE
1BC6	48%	Bacillus schlegelii	7-FE FERREDOXIN FROM BACILLUS SCHLEGELII, NMR, 20 STRUCTURES
1BWE	47%	Bacillus schlegelii	ARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGELII FE7S8 FERREDOXIN
1BQX	47%	Bacillus schlegelii	ARTIFICIAL FE8S8 FERREDOXIN: THE D13C VARIANT OF BACILLUS SCHLEGELII FE7S8 FERREDOXIN
1FCA	44%	Clostridium acidurici	STRUCTURE OF THE FERREDOXIN FROM CLOSTRIDIUM ACIDURICI: MODEL AT 1.8 ANGSTROMS RESOLUTION
1DUR	44%	Peptoniphilus asaccharolyticus	Replacement for 1FDX 2(4FE4S) ferredoxin from (NOW) Peptostreptococcus asaccharolyticus
1G3O	43%	Azotobacter vinelandii	CRYSTAL STRUCTURE OF V19E MUTANT OF FERREDOXIN I
1FRJ	43%	Azotobacter vinelandii	AZOTOBACTER VINELANDII FERREDOXIN I: ALTERATION OF INDIVIDUAL SURFACE CHARGES AND THE [4FE-4S] CLUSTER REDUCTION POTENTIAL

Links to additional information on fdxA:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.494 (from Jeremy Rock's lab)
- BioCyc
- Systems Biology

Amino Acid Sequence

VTYVIGSECVDVMDKSCVQECPVDCIYEGARMLYINPDECVDCGACKPACRVEAIYWEGDLPDDQHQHLGDNAAFFHQVLPGRVAPLGSPGGAAAVGPIG
VDTPLVAAIPVECP

(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: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 8 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 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
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:
- Rv1353c (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv3133c (devR) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3133c (devR)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Proc. Natl. Acad. Sci. U.S.A. 2007	akankshajain.21	IEP	17609369	co-expression(Functional linkage)
Interaction	Regulatory Rv2031c	akankshajain.21	IEP		co-expression(Functional linkage) A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. Proc. Natl. Acad. Sci. U.S.A. 2007
Interaction	Regulatory Rv3133c	akankshajain.21	IEP		co-expression(Functional linkage) A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. Proc. Natl. Acad. Sci. U.S.A. 2007
Citation	Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Proc. Natl. Acad. Sci. U.S.A. 2007	prabhakarsmail	IEP	17609369	co-expression(Functional linkage)
Interaction	Regulatory Rv2031c	prabhakarsmail	IEP		co-expression(Functional linkage) A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. Proc. Natl. Acad. Sci. U.S.A. 2007
Interaction	Regulatory Rv3133c	prabhakarsmail	IEP		co-expression(Functional linkage) A. Kumar,JC. Toledo,RP. Patel,JR. Lancaster,AJ. Steyn Mycobacterium tuberculosis DosS is a redox sensor and DosT is a hypoxia sensor. Proc. Natl. Acad. Sci. U.S.A. 2007
Interaction	RegulatedBy Rv0981	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.. H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
Interaction	RegulatedBy Rv3133c	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

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