Rv0284 (eccC3)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ESX-3 secretion system protein eccC3
- REFSEQ: hypothetical protein
- PATRIC: Type VII secretion protein EccCa
- TUBERCULIST: ESX conserved component EccC3. ESX-3 type VII secretion system protein. Possible membrane protein.
- NCBI: ESX conserved component EccC3 ESX-3 type VII secretion system protein Possible membrane protein
- updated information (H37Rv4):
  - gene name: eccC3
  - function:
  - reference:
Type: Essential
Start: 345635
End: 349627
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005887 - integral component of plasma membrane (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005524 - ATP binding (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000166 - nucleotide binding (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
6J17	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	ATPase
6SGX	70%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 1 of the ESX-3 core complex
6SGW	70%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of the ESX-3 core complex
6UMM	69%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	A complete structure of the ESX-3 translocon complex
6SGZ	57%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 2 of the ESX-3 core complex
4N1A	35%	Thermomonospora curvata	Thermomonospora curvata EccC (ATPases 2 and 3) in complex with a signal sequence peptide

Links to additional information on eccC3:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -6.314 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- Photo of spot titer

Amino Acid Sequence

VSRLIFEARRRLAPPSSHQGTIIIEAPPELPRVIPPSLLRRALPYLIGILIVGMIVALVATGMRVISPQTLFFPFVLLLAATALYRGNDKKMRTEEVDAE
RADYLRYLSVVRDNIRAQAAEQRASALWSHPDPTALASVPGSRRQWERDPHDPDFLVLRAGRHTVPLATTLRVNDTADEIDLEPVSHSALRSLLDTQRSI
GDVPTGIDLTKVSPITVLGERAQVRAVLRAWIAQAVTWHDPTVLGVALAARDLEGRDWNWLKWLPHVDIPGRLDALGPARNLSTDPDELIALLGPVLADR
PAFTGQPTDALRHLLIVVDDPDYDLGASPLAVGRAGVTVVHCSASAPHREQYSDPEKPILRVAHGAIERWQTGGWQPYIDAADQFSADEAAHLARRLSRW
DSNPTHAGLRSAATRGASFTTLLGIEDASRLDVPALWAPRRRDEELRVPIGVTGTGEPLMFDLKDEAEGGMGPHGLMIGMTGSGKSQTLMSILLSLLTTH
SAERLIVIYADFKGEAGADSFRDFPQVVAVISNMAEKKSLADRFADTLRGEVARREMLLREAGRKVQGSAFNSVLEYENAIAAGHSLPPIPTLFVVADEF
TLMLADHPEYAELFDYVARKGRSFRIHILFASQTLDVGKIKDIDKNTAYRIGLKVASPSVSRQIIGVEDAYHIESGKEHKGVGFLVPAPGATPIRFRSTY
VDGIYEPPQTAKAVVVQSVPEPKLFTAAAVEPDPGTVIADTDEQEPADPPRKLIATIGEQLARYGPRAPQLWLPPLDETIPLSAALARAGVGPRQWRWPL
GEIDRPFEMRRDPLVFDARSSAGNMVIHGGPKSGKSTALQTFILSAASLHSPHEVSFYCLDYGGGQLRALQDLAHVGSVASALEPERIRRTFGELEQLLL
SRQQREVFRDRGANGSTPDDGFGEVFLVIDNLYGFGRDNTDQFNTRNPLLARVTELVNVGLAYGIHVIITTPSWLEVPLAMRDGLGLRLELRLHDARDSN
VRVVGALRRPADAVPHDQPGRGLTMAAEHFLFAAPELDAQTNPVAAINARYPGMAAPPVRLLPTNLAPHAVGELYRGPDQLVIGQREEDLAPVILDLAAN
PLLMVFGDARSGKTTLLRHIIRTVREHSTADRVAFTVLDRRLHLVDEPLFPDNEYTANIDRIIPAMLGLANLIEARRPPAGMSAAELSRWTFAGHTHYLI
IDDVDQVPDSPAMTGPYIGQRPWTPLIGLLAQAGDLGLRVIVTGRATGSAHLLMTSPLLRRFNDLQATTLMLAGNPADSGKIRGERFARLPAGRAILLTD
SDSPTYVQLINPLVDAAAVSGETQQKGSQS

(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: 1.000000; 61 non-insertions in a row out of 61 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 61 non-insertions in a row out of 61 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 61 non-insertions in a row out of 61 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 61 non-insertions in a row out of 61 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 61 non-insertions in a row out of 61 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.02
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:
- Rv0023 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0967 (csoR) (Direct binding)
- Rv1353c (-) (Direct binding)
- Rv0047c (-) (Upstream of operon)
- Rv2359 (zur) (Upstream of operon)

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:
- Rv0023 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. GM. Rodriguez, MI. Voskuil et al. Infect. Immun. 2002	gaat3s	IGC	12065475	Gene Neighborhood (Functional linkage)
Interaction	Regulatory Rv2359	gaat3s	IGC		Gene Neighborhood (Functional linkage) GM. Rodriguez, MI. Voskuil et al. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002
Interaction	Regulatory Rv2711	gaat3s	IGC		Gene Neighborhood (Functional linkage) GM. Rodriguez, MI. Voskuil et al. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002
Citation	Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. A. Maciag, E. Dainese et al. J. Bacteriol. 2007	gaat3s	IGC	17098899	Gene Neighborhood (Functional linkage)
Interaction	Regulatory Rv2359	gaat3s	IGC		Gene Neighborhood (Functional linkage) A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Interaction	Regulatory Rv2711	gaat3s	IGC		Gene Neighborhood (Functional linkage) A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Citation	Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. A. Maciag, A. Piazza et al. BMC Microbiol. 2009	gaat3s	IGC	19257911	Gene Neighborhood (Functional linkage)
Interaction	Regulatory Rv2359	gaat3s	IGC		Gene Neighborhood (Functional linkage) A. Maciag, A. Piazza et al. Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. BMC Microbiol. 2009
Interaction	Regulatory Rv2711	gaat3s	IGC		Gene Neighborhood (Functional linkage) A. Maciag, A. Piazza et al. Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. BMC Microbiol. 2009
Interaction	RegulatedBy Rv2359	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.. A. Maciag, E. Dainese et al. Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. J. Bacteriol. 2007
Interaction	RegulatedBy Rv2359	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 Rv2711	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.. GM. Rodriguez, MI. Voskuil et al. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002

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