Rv3634c (galE1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: UDP-glucose 4-epimerase
- REFSEQ: UDP-glucose 4-epimerase GALE1 (galactowaldenase) (UDP-galactose 4-epimerase) (uridine diphosphate galactose 4-epimerase) (uridine diphospho-galactose 4-epimerase)
- PATRIC: UDP-glucose 4-epimerase (EC 5.1.3.2)
- TUBERCULIST: UDP-glucose 4-epimerase GalE1 (galactowaldenase) (UDP-galactose 4-epimerase) (uridine diphosphate galactose 4-epimerase) (uridine diphospho-galactose 4-epimerase)
- NCBI: UDP-glucose 4-epimerase GalE1 (galactowaldenase) (UDP-galactose 4-epimerase) (uridine diphosphate galactose 4-epimerase) (uridine diphospho-galactose 4-epimerase)
- updated information (H37Rv4):
  - gene name: galE1
  - function:
  - reference: Tardeshi (2017), PMID: 28403215
Type: Not Target
Start: 4072667
End: 4073611
Operon:

Trans-membrane region:
Role: I.C.3 - Sugar nucleotides
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0016853 - isomerase activity (Uniprot)
- GO:0006012 - galactose metabolic process (Uniprot)
- GO:0005975 - carbohydrate metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0003978 - UDP-glucose 4-epimerase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- UDPG[c] <=> UDPGAL[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
4ZRN	45%	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)	Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) with UDP-glucose from Hyperthermophilic Eubacterium Thermotoga Maritima
4ZRM	45%	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)	Crystal Structure of UDP-Glucose 4-Epimerase (TM0509) from Hyperthermophilic Eubacterium Thermotoga maritima
2P5Y	44%	Thermus thermophilus HB8	Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD
2P5U	44%	Thermus thermophilus HB8	Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD
6WJB	39%	Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)	UDP-GlcNAc C4-epimerase from Pseudomonas protegens in complex with NAD and UDP-GlcNAc
6WJA	38%	Pseudomonas protegens	UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GalNAc
6WJ9	38%	Pseudomonas protegens	UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GlcNAc

Links to additional information on galE1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -5.264 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VRALVTGAAGFIGSTLVDRLLADGHSVVGLDNFATGRATNLEHLADNSAHVFVEADIVTADLHAILEQHRPEVVFHLAAQIDVRRSVADPQFDAAVNVIG
TVRLAEAARQTGVRKIVHTSSGGSIYGTPPEYPTPETAPTDPASPYAAGKVAGEIYLNTFRHLYGLDCSHIAPANVYGPRQDPHGEAGVVAIFAQALLSG
KPTRVFGDGTNTRDYVFVDDVVDAFVRVSADVGGGLRFNIGTGKETSDRQLHSAVAAAVGGPDDPEFHPPRLGDLKRSCLDIGLAERVLGWRPQIELADG
VRRTVEYFRHKHTD

(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; 20 non-insertions in a row out of 20 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 20 non-insertions in a row out of 20 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 20 non-insertions in a row out of 20 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 20 non-insertions in a row out of 20 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 20 non-insertions in a row out of 20 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:
- Rv0260c (-)
- Rv0818 (-)

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:
- Rv0260c (-)
- Rv0818 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. PA. Fontn, V. Aris et al. Mycobacterium tuberculosis Sigma Factor E Regulon Modulates the Host Inflammatory Response. J. Infect. Dis. 2008
Interaction	RegulatedBy Rv3676	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv3676	yamir.moreno	ISO		E.coli orthology based inference. Orthologous pair regulator-target found in E.coli. authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
Name	UDP-Glucose-4-epimerase: formation of UDP-Galactopyranosem, the first step in the formation of UDP-Galactofuranose the donor of galactofuranosyl residues	mjackson	IDA		UDP-Galactofuranose synthesis
Citation	Biosynthetic origin of mycobacterial cell wall galactofuranosyl residues. A. Weston,RJ. Stern,RE. Lee,PM. Nassau,D. Monsey,SL. Martin,MS. Scherman,GS. Besra,K. Duncan,MR. McNeil Tuber. Lung Dis. 1997	mmcneil		9692181	UDP-Glucose-4-epimerase: formation of UDP-Galp the first step in the formation of UDP-Galf the donor of galactofuranosyl residues. Standard pathway; enzymatic evidence
Term	GO:0009226 nucleotide-sugar biosynthetic process - NR	mmcneil	NR		UDP-Glucose-4-epimerase: formation of UDP-Galp the first step in the formation of UDP-Galf the donor of galactofuranosyl residues. Standard pathway; enzymatic evidence A. Weston,RJ. Stern,RE. Lee,PM. Nassau,D. Monsey,SL. Martin,MS. Scherman,GS. Besra,K. Duncan,MR. McNeil Biosynthetic origin of mycobacterial cell wall galactofuranosyl residues. Tuber. Lung Dis. 1997
Citation	Biosynthetic origin of mycobacterial cell wall galactofuranosyl residues. A. Weston,RJ. Stern,RE. Lee,PM. Nassau,D. Monsey,SL. Martin,MS. Scherman,GS. Besra,K. Duncan,MR. McNeil Tuber. Lung Dis. 1997	extern:JZUCKER		9692181	Assay of protein purified to homogeneity from its native host
Term	EC:5.1.3.2 UDP-glucose 4-epimerase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from its native host A. Weston,RJ. Stern,RE. Lee,PM. Nassau,D. Monsey,SL. Martin,MS. Scherman,GS. Besra,K. Duncan,MR. McNeil Biosynthetic origin of mycobacterial cell wall galactofuranosyl residues. Tuber. Lung Dis. 1997

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