Rv0215c (fadE3)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: acyl-CoA dehydrogenase fadE3
- REFSEQ: acyl-CoA dehydrogenase FADE3
- PATRIC: Acyl-CoA dehydrogenase short-chain specific (EC 1.3.99.2)
- TUBERCULIST: Probable acyl-CoA dehydrogenase FadE3
- NCBI: Probable acyl-CoA dehydrogenase FadE3
- updated information (H37Rv4):
  - gene name: fadE3
  - function:
  - reference:
Type: Not Target
Start: 257783
End: 258856
Operon:

Trans-membrane region:
Role: I.A.3 - Fatty acids
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0050660 - flavin adenine dinucleotide binding (Uniprot)
- GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0008152 - metabolic process (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
4IV6	71%	Mycobacterium smegmatis	X-ray crystal structure of an isovaleryl-CoA dehydrogenase from Mycobacterium smegmatis
5LNX	39%	Bacillus subtilis (strain 168)	Crystal structure of MmgC, an acyl-CoA dehydrogenase from bacillus subtilis.
4U83	39%	Brucella abortus	Structure of Brucella Abortus Butyryl-CoA dehydrogenase
6ES9	39%	Paracoccus denitrificans (strain Pd 1222)	Methylsuccinyl-CoA dehydrogenase of Paracoccus denitrificans with bound flavin adenine dinucleotide
5OL2	37%	Clostridioides difficile	The electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile
2D29	37%	Thermus thermophilus	Structural study on project ID TT0172 from Thermus thermophilus HB8
2CX9	37%	Thermus thermophilus	Crystal structure of acyl-CoA dehydrogenase
1WS9	37%	Thermus thermophilus	Crystal structure of project ID TT0172 from Thermus thermophilus HB8
4N5F	37%	Burkholderia cenocepacia	Crystal Structure of a Putative acyl-CoA dehydrogenase with bound FADH2 from Burkholderia cenocepacia J2315
6FAH	36%	Acetobacterium woodii (strain ATCC 29683 / DSM 1030 / JCM 2381 / KCTC 1655 / WB1)	Molecular basis of the flavin-based electron-bifurcating caffeyl-CoA reductase reaction

Links to additional information on fadE3:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.193 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VRNELNDDEAMLVATVRAFIDRDVKPTVREVEHANSYPEAWIEQMKHIGIYGLAIDEQYGGSPVSMPCYVQVTQELARGWMSLAGAMGGHTVVAKLLTLF
GTEEQRRTYLPPMASGELRATMALTEPGGGSDLQNMSTTALADGPEGSAGLLINGCKTWISNARRSGLFAVLCKTDPNATPRHQGMSIVLVEPGPGLTVS
RDLPKLGYKGVESCELSFDNLRVPVSAILGGAMGQGFSQMMKGLETGRIQVAARALGVATAALEDSLAYAQQRESFGRPIWQHQAVGNYLADMATKLTAA
RQLTRYAAERYDSGQRCDMEAGMAKLFASEVAMEIALNAVRIHGGYGYSTEYDVERR

(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
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 18 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 18 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 18 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 18 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 18 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 2.33
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

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:
- No bindings to other targets were found.

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv0214	ahal4789	NAS		Co-expression (Functional linkage) J. Daniel, C. Deb et al. Induction of a novel class of diacylglycerol acyltransferases and triacylglycerol accumulation in Mycobacterium tuberculosis as it goes into a dormancy-like state in culture. J. Bacteriol. 2004
Interaction	PhysicalInteraction Rv0217c	shahanup86	NAS		Co-expression (Functional linkage) J. Daniel, C. Deb et al. Induction of a novel class of diacylglycerol acyltransferases and triacylglycerol accumulation in Mycobacterium tuberculosis as it goes into a dormancy-like state in culture. J. Bacteriol. 2004

TB Genome Annotation Portal