Rv3891c (esxD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: esat-6 like protein esxD
- REFSEQ: ESAT-6 like protein EsxD
- PATRIC: Esat-6 like protein EsxD
- TUBERCULIST: Possible ESAT-6 like protein EsxD
- NCBI: Possible ESAT-6 like protein EsxD
- updated information (H37Rv4):
  - gene name: esxD
  - function:
  - reference:
Type: Not Target
Start: 4374049
End: 4374372
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0005576 - extracellular region (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): (none with >35% aa id)
Links to additional information on esxD:
- KEGG - nucleotide and amino acid sequences of gene
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.002 (from Jeremy Rock's lab)
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VADTIQVTPQMLRSTANDIQANMEQAMGIAKGYLANQENVMNPATWSGTGVVASHMTATEITNELNKVLTGGTRLAEGLVQAAALMEGHEADSQTAFQAL
FGASHGS

(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 9 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 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; 2 non-insertions in a row out of 9 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.03
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:
- Rv0324 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0022c (whiB5)
- Rv0023 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv3891c (esxD)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002
Citation	Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. KL. Lightbody, D. Ilghari et al. J. Biol. Chem. 2008	shahanup86	TAS	18430736	Structural Analysis
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008
Citation	Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. B. Callahan, K. Nguyen et al. J. Bacteriol. 2010	shahanup86	TAS	19854905	Structural Analysis
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010
Citation	Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr J. Biol. Chem. 2002	shahanup86	TAS	11940590	Spectrophotometric
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002
Citation	Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. KL. Lightbody, D. Ilghari et al. J. Biol. Chem. 2008	shahanup86	TAS	18430736	Spectrophotometric
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008
Citation	Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. B. Callahan, K. Nguyen et al. J. Bacteriol. 2010	shahanup86	TAS	19854905	Spectrophotometric
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010
Citation	The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. NC. Gey Van Pittius, J. Gamieldien et al. Genome Biol. 2001	shahanup86	TAS	11597336	Structural Analysis
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001
Citation	Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr J. Biol. Chem. 2002	shahanup86	TAS	11940590	Structural Analysis
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Structural Analysis B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010
Citation	The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. NC. Gey Van Pittius, J. Gamieldien et al. Genome Biol. 2001	shahanup86	TAS	11597336	Spectrophotometric
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008
Interaction	PhysicalInteraction Rv3890c	shahanup86	TAS		Spectrophotometric B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010

Property

Value

Creator

Evidence

PMID

Comment

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002

Citation

Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. KL. Lightbody, D. Ilghari et al. J. Biol. Chem. 2008

shahanup86

TAS

18430736

Structural Analysis

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008

Citation

Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. B. Callahan, K. Nguyen et al. J. Bacteriol. 2010

shahanup86

TAS

19854905

Structural Analysis

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010

Citation

Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr J. Biol. Chem. 2002

shahanup86

TAS

11940590

Spectrophotometric

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
authors,PS. Renshaw,P. Panagiotidou,A. Whelan,SV. Gordon,RG. Hewinson,RA. Williamson,MD. Carr Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence. J. Biol. Chem. 2002

Citation

shahanup86

TAS

18430736

Spectrophotometric

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
KL. Lightbody, D. Ilghari et al. Molecular features governing the stability and specificity of functional complex formation by Mycobacterium tuberculosis CFP-10/ESAT-6 family proteins. J. Biol. Chem. 2008

Citation

Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. B. Callahan, K. Nguyen et al. J. Bacteriol. 2010

shahanup86

TAS

19854905

Spectrophotometric

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010

Citation

The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. NC. Gey Van Pittius, J. Gamieldien et al. Genome Biol. 2001

shahanup86

TAS

11597336

Structural Analysis

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001

Citation

shahanup86

TAS

11940590

Structural Analysis

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Structural Analysis
B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010

Citation

The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. NC. Gey Van Pittius, J. Gamieldien et al. Genome Biol. 2001

shahanup86

TAS

11597336

Spectrophotometric

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
NC. Gey Van Pittius, J. Gamieldien et al. The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol. 2001

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Interaction

PhysicalInteraction Rv3890c

shahanup86

TAS

Spectrophotometric
B. Callahan, K. Nguyen et al. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J. Bacteriol. 2010

Comments