Rv3409c (choD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: cholesterol oxidase
- REFSEQ: cholesterol oxidase precursor
- PATRIC: Cholesterol oxidase (EC 1.1.3.6)
- TUBERCULIST: Cholesterol oxidase ChoD (cholesterol-O2 oxidoreductase)
- NCBI: Cholesterol oxidase ChoD (cholesterol-O2 oxidoreductase)
- updated information (H37Rv4):
  - gene name: choD
  - function:
  - reference:
Type: Not Target
Start: 3826991
End: 3828727
Operon:

Trans-membrane region:
Role: I.A.3 - Fatty acids
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0016995 - cholesterol oxidase activity (Uniprot)
- GO:0016853 - isomerase activity (Uniprot)
- GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0008203 - cholesterol metabolic process (Uniprot)
- GO:0008202 - steroid metabolic process (Uniprot)
- GO:0006694 - steroid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0004769 - steroid delta-isomerase 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): (none with >35% aa id)
Links to additional information on choD:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.729 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MKPDYDVLIIGSGFGGSVTALRLTEKGYRVGVLEAGRRFSDEEFAKTSWDLRKFLWAPRLGCYGIQRIHPLRNVMILAGAGVGGGSLNYANTLYVPPEPF
FADQQWSHITDWRGELMPHYQQAQRMLGVVQNPTFTDADRIVKEVADEMGFGDTWVPTPVGVFFGPDGTKTPGKTVPDPYFGGAGPARTGCLECGCCMTG
CRHGAKNTLVKNYLGLAESAGAQVIPMTTVKGFERRSDGLWEVRTVRTGSWLRRDRRTFTATQLVLAAGTWGTQHLLFKMRDRGRLPGLSKRLGVLTRTN
SESIVGAATLKVNPDLDLTHGVAITSSIHPTADTHIEPVRYGKGSNAMGLLQTLMTDGSGPQGTDVPRWRQLLQTASQDPRGTIRMLNPRQWSERTVIAL
VMQHLDNSITTFTKRGKLGIRWYSSKQGHGEPNPTWIPIGNQVTRRIAAKIDGVAGGTWGELFNIPLTAHFLGGAVIGDDPEHGVIDPYHRVYGYPTLYV
VDGAAISANLGVNPSLSIAAQAERAASLWPNKGETDRRPPQGEPYRRLAPIQPAHPVVPADAPGALRWLPIDPVSNAG

(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; 2 non-insertions in a row out of 22 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 22 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 22 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.041950; 3 non-insertions in a row out of 22 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000150; 2 non-insertions in a row out of 22 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: 0.33
Growth-Advantage	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:
- Rv0047c (-) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv3249c (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0818 (-)
- Rv1956 (higA)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Cholesterol oxidase is required for virulence of Mycobacterium tuberculosis. A. Brzostek, B. Dziadek et al. FEMS Microbiol. Lett. 2007	extern:JZUCKER		17651430	Inferred from mutant phenotype
Term	EC:1.1.3.6 Cholesterol oxidase. - NR	extern:JZUCKER	NR		Inferred from mutant phenotype A. Brzostek, B. Dziadek et al. Cholesterol oxidase is required for virulence of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2007

TB Genome Annotation Portal