Rv2207 (cobT)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase
- REFSEQ: nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
- PATRIC: Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21)
- TUBERCULIST: Probable nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase CobT
- NCBI: Probable nicotinate-nucleotide-dimethylbenzimidazol phosphoribosyltransferase CobT
- updated information (H37Rv4):
  - gene name: cobT
  - function:
  - reference:
Type: Not Target
Start: 2471411
End: 2472496
Operon:

Trans-membrane region:
Role: I.G.13 - Cobalamin
GO terms:
- GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0009236 - cobalamin biosynthetic process (Uniprot)
- GO:0009163 - nucleoside biosynthetic process (Uniprot)
- GO:0008939 - nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity (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
1WX1	49%	Thermus thermophilus HB8	Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8
1J33	49%	Thermus thermophilus	Crystal structure of CobT from Thermus thermophilus HB8
4KQK	36%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol
4KQJ	36%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT S80Y/Q88M/L175M complexed with p-cresol and NaMN
4KQG	35%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT E174A complexed with DMB
4KQF	35%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT E174A complexed with adenine
1D0V	35%	Salmonella typhimurium	CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE:5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH ITS REACTION PRODUCTS DETERMINED TO 1.9 A RESOLUTION
1D0S	35%	Salmonella typhimurium	CRYSTAL STRUCTURE OF NICOTINATE MONONUCLEOTIDE : 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH 5, 6-DIMETHYLBENZIMIDAZOLE
4KQI	35%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT E317A complexed with its reaction products
4KQH	35%	Salmonella enterica subsp. enterica serovar Typhimurium	Crystal structure of CobT E317A

Links to additional information on cobT:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -7.656 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MIGFAPVSTPDAAAEAAARARQDSLTKPRGALGSLEDLSVWVASCQQRCPPRQFERARVVVFAGDHGVARSGVSAYPPEVTAQMVANIDAGGAAINALAD
VAGATVRVADLAVDADPLSERIGAHKVRRGSGNIATEDALTNDETAAAITAGQQIADEEVDAGADLLIAGDMGIGNTTAAAVLVAALTDAEPVAVVGFGT
GIDDAGWARKTAAVRDALFRVRPVLPDPVGLLRCAGGADLAAIAGFCAQAAVRRTPLLLDGVAVTAAALVAERLAPGAHRWWQAGHRSSEPGHGLALAAL
GLDPIVDLHMRLGEGTGAAVALMVLRAAVAALSSMATFTEAGVSTRSVDGVDRTAPPAVSP

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.968600; 8 non-insertions in a row out of 8 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.995550; 8 non-insertions in a row out of 8 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.987400; 7 non-insertions in a row out of 8 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.759350; 5 non-insertions in a row out of 8 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.994100; 8 non-insertions in a row out of 8 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

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:
- No bindings to other targets were found.

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.

TB Genome Annotation Portal