Rv0283 (eccB3)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ESX-3 secretion system protein eccB3
- REFSEQ: hypothetical protein
- PATRIC: Type VII secretion protein EccB
- TUBERCULIST: ESX conserved component EccB3. ESX-3 type VII secretion system protein. Possible membrane protein.
- NCBI: ESX conserved component EccB3 ESX-3 type VII secretion system protein Possible membrane protein
- updated information (H37Rv4):
  - gene name: eccB3
  - function:
  - reference:
Type: Essential
Start: 344022
End: 345638
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016787 - hydrolase activity (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:0005576 - extracellular region (Uniprot)
- GO:0005524 - ATP binding (Uniprot)
- GO:0000166 - nucleotide binding (Uniprot)
- GO:0043022 - ribosome binding (FLUTE) (FLUTE Assigned!)
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
6SGW	82%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of the ESX-3 core complex
6SGZ	82%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 2 of the ESX-3 core complex
6SGX	82%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of protomer 1 of the ESX-3 core complex
6UMM	81%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	A complete structure of the ESX-3 translocon complex
6SGY	63%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of EccB3 dimer from the ESX-3 core complex
5CYU	37%	Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)	Structure of the soluble domain of EccB1 from the Mycobacterium smegmatis ESX-1 secretion system.
4KK7	37%	Mycobacterium tuberculosis	Structure of EccB1 from the type VII (ESX-1) secretion system of Mycobacterium tuberculosis.
5EBD	36%	Mycobacterium tuberculosis	Crystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P21 (state IV)
5EBC	36%	Mycobacterium tuberculosis	Crystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P21 (state III)
3X3N	36%	Mycobacterium tuberculosis	Crystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P21

Links to additional information on eccB3:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -7.014 (from Jeremy Rock's lab)

Amino Acid Sequence

MTNQQHDHDFDHDRRSFASRTPVNNNPDKVVYRRGFVTRHQVTGWRFVMRRIAAGIALHDTRMLVDPLRTQSRAVLMGVLIVITGLIGSFVFSLIRPNGQ
AGSNAVLADRSTAALYVRVGEQLHPVLNLTSARLIVGRPVSPTTVKSTELDQFPRGNLIGIPGAPERMVQNTSTDANWTVCDGLNAPSRGGADGVGVTVI
AGPLEDTGARAAALGPGQAVLVDSGAGTWLLWDGKRSPIDLADHAVTSGLGLGADVPAPRIIASGLFNAIPEAPPLTAPIIPDAGNPASFGVPAPIGAVV
SSYALKDSGKTISDTVQYYAVLPDGLQQISPVLAAILRNNNSYGLQQPPRLGADEVAKLPVSRVLDTRRYPSEPVSLVDVTRDPVTCAYWSKPVGAATSS
LTLLAGSALPVPDAVHTVELVGAGNGGVATRVALAAGTGYFTQTVGGGPDAPGAGSLFWVSDTGVRYGIDNEPQGVAGGGKAVEALGLNPPPVPIPWSVL
SLFVPGPTLSRADALLAHDTLVPDSRPARPVSAEGGYR

(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; 24 non-insertions in a row out of 24 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 24 non-insertions in a row out of 24 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 24 non-insertions in a row out of 24 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 24 non-insertions in a row out of 24 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 24 non-insertions in a row out of 24 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:
- Rv1776c (-) (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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