Rv0827c (kmtR)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ArsR family transcriptional regulator
- REFSEQ: transcriptional regulatory protein
- PATRIC: transcriptional regulator ArsR family
- TUBERCULIST: Metal sensor transcriptional regulator KmtR (ArsR-SmtB family)
- NCBI: Metal sensor transcriptional regulator KmtR (ArsR-SmtB family)
- updated information (H37Rv4):
  - gene name: kmtR
  - function:
  - reference:
Type: Not Target
Start: 920741
End: 921133
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0032025 - response to cobalt ion (Uniprot)
- GO:0010045 - response to nickel cation (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0003700 - DNA binding transcription factor 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
4ON0	42%	Sinorhizobium fredii	Crystal Structure of NolR from Sinorhizobium fredii in complex with oligo AA DNA
4OMZ	42%	Sinorhizobium fredii	Crystal Structure of NolR from Sinorhizobium fredii
4OMY	42%	Sinorhizobium fredii	Crystal Structure of SeMet NolR from Sinorhizobium fredii in complex with oligo AT DNA
3PQK	38%	Xylella fastidiosa	Crystal Structure of the transcriptional repressor BigR from Xylella fastidiosa
3PQJ	38%	Xylella fastidiosa	Crystal Structure of the transcriptional repressor BigR from Xylella fastidiosa
1R22	37%	Synechococcus elongatus PCC 7942	Crystal structure of the cyanobacterial metallothionein repressor SmtB (C14S/C61S/C121S mutant) in the Zn2alpha5-form
4OOI	37%	Vibrio cholerae	Reduced HlyU from Vibrio cholerae N16961
4K2E	37%	Vibrio cholerae	HlyU from Vibrio cholerae N16961
6O8O	36%	Rhodobacter capsulatus	Crystal Structure of C9S disulfide state of Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.
6O8N	36%	Rhodobacter capsulatus	Crystal Structure of C9S tetrasulfide state of Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.

Links to additional information on kmtR:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.376 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MYADSGPDPLPDDQVCLVVEVFRMLADATRVQVLWSLADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRDGTTIFYRLENEHVRQLVIDAVFNA
EHAGPGIPRHHRAAGGLQSVAKASATKDVG

(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 6 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 6 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 6 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 7 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 7 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: 0.91
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

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

Binds To:
- Rv0825c (-) (Direct binding)
- Rv0826 (-) (Direct binding)
- Rv0827c (kmtR) (Direct binding)
- Rv3660c (-) (Direct binding)
- Rv3661 (-) (Direct binding)
Bound By:
- Rv0827c (kmtR) (Direct binding)
- Rv2034 (-) (Direct binding)

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

Upregulates:
Upregulated by:
Downregulates:
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Activates Rv2025c	akankshajain.21	IDA		Band Shift DR. Campbell, KE. Chapman et al. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J. Biol. Chem. 2007
Interaction	Activates Rv2025c	prabhakarsmail	IDA		Band Shift DR. Campbell, KE. Chapman et al. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J. Biol. Chem. 2007
Citation	Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. DR. Campbell, KE. Chapman et al. J. Biol. Chem. 2007	diponlove	IMP	17726022	Co-expression (Functional linkage)
Interaction	Transcription Rv2025c	diponlove	IMP		Co-expression (Functional linkage) DR. Campbell, KE. Chapman et al. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J. Biol. Chem. 2007
Interaction	Transcription Rv0827c	diponlove	IMP		Co-expression (Functional linkage) DR. Campbell, KE. Chapman et al. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J. Biol. Chem. 2007
Interaction	Transcription Rv0827c	diponlove	IMP		Co-expression (Functional linkage) DR. Campbell, KE. Chapman et al. Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. J. Biol. Chem. 2007
Interaction	RegulatedBy Rv0981	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.. H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006

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