Rv2952 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: phthiotriol/phenolphthiotriol dimycocerosates methyltransferase
- REFSEQ: methyltransferase (methylase)
- PATRIC: Phthiotriol/phenolphthiotriol dimycocerosates methyltransferase
- TUBERCULIST: Possible methyltransferase (methylase)
- NCBI: Possible methyltransferase (methylase)
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 3304441
End: 3305253
Operon:

Trans-membrane region:
Role: IV.H - Miscellaneous transferases
GO terms:
- GO:0071770 - DIM/DIP cell wall layer assembly (Uniprot)
- GO:0032259 - methylation (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0008171 - O-methyltransferase activity (Uniprot)
- GO:0008168 - methyltransferase activity (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- SAM[c] + PPTT[c] -> SAH[c] + PPTC[c]
- SAM[c] + PTT[c] -> SAH[c] + PTC[c]
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
2GS9	39%	Thermus thermophilus	Crystal structure of TT1324 from Thermus thermophilis HB8
1VLM	36%	Thermotoga maritima	Crystal structure of SAM-dependent methyltransferase, possible histamine N-methyltransferase (TM1293) from Thermotoga maritima at 2.20 A resolution
3L8D	35%	Bacillus thuringiensis	Crystal structure of methyltransferase from Bacillus Thuringiensis

Links to additional information on Rv2952:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.98 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MAFSRTHSLLARAGSTSTYKRVWRYWYPLMTRGLGNDEIVFINWAYEEDPPMDLPLEASDEPNRAHINLYHRTATQVDLGGKQVLEVSCGHGGGASYLTR
TLHPASYTGLDLNQAGIKLCKKRHRLPGLDFVRGDAENLPFDDESFDVVLNVEASHCYPHFRRFLAEVVRVLRPGGYFPYADLRPNNEIAAWEADLAATP
LRQLSQRQINAEVLRGIGNNSQKSRDLVDRHLPAFLRFAGREFIGVQGTQLSRYLEGGELSYRMYCFTKD

(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 16 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 16 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 16 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 16 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 16 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: 0.93
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv0302 (-) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv3133c (devR) (Direct binding)

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Name	SAM-dependent O-methyltransferase involved in the formation of (phenol)phthiocerol dimycocerosates from (phenol)phthiodiolone dimycocerosates. Catalyzes the transfer of a methyl group to the third hydroxyl group of (phenol)phthiotriol in phthiocerol dimycocerosates and glycosylated phenolphthiotriol dimycocerosates	mjackson	IMP		Phthiocerol dimycocerosates (PDIM), phenolic glycolipids (PGL) and para-hydroxybenzoic acid derivatives
Other	TBPWY:Phthiocerol dimycocerosates, PGL & pHBAD	mjackson			SAM-dependent O-methyltransferase involved in the formation of (phenol)phthiocerol dimycocerosates from (phenol)phthiodiolone dimycocerosates. Catalyzes the transfer of a methyl group to the third hydroxyl group of (phenol)phthiotriol in phthiocerol dimycocerosates and glycosylated phenolphthiotriol dimycocerosates (phenotypic [mycobacterial recombinant strains]) R. Simone, P. Constant et al. Molecular dissection of the biosynthetic relationship between phthiocerol and phthiodiolone dimycocerosates and their critical role in the virulence and permeability of Mycobacterium tuberculosis. FEBS J. 2007
Citation	Molecular dissection of the role of two methyltransferases in the biosynthesis of phenolglycolipids and phthiocerol dimycoserosate in the Mycobacterium tuberculosis complex. E. Prez, P. Constant et al. J. Biol. Chem. 2004	mjackson		15292265	SAM-dependent O-methyltransferase involved in the formation of (phenol)phthiocerol dimycocerosates from (phenol)phthiodiolone dimycocerosates. Catalyzes the transfer of a methyl group to the third hydroxyl group of (phenol)phthiotriol in phthiocerol dimycocerosates and glycosylated phenolphthiotriol dimycocerosates (phenotypic [mycobacterial recombinant strains])
Other	TBPWY:Phthiocerol dimycocerosates, PGL & pHBAD	mjackson			SAM-dependent O-methyltransferase involved in the formation of (phenol)phthiocerol dimycocerosates from (phenol)phthiodiolone dimycocerosates. Catalyzes the transfer of a methyl group to the third hydroxyl group of (phenol)phthiotriol in phthiocerol dimycocerosates and glycosylated phenolphthiotriol dimycocerosates (phenotypic [mycobacterial recombinant strains]) E. Prez, P. Constant et al. Molecular dissection of the role of two methyltransferases in the biosynthesis of phenolglycolipids and phthiocerol dimycoserosate in the Mycobacterium tuberculosis complex. J. Biol. Chem. 2004
Citation	Molecular dissection of the biosynthetic relationship between phthiocerol and phthiodiolone dimycocerosates and their critical role in the virulence and permeability of Mycobacterium tuberculosis. R. Simone, P. Constant et al. FEBS J. 2007	mjackson		17371506	SAM-dependent O-methyltransferase involved in the formation of (phenol)phthiocerol dimycocerosates from (phenol)phthiodiolone dimycocerosates. Catalyzes the transfer of a methyl group to the third hydroxyl group of (phenol)phthiotriol in phthiocerol dimycocerosates and glycosylated phenolphthiotriol dimycocerosates (phenotypic [mycobacterial recombinant strains])
Citation	Characterization of three glycosyltransferases involved in the biosynthesis of the phenolic glycolipid antigens from the Mycobacterium tuberculosis complex. E. Prez, P. Constant et al. J. Biol. Chem. 2004	jjmcfadden		15292272	Inferred from direct assay
Term	EC:2.1.1.- Transferases. Transferring one-carbon groups. Methyltransferases. - NR	jjmcfadden	NR		Inferred from direct assay E. Prez, P. Constant et al. Characterization of three glycosyltransferases involved in the biosynthesis of the phenolic glycolipid antigens from the Mycobacterium tuberculosis complex. J. Biol. Chem. 2004

TB Genome Annotation Portal