Rv0456A (mazF1)

Current annotations:
- TUBERCULIST: Possible toxin MazF1
- NCBI: Possible toxin MazF1
- updated information (H37Rv4):
  - gene name: mazF1
  - function:
  - reference:
Type: Not Target
Start: 547076
End: 547357
Operon:

Trans-membrane region:
Role: -
GO terms:
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0003677 - DNA 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
6KYT	60%	Mycobacterium tuberculosis H37Rv	The structure of the M. tb toxin MazEF-mt1 complex
6KYS	60%	Mycobacterium tuberculosis H37Rv	The structure of the M. tb toxin MazF-mt1
5HJZ	60%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Structure of M. tuberculosis MazF-mt1 (Rv2801c) in complex with RNA
6L29	57%	Mycobacterium tuberculosis	The structure of the MazF-mt1 mutant
6L2A	56%	Mycobacterium tuberculosis	The structure of the M. tb toxin MazEF-mt1 complex
6A6X	40%	Mycobacterium tuberculosis	The crystal structure of the Mtb MazE-MazF-mt9 complex
5WYG	40%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	The crystal structure of the apo form of Mtb MazF

Links to additional information on mazF1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.133 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MLRGEIWQVDLDPARGSAANMRRPAVIVSNDRANAAAIRLDRGVVPVVPVTSNTEKVPIPGVVAGSERWPGRRFEGAGPAGWIRRCATSPLPS

(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
Too-Short	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 4 sites
Too-Short	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 4 sites
Too-Short	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 4 sites
Too-Short	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 4 sites
Too-Short	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: -1.000000; 1 non-insertions in a row out of 4 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv0023 (-) (Direct binding)
- Rv0047c (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0324 (-) (Direct binding)
- Rv0465c (-) (Direct binding)
- Rv0472c (-) (Direct binding)
- Rv0757 (phoP) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1460 (-) (Direct binding)
- Rv1776c (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv3133c (devR) (Direct binding)
- Rv3246c (mtrA) (Direct binding)
- Rv3574 (kstR) (Direct binding)
- Rv3597c (lsr2) (Direct binding)
- Rv3765c (tcrX) (Direct binding)
- Rv3855 (ethR) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3849 (espR)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	priyadarshinipriyanka2001	TAS	19016878	None
Citation	Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. authors,HR. Ramage,LE. Connolly,JS. Cox PLoS Genet. 2009	jlew		20011113	MazF homolog, Not toxic when expressed in Msmeg
Citation	Characterization of mRNA interferases from Mycobacterium tuberculosis. authors,L. Zhu,Y. Zhang,JS. Teh,J. Zhang,N. Connell,H. Rubin,M. Inouye J. Biol. Chem. 2006	jlew		16611633	None
Symbol	mazF-mt2	jlew			authors,L. Zhu,Y. Zhang,JS. Teh,J. Zhang,N. Connell,H. Rubin,M. Inouye Characterization of mRNA interferases from Mycobacterium tuberculosis. J. Biol. Chem. 2006

TB Genome Annotation Portal