Rv1208 (gpgS)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: glucosyl-3-phosphoglycerate synthase
- REFSEQ: putative glucosyl-3-phosphoglycerate synthase
- PATRIC: Glycosyltransferases involved in cell wall biogenesis
- TUBERCULIST: Probable glucosyl-3-phosphoglycerate synthase GpgS
- NCBI: Probable glucosyl-3-phosphoglycerate synthase GpgS
- updated information (H37Rv4):
  - gene name: gpgS
  - function:
  - reference:
Type: Essential
Start: 1352144
End: 1353118
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0046872 - metal ion binding (Uniprot)
- GO:0042803 - protein homodimerization activity (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016758 - transferase activity, transferring hexosyl groups (Uniprot)
- GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0006011 - UDP-glucose metabolic process (Uniprot)
- GO:0000287 - magnesium ion 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: 4de7, 3e25, 4ddz, 4dec, 3e26
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
5JUD	100%	Mycobacterium bovis AF2122/97	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with uridine-diphosphate (UDP) - GpgS*UDP
5JUC	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgSGPGUDP*Mn2+_2
5JT0	100%	Mycobacterium tuberculosis	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgSGPGUDP*Mn2+
5JSX	100%	Mycobacterium tuberculosis H37Ra	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+ and uridine-diphosphate-glucose (UDP-Glc)
5JQX	100%	Mycobacterium tuberculosis H37Rv	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with phosphoglyceric acid (PGA) - GpgS*PGA
5JQQ	100%	Mycobacterium tuberculosis H37Ra	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form
4Y9X	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and phosphoglyceric acid (PGA) - GpgS Mn2+ UDP-Glc PGA-3
4Y7G	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and glycerol 3-phosphate (G3P) - GpgS Mn2+ UDP-Glc G3P
4Y7F	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and 3-(phosphonooxy)propanoic acid (PPA) - GpgS Mn2+ UDP-Glc PPA
4Y6U	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterial protein

Links to additional information on gpgS:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -4.054 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTASELVAGDLAGGRAPGALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVS
REQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRP
ELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDD
SDYTRHTWPVSLVDRPPMKVMRPR

(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: 0.999550; 14 non-insertions in a row out of 14 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.999950; 14 non-insertions in a row out of 14 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 14 non-insertions in a row out of 14 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999950; 14 non-insertions in a row out of 14 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 14 non-insertions in a row out of 14 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.09
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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1353c (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1049 (-) (Direct binding)
- Rv1353c (-) (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:
- Rv1353c (-)

Property	Value	Creator	Evidence	PMID	Comment
Symbol	gpgS	mjackson	IDA		Other (lipo)polysaccharides [Methylglucose lipolysaccharides, glycogen and capsular alpha-1,4 glucan]
Name	Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis	mjackson	IDA		Other (lipo)polysaccharides [Methylglucose lipolysaccharides, glycogen and capsular alpha-1,4 glucan]
Symbol	gpgS	mjackson	IMP		Other (lipo)polysaccharides [Methylglucose lipolysaccharides, glycogen and capsular alpha-1,4 glucan]
Name	Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis	mjackson	IMP		Other (lipo)polysaccharides [Methylglucose lipolysaccharides, glycogen and capsular alpha-1,4 glucan]
Symbol	gpgS	mjackson			Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic) N. Empadinhas, L. Albuquerque et al. Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase. FEMS Microbiol. Lett. 2008
Citation	Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase. N. Empadinhas, L. Albuquerque et al. FEMS Microbiol. Lett. 2008	mjackson		18221489	Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic)
Other	TBPWY:(MGLP and alpha-1,4 glucans)	mjackson			Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic) N. Empadinhas, L. Albuquerque et al. Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase. FEMS Microbiol. Lett. 2008
Symbol	gpgS	mjackson			Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic) D. Kaur, H. Pham et al. Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria. PLoS ONE 2009
Citation	Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria. D. Kaur, H. Pham et al. PLoS ONE 2009	mjackson		19421329	Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic)
Other	TBPWY:(MGLP and alpha-1,4 glucans)	mjackson			Glucosyl-3-phosphoglycerate synthase involved in methylglucose lipolysaccharide synthesis (phenotypic [mycobacterial recombinant strains]; enzymatic) D. Kaur, H. Pham et al. Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria. PLoS ONE 2009

TB Genome Annotation Portal