Rv2200c (ctaC)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: cytochrome c oxidase subunit 2
- REFSEQ: transmembrane cytochrome C oxidase subunit II CtaC
- PATRIC: Cytochrome c oxidase polypeptide II (EC 1.9.3.1)
- TUBERCULIST: Probable transmembrane cytochrome C oxidase (subunit II) CtaC
- NCBI: Probable transmembrane cytochrome C oxidase (subunit II) CtaC
- updated information (H37Rv4):
  - gene name: ctaC
  - function:
  - reference:
Type: Not Target
Start: 2463660
End: 2464751
Operon:

Trans-membrane region:
Role: I.B.6.a - aerobic
GO terms:
- GO:1902600 - proton transmembrane transport (Uniprot)
- GO:0070469 - respiratory chain (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0044121 - growth of symbiont in host organelle (Uniprot)
- GO:0042773 - ATP synthesis coupled electron transport (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0009319 - cytochrome o ubiquinol oxidase complex (Uniprot)
- GO:0005887 - integral component of plasma membrane (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005507 - copper ion binding (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	75%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
6ADQ	75%	Mycobacterium smegmatis MC2 51	Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
4W9Z	35%	Bradyrhizobium diazoefficiens	Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum

Links to additional information on ctaC:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -8.533 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VTPRGPGRLQRLSQCRPQRGSGGPARGLRQLALAAMLGALAVTVSGCSWSEALGIGWPEGITPEAHLNRELWIGAVIASLAVGVIVWGLIFWSAVFHRKK
NTDTELPRQFGYNMPLELVLTVIPFLIISVLFYFTVVVQEKMLQIAKDPEVVIDITSFQWNWKFGYQRVNFKDGTLTYDGADPERKRAMVSKPEGKDKYG
EELVGPVRGLNTEDRTYLNFDKVETLGTSTEIPVLVLPSGKRIEFQMASADVIHAFWVPEFLFKRDVMPNPVANNSVNVFQIEEITKTGAFVGHCAEMCG
TYHSMMNFEVRVVTPNDFKAYLQQRIDGKTNAEALRAINQPPLAVTTHPFDTRRGELAPQPVG

(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; 18 non-insertions in a row out of 20 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 18 non-insertions in a row out of 20 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 18 non-insertions in a row out of 20 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 18 non-insertions in a row out of 21 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 18 non-insertions in a row out of 21 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.05
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

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

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1353c (-) (Direct binding)
- Rv2250c (-) (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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
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 Rv2193	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
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
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 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 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	Operon Rv2193	harsharohiratruefriend	TAS		BD. Kana, EA. Weinstein et al. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J. Bacteriol. 2001
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	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	RegulatedBy Rv2710	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.. JH. Lee, PC. Karakousis et al. Roles of SigB and SigF in the Mycobacterium tuberculosis sigma factor network. J. Bacteriol. 2008
Interaction	RegulatedBy Rv3286c	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.. EP. Williams, JH. Lee et al. Mycobacterium tuberculosis SigF regulates genes encoding cell wall-associated proteins and directly regulates the transcriptional regulatory gene phoY1. J. Bacteriol. 2007

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