Rv2193 (ctaE)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: cytochrome c oxidase subunit III
- REFSEQ: cytochrome C oxidase subunit III
- PATRIC: Cytochrome c oxidase polypeptide III (EC 1.9.3.1)
- TUBERCULIST: Probable cytochrome C oxidase (subunit III) CtaE
- NCBI: Probable cytochrome C oxidase (subunit III) CtaE
- updated information (H37Rv4):
  - gene name: ctaE
  - function:
  - reference:
Type: Not Target
Start: 2456901
End: 2457512
Operon:

Trans-membrane region:
Role: I.B.6.a - aerobic
GO terms:
- GO:1902600 - proton transmembrane transport (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0022904 - respiratory electron transport chain (Uniprot)
- GO:0019646 - aerobic electron transport chain (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0015002 - heme-copper terminal oxidase activity (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0004129 - cytochrome-c oxidase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- 0.5 O2[c] + 2 HEME_FE2[c] -> 6 H[c] + 2 HEME_FE3[c]
- MKH2[c] + 2 HEME_FE3[c] <=> MK[c] + 2 HEME_FE2[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):

PDB	aa ident	species	PDB title
6HWH	87%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
6ADQ	87%	Mycobacterium smegmatis MC2 51	Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
5Z62	39%	Homo sapiens	Structure of human cytochrome c oxidase
6NMP	36%	Bos taurus	SFX structure of oxidized cytochrome c oxidase at room temperature
6NMF	36%	Bos taurus	SFX structure of reduced cytochrome c oxidase at room temperature
6NKN	36%	Bos taurus	Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature
6JY4	36%	Bos taurus	Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State
6JY3	36%	Bos taurus	Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
6JUW	36%	Bos taurus	BOVINE HEART CYTOCHROME C OXIDASE IN CATALITIC INTERMEDIATES AT 1.80 ANGSTROM RESOLUTION
6J8M	36%	Bos taurus	Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray

Links to additional information on ctaE:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -8.948 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VTSAVGTSGTAITSRVHSLNRPNMVSVGTIVWLSSELMFFAGLFAFYFSARAQAGGNWPPPPTELNLYQAVPVTLVLIASSFTCQMGVFAAERGDIFGLR
RWYVITFLMGLFFVLGQAYEYRNLMSHGTSIPSSAYGSVFYLATGFHGLHVTGGLIAFIFLLVRTGMSKFTPAQATASIVVSYYWHFVDIVWIALFTVIY
FIR

(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: 0.999900; 17 non-insertions in a row out of 17 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 17 non-insertions in a row out of 17 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 17 non-insertions in a row out of 17 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 16 non-insertions in a row out of 17 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 17 non-insertions in a row out of 17 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.04
Growth-Defect	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:
- Rv0324 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0324 (-) (Direct binding)
- Rv2034 (-) (Direct binding)

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:
- Rv0324 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Operon Rv2200c	harsharohiratruefriend	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2196	ashwinigbhat	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2195	ashwinigbhat	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2196	priti.priety	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2195	priti.priety	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2194	priti.priety	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2194	ashwinigbhat	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2196	priti.priety	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Citation	Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. BD. Kana, EA. Weinstein et al. J. Bacteriol. 2001	ashwinigbhat	TAS	11717265	Coexpression
Interaction	PhysicalInteraction Rv2194	ashwinigbhat	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2195	ashwinigbhat	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2196	ashwinigbhat	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Citation	Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. BD. Kana, EA. Weinstein et al. J. Bacteriol. 2001	harsharohiratruefriend	TAS	11717265	None
Interaction	Operon Rv2200c	harsharohiratruefriend	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	Operon Rv3043c	harsharohiratruefriend	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Citation	Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. BD. Kana, EA. Weinstein et al. J. Bacteriol. 2001	priti.priety	TAS	11717265	Coexpression
Interaction	PhysicalInteraction Rv2194	priti.priety	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv2195	priti.priety	TAS		Coexpression BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
Interaction	PhysicalInteraction Rv1451	ashwinigbhat	ISA		Co-occurrence (Functional linkage) authors,M. Strong,TG. Graeber,M. Beeby,M. Pellegrini,MJ. Thompson,TO. Yeates,D. Eisenberg Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003
Interaction	PhysicalInteraction Rv1451	priti.priety	ISA		Co-occurrence (Functional linkage) authors,M. Strong,TG. Graeber,M. Beeby,M. Pellegrini,MJ. Thompson,TO. Yeates,D. Eisenberg Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 2003
Interaction	RegulatedBy Rv0348	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.. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
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

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