Rv1960c (parD1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: antitoxin
- REFSEQ: hypothetical protein
- PATRIC: Antitoxin ParD1
- TUBERCULIST: Possible antitoxin ParD1
- NCBI: Possible antitoxin ParD1
- updated information (H37Rv4):
  - gene name: parD1
  - function:
  - reference:
Type: Not Target
Start: 2203974
End: 2204225
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0045927 - positive regulation of growth (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0005515 - protein 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

3KXE 59% Caulobacter crescentus NA1000 A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex
Links to additional information on parD1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.418 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
3KXE	59%	Caulobacter crescentus NA1000	A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex

Amino Acid Sequence

VGKNTSFVLDEHYSAFIDGEIAAGRYRSASEVIRSALRLLEDRETQLRALREALEAGERSGSSTPFDFDGFLGRKRADASRGR

(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; 1 non-insertions in a row out of 4 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 4 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 4 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 4 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 4 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: 2.47
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:
Bound By:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv2034 (-) (Direct binding)
- Rv3574 (kstR) (Direct binding)

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

Upregulates:
Upregulated by:
- Rv0023 (-)
- Rv1960c (parD1)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv1960c (parD1)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	InhibitedBy Rv2142c	harsharohiratruefriend	ISA		operon(Functional linkage) authors,K. Simola,RK. Selander,A. de la Chapelle,G. Corneo,E. Ginelli Molecular basis of chromosome banding. I. The effect of mouse DNA fractions on two fluorescent dyes in vitro. Chromosoma 1975
Interaction	InhibitedBy Rv2142c	harsharohiratruefriend	ISA		operon(Functional linkage) authors,KM. Dalton,S. Crosson A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Biochemistry 2010
Interaction	InhibitedBy Rv2142c	harsharohiratruefriend	ISA		operon(Functional linkage) authors,V. Anantharaman,L. Aravind New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol. 2003
Interaction	InhibitedBy Rv2142c	harsharohiratruefriend	ISA		operon(Functional linkage) authors,K. Gerdes,SK. Christensen,A. Lbner-Olesen Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005
Interaction	Inhibits Rv1959c	akankshajain.21	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	Inhibits Rv1959c	prabhakarsmail	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	akankshajain.21	IDA	19016878	Spectrophotometric analysis
Interaction	Inhibits Rv1959c	akankshajain.21	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	prabhakarsmail	IDA	19016878	Spectrophotometric analysis
Interaction	Inhibits Rv1959c	prabhakarsmail	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Symbol	ParD1	jlew			Relieves toxin activity. We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin. authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	jlew		19016878	Relieves toxin activity. We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin.
Symbol	Par DE-1	rslayden			Conserved hypothetical protein, similar to O85269
Other	start:2203974	rslayden			Conserved hypothetical protein, similar to O85269
Other	stop:2204225	rslayden			Conserved hypothetical protein, similar to O85269
Other	strand:+	rslayden			Conserved hypothetical protein, similar to O85269
Symbol	Par DE-1	rslayden			AF102990
Other	start:2203974	rslayden			AF102990
Other	stop:2204225	rslayden			AF102990
Other	strand:+	rslayden			AF102990
Symbol	Par DE-1	rslayden			AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).
Other	start:2203974	rslayden			AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).
Other	stop:2204225	rslayden			AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).
Other	strand:+	rslayden			AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).

Property

Value

Creator

Evidence

PMID

Comment

Interaction

InhibitedBy Rv2142c

harsharohiratruefriend

ISA

operon(Functional linkage)
authors,K. Simola,RK. Selander,A. de la Chapelle,G. Corneo,E. Ginelli Molecular basis of chromosome banding. I. The effect of mouse DNA fractions on two fluorescent dyes in vitro. Chromosoma 1975

Interaction

InhibitedBy Rv2142c

harsharohiratruefriend

ISA

operon(Functional linkage)
authors,KM. Dalton,S. Crosson A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex. Biochemistry 2010

Interaction

InhibitedBy Rv2142c

harsharohiratruefriend

ISA

operon(Functional linkage)
authors,V. Anantharaman,L. Aravind New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol. 2003

Interaction

InhibitedBy Rv2142c

harsharohiratruefriend

ISA

operon(Functional linkage)
authors,K. Gerdes,SK. Christensen,A. Lbner-Olesen Prokaryotic toxin-antitoxin stress response loci. Nat. Rev. Microbiol. 2005

Interaction

Inhibits Rv1959c

akankshajain.21

IDA

Spectrophotometric analysis
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Interaction

Inhibits Rv1959c

prabhakarsmail

IDA

Spectrophotometric analysis
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Citation

Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009

akankshajain.21

IDA

19016878

Spectrophotometric analysis

Interaction

Inhibits Rv1959c

akankshajain.21

IDA

Spectrophotometric analysis
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Citation

Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009

prabhakarsmail

IDA

19016878

Spectrophotometric analysis

Interaction

Inhibits Rv1959c

prabhakarsmail

IDA

Spectrophotometric analysis
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Symbol

ParD1

jlew

Relieves toxin activity. We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin.
authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009

Citation

Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009

jlew

19016878

Symbol

Par DE-1

rslayden

Conserved hypothetical protein, similar to O85269

Other

start:2203974

rslayden

Conserved hypothetical protein, similar to O85269

Other

stop:2204225

rslayden

Conserved hypothetical protein, similar to O85269

Other

strand:+

rslayden

Conserved hypothetical protein, similar to O85269

Symbol

Par DE-1

rslayden

AF102990

Other

start:2203974

rslayden

AF102990

Other

stop:2204225

rslayden

AF102990

Other

strand:+

rslayden

AF102990

Symbol

Par DE-1

rslayden

AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).

Other

start:2203974

rslayden

AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).

Other

stop:2204225

rslayden

AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).

Other

strand:+

rslayden

AF102990_51 hypothetical protein of Yersinia enterocolitica (80 aa), FASTA scores: opt: 149, E(): 0.00037, (42 .1% identity in 57 aa overlap).

Comments