Rv3263 (MamA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: methyltransferase
- REFSEQ: DNA methylase (modification methylase) (methyltransferase)
- PATRIC: probable DNA methylase
- TUBERCULIST: Probable DNA methylase (modification methylase) (methyltransferase)
- NCBI: Probable DNA methylase (modification methylase) (methyltransferase)
- updated information (H37Rv4):
  - gene name: mamA
  - function: primary DNA methylase; methylates adenosine at consensus sites CTGGAG
  - reference: Shell (2013) PMID: 23853579
Type: Not Target
Start: 3643177
End: 3644838
Operon:

Trans-membrane region:
Role: II.A.5 - DNA replication, repair, recombination and restriction/modification
GO terms:
- GO:0032259 - methylation (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0008168 - methyltransferase activity (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0003676 - nucleic acid binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- 5 ATP[c] + 5 GLU[c] + F420[0][c] -> F420[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): (none with >35% aa id)
Links to additional information on MamA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.461 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- Pubmed - (Shell et al., 2013)
- Pubmed - RNA-seq data in GEO

Amino Acid Sequence

MQPSHPTRPGAVIRYVGSSLDTCPMTTFAGKTAASADKVRGGYYTPPAVARFLAHWVHQAGPKILEPSCGDGRILRELSAITDHAHGVELVAREAKKSRD
FASVDTENLFTWLHKTQLGSWDGVAGNPPYIRFGNWASEQRDPALELMRRVGLRPTKLTNAWVPFVVASTTLARDGGRVGLVVPAELLQVTYAAQLREFL
LSRYREITLVTFERLVFDGILQEVVLFCGVVGPGPAHIRTVRLGDANDLNALGDKDFTNESAPALLHEKEKWTKYFLDPAQIRLLRGLKQSATMIRLGEL
ADVDVGIVTGRNSFFTFTDAKAQALGLRAHCVPLVSRSAQLSGLIYDEDCRACDVAGNHRTWLLDAADYPTDPALVAHITAGEAAGVHLGYKCSIRKPWW
STPSLWMPDLFMLRQIHFAPRLTVNAAAATSTDTVHRVRLDPNVDPATLAAVFHNSATFAFAEIMGRSYGGGILELEPREAEQLPMPPPAYGSAELAQDV
DLLLKANEIDKALDVVDRHVLIDGLGLSPRLVAGCRAAWLTLRDRRTKRGSRR

(Nucleotide sequence available on KEGG)

Additional Information

Identified as the primary DNA methylase.
Recognized CTGGAG, methylates adenosines.
(Shell et al., 2013)

The RNA-Seq dataset was deposited in NCBI GEO with accession number GSE52551.
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52551

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; 3 non-insertions in a row out of 29 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 29 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 29 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 30 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 30 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: 0.65
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.

collected by: Scarlet Shell (c. 2013)
GEO accession: GSE52551
counts/RPKMs: RNA_delta_Rv3263_expr.dat, RNA_H37Rv_SS1_expr.dat
DeSeq analysis: DeSeq_delta_Rv3263_expr.xlsx (differentially expressed genes with qval<0.05 are marked in yellow)

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:
- Rv2250c (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv3223c (sigH)
- Rv3849 (espR)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Translation Rv3259	shahanup86	ISA		Gene Neighborhood (Functional linkage) KP. Choi, TB. Bair et al. Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG. J. Bacteriol. 2001
Interaction	Translation Rv3259	vashishtrv	ISA		Gene Neighborhood (Functional linkage) KP. Choi, TB. Bair et al. Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG. J. Bacteriol. 2001
Citation	Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F(420) and FO biosynthesis. KP. Choi, N. Kendrick et al. J. Bacteriol. 2002	jjmcfadden		11948155	Inferred from direct assay
Term	EC:2.1.1.37 DNA (cytosine-5-)-methyltransferase. - NR	jjmcfadden	NR		Inferred from direct assay KP. Choi, N. Kendrick et al. Demonstration that fbiC is required by Mycobacterium bovis BCG for coenzyme F(420) and FO biosynthesis. J. Bacteriol. 2002

TB Genome Annotation Portal