Rv2188c (pimB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
- REFSEQ: hypothetical protein
- PATRIC: Poly(glycerol-phosphate) alpha-glucosyltransferase (EC 2.4.1.52)
- TUBERCULIST: Mannosyltransferase PimB
- NCBI: Mannosyltransferase PimB
- updated information (H37Rv4):
  - gene name: pimB
  - function:
  - reference:
Type: Essential
Start: 2449993
End: 2451150
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0097502 - mannosylation (Uniprot)
- GO:0046488 - phosphatidylinositol metabolic process (Uniprot)
- GO:0043750 - phosphatidylinositol alpha-mannosyltransferase activity (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0033164 - glycolipid 6-alpha-mannosyltransferase activity (Uniprot)
- GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0009247 - glycolipid biosynthetic process (Uniprot)
- GO:0008654 - phospholipid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0000030 - mannosyltransferase 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
3OKP	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' bound to GDP-Man (orthorhombic crystal form)
3OKC	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' bound to GDP (orthorhombic crystal form)
3OKA	50%	Corynebacterium glutamicum	Crystal structure of Corynebacterium glutamicum PimB' in complex with GDP-Man (triclinic crystal form)

Links to additional information on pimB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -2.75 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VSRVLLVTNDFPPRRGGIQSYLGEFVGRLVGSRAHAMTVYAPQWKGADAFDDAARAAGYRVVRHPSTVMLPGPTVDVRMRRLIAEHDIETVWFGAAAPLA
LLAPRARLAGASRVLASTHGHEVGWSMLPVARSVLRRIGDGTDVVTFVSSYTRSRFASAFGPAASLEYLPPGVDTDRFRPDPAARAELRKRYRLGERPTV
VCLSRLVPRKGQDTLVTALPSIRRRVDGAALVIVGGGPYLETLRKLAHDCGVADHVTFTGGVATDELPAHHALADVFAMPCRTRGAGMDVEGLGIVFLEA
SAAGVPVIAGNSGGAPETVQHNKTGLVVDGRSVDRVADAVAELLIDRDRAVAMGAAGREWVTAQWRWDTLAAKLADFLRGDDAAR

(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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 19 non-insertions in a row out of 19 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 19 non-insertions in a row out of 19 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 19 non-insertions in a row out of 19 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 19 non-insertions in a row out of 19 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 19 non-insertions in a row out of 19 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.07
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:
- Rv0880 (-) (Direct binding)
- Rv1990c (-) (Direct binding)
- Rv2034 (-) (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	GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase	mjackson	IDA		PIM, LM and LAM biosynthesis
Symbol	pimB'	mjackson	IMP		PIM, LM and LAM biosynthesis
Name	GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase	mjackson	IMP		PIM, LM and LAM biosynthesis
Symbol	pimB'	mjackson	IDA		PIM, LM and LAM biosynthesis
Other	TBPWY:PIM, LM and LAM biosynthesis	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) ME. Guerin, D. Kaur et al. New insights into the early steps of phosphatidylinositol mannoside biosynthesis in mycobacteria: PimB' is an essential enzyme of Mycobacterium smegmatis. J. Biol. Chem. 2009
Symbol	pimB'	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) DJ. Lea-Smith, KL. Martin et al. Analysis of a new mannosyltransferase required for the synthesis of phosphatidylinositol mannosides and lipoarbinomannan reveals two lipomannan pools in corynebacterineae. J. Biol. Chem. 2008
Citation	Analysis of a new mannosyltransferase required for the synthesis of phosphatidylinositol mannosides and lipoarbinomannan reveals two lipomannan pools in corynebacterineae. DJ. Lea-Smith, KL. Martin et al. J. Biol. Chem. 2008	mjackson		18178556	GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic)
Other	TBPWY:PIM, LM and LAM biosynthesis	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) DJ. Lea-Smith, KL. Martin et al. Analysis of a new mannosyltransferase required for the synthesis of phosphatidylinositol mannosides and lipoarbinomannan reveals two lipomannan pools in corynebacterineae. J. Biol. Chem. 2008
Symbol	pimB'	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) AK. Mishra, S. Batt et al. Characterization of the Corynebacterium glutamiucm{Delta}pimB'{Delta}mgtA double deletion mutant and the role of Mycobacterium tuberculosis orthologoues Rv2188c and Rv0557 in glycolipid biosynthesis. J. Bacteriol. 2009
Citation	Characterization of the Corynebacterium glutamiucm{Delta}pimB'{Delta}mgtA double deletion mutant and the role of Mycobacterium tuberculosis orthologoues Rv2188c and Rv0557 in glycolipid biosynthesis. AK. Mishra, S. Batt et al. J. Bacteriol. 2009	mjackson		19395496	GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic)
Other	TBPWY:PIM, LM and LAM biosynthesis	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) AK. Mishra, S. Batt et al. Characterization of the Corynebacterium glutamiucm{Delta}pimB'{Delta}mgtA double deletion mutant and the role of Mycobacterium tuberculosis orthologoues Rv2188c and Rv0557 in glycolipid biosynthesis. J. Bacteriol. 2009
Symbol	pimB'	mjackson			GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic) ME. Guerin, D. Kaur et al. New insights into the early steps of phosphatidylinositol mannoside biosynthesis in mycobacteria: PimB' is an essential enzyme of Mycobacterium smegmatis. J. Biol. Chem. 2009
Citation	New insights into the early steps of phosphatidylinositol mannoside biosynthesis in mycobacteria: PimB' is an essential enzyme of Mycobacterium smegmatis. ME. Guerin, D. Kaur et al. J. Biol. Chem. 2009	mjackson		19638342	GDP-Man-dependent alpha-1,6-phosphatidylinositol mannosyltransferase (phenotypic [corynebacterial recombinant strains]; enzymatic)

TB Genome Annotation Portal