Rv3537 (kstD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 3-oxosteroid 1-dehydrogenase
- REFSEQ: 3-ketosteroid-delta-1-dehydrogenase
- PATRIC: 3-oxosteroid 1-dehydrogenase (EC 1.3.99.4)
- TUBERCULIST: Probable dehydrogenase
- NCBI: Probable dehydrogenase
- updated information (H37Rv4):
  - gene name: kstD
  - function:
  - reference:
Coordinates in H37Rv: 3975369 - 3977060
Gene length: 1692 bp (with stop codon), 563 aa (without stop codon)
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0047571 - 3-oxosteroid 1-dehydrogenase activity (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0016042 - lipid catabolic process (Uniprot)
- GO:0008202 - steroid metabolic process (Uniprot)
- GO:0006707 - cholesterol catabolic process (Uniprot)
- GO:0006694 - steroid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- 4ADSD[c] -> ADD[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
4C3Y	39%	RHODOCOCCUS ERYTHROPOLIS	Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
4C3X	39%	RHODOCOCCUS ERYTHROPOLIS	Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1

Links to additional information on kstD:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.983 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTVQEFDVVVVGSGAAGMVAALVAAHRGLSTVVVEKAPHYGGSTARSGGGVWIPNNEVLKRRGVRDTPEAARTYLHGIVGEIVEPERIDAYLDRGPEMLS
FVLKHTPLKMCWVPGYSDYYPEAPGGRPGGRSIEPKPFNARKLGADMAGLEPAYGKVPLNVVVMQQDYVRLNQLKRHPRGVLRSMKVGARTMWAKATGKN
LVGMGRALIGPLRIGLQRAGVPVELNTAFTDLFVENGVVSGVYVRDSHEAESAEPQLIRARRGVILACGGFEHNEQMRIKYQRAPITTEWTVGASANTGD
GILAAEKLGAALDLMDDAWWGPTVPLVGKPWFALSERNSPGSIIVNMSGKRFMNESMPYVEACHHMYGGEHGQGPGPGENIPAWLVFDQRYRDRYIFAGL
QPGQRIPSRWLDSGVIVQADTLAELAGKAGLPADELTATVQRFNAFARSGVDEDYHRGESAYDRYYGDPSNKPNPNLGEVGHPPYYGAKMVPGDLGTKGG
IRTDVNGRALRDDGSIIDGLYAAGNVSAPVMGHTYPGPGGTIGPAMTFGYLAALHIADQAGKR

(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

Rv3537/kstD, gene len: 1691 bp, num TA sites: 37

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	no data	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	non-essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	YES (LFC=-2.92)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	growth defect	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	growth defect	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=-0.657)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.82)	YM rich vs minimal medium	resampling

Analysis of Positive Selection in Clinical Isolates new

data from Culviner et al (2025) (55,259 Mtb clinical isolates)
- overall pN/pS for Rv3537: 0.527738601
- lineage-specific pN/pS in L1: 0.370125395
- lineage-specific pN/pS in L2: 0.616875658
- lineage-specific pN/pS in L3: 0.528750564
- lineage-specific pN/pS in L4: 0.595253212

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	2.11 (0.37)	2.25 (0.57)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

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:
- Rv3574 (kstR) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
- Rv0681 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv3574 (kstR)

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 Rv3416	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv3414c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv2021c	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv1956	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0491	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0117	yamir.moreno	IDA		One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
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
Term	EC:1.3.99.4 3-oxosteroid 1-dehydrogenase. - NR	nsampson	NR		Assay of protein purified to homogeneity from a heterlogous host authors,JK. Capyk,I. Casabon,R. Gruninger,NC. Strynadka,LD. Eltis Activity of 3-ketosteroid 9-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. J. Biol. Chem. 2011
Citation	Activity of 3-ketosteroid 9-hydroxylase (KshAB) indicates cholesterol side chain and ring degradation occur simultaneously in Mycobacterium tuberculosis. authors,JK. Capyk,I. Casabon,R. Gruninger,NC. Strynadka,LD. Eltis J. Biol. Chem. 2011	nsampson		21987574	Assay of protein purified to homogeneity from a heterlogous host
Citation	3-Keto-5alpha-steroid Delta(1)-dehydrogenase from Rhodococcus erythropolis SQ1 and its orthologue in Mycobacterium tuberculosis H37Rv are highly specific enzymes that function in cholesterol catabolism. J. Knol, K. Bodewits et al. Biochem. J. 2008	extern:JZUCKER		18031290	Assay of protein purified to homogeneity from its native host
Term	EC:1.3.99.4 3-oxosteroid 1-dehydrogenase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from its native host J. Knol, K. Bodewits et al. 3-Keto-5alpha-steroid Delta(1)-dehydrogenase from Rhodococcus erythropolis SQ1 and its orthologue in Mycobacterium tuberculosis H37Rv are highly specific enzymes that function in cholesterol catabolism. Biochem. J. 2008

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