Rv1106c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 3 beta-hydroxysteroid dehydrogenase/Delta 5-4-isomerase
- REFSEQ: cholesterol dehydrogenase
- PATRIC: PROBABLE CHOLESTEROL DEHYDROGENASE
- TUBERCULIST: 3-beta-hydroxysteroid dehydrogenase
- NCBI: 3-beta-hydroxysteroid dehydrogenase
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 1232844
End: 1233956
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0102294 - cholesterol dehydrogenase activity (Uniprot)
- GO:0070403 - NAD+ binding (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0030283 - testosterone dehydrogenase [NAD(P)] activity (Uniprot)
- GO:0016853 - isomerase activity (Uniprot)
- GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016042 - lipid catabolic process (Uniprot)
- GO:0008202 - steroid metabolic process (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006694 - steroid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005737 - cytoplasm (Uniprot)
- GO:0004769 - steroid delta-isomerase activity (Uniprot)
- GO:0003854 - 3-beta-hydroxy-delta5-steroid dehydrogenase activity (Uniprot)
- GO:0003824 - catalytic activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- H[c] + NAD[c] + CHOLESTEROL[c] -> NADH[c] + CHOLESTENONE[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
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
6JKH	36%	Homo sapiens	cholesterol-decarboxylating enzyme 2
6JKG	36%	Homo sapiens	cholesterol-decarboxylating enzyme 1

Links to additional information on Rv1106c:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.312 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MLRRMGDASLTTELGRVLVTGGAGFVGANLVTTLLDRGHWVRSFDRAPSLLPAHPQLEVLQGDITDADVCAAAVDGIDTIFHTAAIIELMGGASVTDEYR
QRSFAVNVGGTENLLHAGQRAGVQRFVYTSSNSVVMGGQNIAGGDETLPYTDRFNDLYTETKVVAERFVLAQNGVDGMLTCAIRPSGIWGNGDQTMFRKL
FESVLKGHVKVLVGRKSARLDNSYVHNLIHGFILAAAHLVPDGTAPGQAYFINDAEPINMFEFARPVLEACGQRWPKMRISGPAVRWVMTGWQRLHFRFG
FPAPLLEPLAVERLYLDNYFSIAKARRDLGYEPLFTTQQALTECLPYYVSLFEQMKNEARAEKTAATVKP

(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; 1 non-insertions in a row out of 17 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 17 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 0 non-insertions in a row out of 17 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: 1.15
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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv1990c (-) (Upstream of operon)

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv3574	priyadarshinipriyanka2001	IEP		Co-expression (Functional linkage) SL. Kendall,P. Burgess,R. Balhana,M. Withers,A. Ten Bokum,JS. Lott,C. Gao,I. Uhia Castro,NG. Stoker Cholesterol utilisation in mycobacteria is controlled by two TetR-type transcriptional regulators; kstR and kstR2. Microbiology (Reading, England) 2010
Interaction	Regulatory Rv3574	priyadarshinipriyanka2001	IEP		Co-expression (Functional linkage) SL. Kendall, M. Withers et al. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol. Microbiol. 2007
Interaction	RegulatedBy Rv3574	yamir.moreno	ISO		M.smegmatis orthology based inference. Orthologous pair regulator-target found in M.smegmatis. SL. Kendall, M. Withers et al. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol. Microbiol. 2007
Interaction	RegulatedBy Rv2711	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Citation	Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. X. Yang, E. Dubnau et al. Biochemistry 2007	nsampson		17630785	Assay of protein purified to homogeneity from a heterlogous host
Term	EC:5.3.3.1 Steroid Delta-isomerase. - NR	nsampson	NR		Assay of protein purified to homogeneity from a heterlogous host X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Term	EC:1.1.1.145 3-beta-hydroxy-Delta(5)-steroid dehydrogenase. - NR	nsampson	NR		Assay of protein purified to homogeneity from a heterlogous host X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Citation	Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. X. Yang, E. Dubnau et al. Biochemistry 2007	nsampson		17630785	Reaction blocked in mutant
Term	EC:5.3.3.1 Steroid Delta-isomerase. - NR	nsampson	NR		Reaction blocked in mutant X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Term	EC:1.1.1.145 3-beta-hydroxy-Delta(5)-steroid dehydrogenase. - NR	nsampson	NR		Reaction blocked in mutant X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Symbol	hsd	rslayden			X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Citation	Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. X. Yang, E. Dubnau et al. Biochemistry 2007	rslayden		17630785	None
Term	EC:1.1.1.145 3-beta-hydroxy-Delta(5)-steroid dehydrogenase. - NR	rslayden	NR		X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Term	EC:5.3.3.1 Steroid Delta-isomerase. - NR	rslayden	NR		X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Other	product:cholest-4-en-3-one	rslayden			X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Citation	Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. X. Yang, E. Dubnau et al. Biochemistry 2007	extern:JZUCKER		17630785	Assay of protein purified to homogeneity from its native host
Term	EC:1.5.1.30 Flavin reductase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from its native host X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007
Term	EC:1.3.1.24 Biliverdin reductase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from its native host X. Yang, E. Dubnau et al. Rv1106c from Mycobacterium tuberculosis is a 3beta-hydroxysteroid dehydrogenase. Biochemistry 2007

TB Genome Annotation Portal