Rv3790 (dprE1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: oxidoreductase
- REFSEQ: oxidoreductase
- PATRIC: Oxidoreductase FAD-binding protein
- TUBERCULIST: Decaprenylphosphoryl-beta-D-ribose 2'-oxidase
- NCBI: Decaprenylphosphoryl-beta-D-ribose 2'-oxidase
- updated information (H37Rv4):
  - gene name: dprE1
  - function:
  - reference:
Type: Essential
Start: 4235779
End: 4237164
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0070592 - cell wall polysaccharide biosynthetic process (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0050660 - flavin adenine dinucleotide binding (Uniprot)
- GO:0046677 - response to antibiotic (Uniprot)
- GO:0045227 - capsule polysaccharide biosynthetic process (Uniprot)
- GO:0042597 - periplasmic space (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0035884 - arabinan biosynthetic process (Uniprot)
- GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0003885 - D-arabinono-1,4-lactone oxidase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- DPPR[c] -> ARAFDPP[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: 4feh, 4fdo, 4fdn, 4ff6, 4fdp
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
6HFW	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis DprE1 in complex with CMP1
6HFV	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis DprE1 in complex with CMP2
6HF3	100%	Mycobacterium tuberculosis	M tuberculosis DprE1 in complex with a covalently bound nitrobenzothiazinone
6HF0	100%	Mycobacterium tuberculosis	M. tuberculosis DprE1 covalently bound to a nitrobenzoxacinone.
6HEZ	100%	Mycobacterium tuberculosis	M tuberculosis DprE1 in complex with BTZ043
6G83	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of M. tuberculosis DprE1 in complex with sPBTZ169 (sulfonylPBTZ)
5OEQ	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA020
5OEP	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis DprE1 in complex with inhibitor TCA481
4PFD	100%	Mycobacterium tuberculosis	Crystal structure of M. tuberculosis in complex with a cBT - non-covalent adduct
4PFA	100%	Mycobacterium tuberculosis	Crystal structure of M. tuberculosis in complex with BTO - covalent adduct

Links to additional information on dprE1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -9.417 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- BioCyc
- Systems Biology
- Mycobrowser
- PATRIC

Amino Acid Sequence

MLSVGATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQ
LMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFI
ADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKS
GTYRGKVQNLTQFYHPLDMFGEWNRAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFV
SELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL

(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; 26 non-insertions in a row out of 27 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 26 non-insertions in a row out of 27 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 26 non-insertions in a row out of 27 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 26 non-insertions in a row out of 28 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 26 non-insertions in a row out of 28 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.04
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:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1816 (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv3286c (sigF)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Term	TBRXN:DCPE decaprenylphosphoryl ribose, arabinofuranose isomerization - IDA	njamshidi	IDA	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	njamshidi	IPI	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose
Term	TBRXN:DCPE decaprenylphosphoryl ribose, arabinofuranose isomerization - IPI	njamshidi	IPI	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	njamshidi	IDA	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose
Symbol	dprE1	mjackson	IDA		Decaprenyl phosphoarabinose synthesis
Name	decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose synthase (AKA Decaprenylphosphoryl-D-ribose oxidase), the first step in epimerizing decaprenyl ribose to decaprenyl arabinose	mjackson	IDA		Decaprenyl phosphoarabinose synthesis
Symbol	dprE1	mmcneil			decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose synthase (AKA Decaprenylphosphoryl-D-ribose oxidase), the first step in epimerizing decaprenyl ribose to decaprenyl arabinose; enzymatic evidence K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	mmcneil		16291675	decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose synthase (AKA Decaprenylphosphoryl-D-ribose oxidase), the first step in epimerizing decaprenyl ribose to decaprenyl arabinose; enzymatic evidence
Term	GO:0009247 glycolipid biosynthetic process - NR	mmcneil	NR		decaprenylphosphoryl-2-keto-beta-D-erythro-pentofuranose synthase (AKA Decaprenylphosphoryl-D-ribose oxidase), the first step in epimerizing decaprenyl ribose to decaprenyl arabinose; enzymatic evidence K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. H. Huang, MS. Scherman et al. J. Biol. Chem. 2005	jjmcfadden		15878857	Inferred from direct assay
Term	EC:1.-.-.- Oxidoreductases. - NR	jjmcfadden	NR		Inferred from direct assay H. Huang, MS. Scherman et al. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. J. Biol. Chem. 2005
Citation	Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. H. Huang, MS. Scherman et al. J. Biol. Chem. 2005	extern:JZUCKER		15878857	Inferred from direct assay
Term	EC:1.-.-.- Oxidoreductases. - NR	extern:JZUCKER	NR		Inferred from direct assay H. Huang, MS. Scherman et al. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. J. Biol. Chem. 2005

TB Genome Annotation Portal