Rv3569c (hsaD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: 45-910-diseco-3-hydroxy-5917-trioxoandrosta-1(10)2-diene-4-oate hydrolase
- REFSEQ: 2-hydroxy-6-oxo-6-phenylhexa-24-dienoate hydrolase BphD
- PATRIC: Poly(3-hydroxyalkanoate) depolymerase
- TUBERCULIST: 49-DHSA hydrolase
- NCBI: 4,9-DHSA hydrolase
- updated information (H37Rv4):
  - gene name: hsaD
  - function:
  - reference:
Type: Not Target
Start: 4010196
End: 4011071
Operon:

Trans-membrane region:
Role: IV.I - Miscellaneous phosphatases, lyases, and hydrolases
GO terms:
- GO:0102296 - 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase activity (Uniprot)
- GO:0044117 - growth of symbiont in host (Uniprot)
- GO:0034820 - 4,9-DSHA hydrolase activity (Uniprot)
- GO:0019439 - aromatic compound catabolic process (Uniprot)
- GO:0018774 - 2,6-dioxo-6-phenylhexa-3-enoate hydrolase activity (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016042 - lipid catabolic process (Uniprot)
- GO:0006694 - steroid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005515 - protein binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- 3 COA[c] + 4ANDROSTENEDIONE[c] -> PYR[c] + 3 PROPIONYLCOA[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: 2vf2, 2wue, 2wud, 2wug, 2wuf
Search for Homologs in PDB

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

PDB	aa ident	species	PDB title
5JZS	100%	Mycobacterium tuberculosis	HsaD bound to 3,5-dichloro-4-hydroxybenzoic acid
5JZB	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of HsaD bound to 3,5-dichlorobenzene sulphonamide
5JZ9	100%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of HsaD bound to 3,5-dichloro-4-hydroxybenzenesulphonic acid
2VF2	100%	MYCOBACTERIUM TUBERCULOSIS	X-ray crystal structure of HsaD from Mycobacterium tuberculosis
2WUG	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPDA
2WUF	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with 4,9DSHA
2WUE	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis in complex with HOPODA
2WUD	99%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of S114A mutant of HsaD from Mycobacterium tuberculosis
2PU5	44%	Burkholderia xenovorans	Crystal Structure of a C-C bond hydrolase, BphD, from Burkholderia xenovorans LB400
2OG1	44%	Burkholderia xenovorans	Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400

Links to additional information on hsaD:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.643 (from Jeremy Rock's lab)

Amino Acid Sequence

MTATEELTFESTSRFAEVDVDGPLKLHYHEAGVGNDQTVVLLHGGGPGAASWTNFSRNIAVLARHFHVLAVDQPGYGHSDKRAEHGQFNRYAAMALKGLF
DQLGLGRVPLVGNSLGGGTAVRFALDYPARAGRLVLMGPGGLSINLFAPDPTEGVKRLSKFSVAPTRENLEAFLRVMVYDKNLITPELVDQRFALASTPE
SLTATRAMGKSFAGADFEAGMMWREVYRLRQPVLLIWGREDRVNPLDGALVALKTIPRAQLHVFGQCGHWVQVEKFDEFNKLTIEFLGGGR

(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: 0.000050; 5 non-insertions in a row out of 14 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.001200; 3 non-insertions in a row out of 14 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 14 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 14 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.999800; 13 non-insertions in a row out of 14 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv0081 (-) (Upstream of operon)
- Rv0678 (-) (Upstream of operon)
- Rv0681 (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv1353c (-) (Upstream of operon)
- Rv1985c (-) (Upstream of operon)
- Rv3574 (kstR) (Upstream of operon)
- Rv3597c (lsr2) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv1353c (-)
- Rv2250c (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

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 Rv3574	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	A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. authors,R. Van der Geize,K. Yam,T. Heuser,MH. Wilbrink,H. Hara,MC. Anderton,E. Sim,L. Dijkhuizen,JE. Davies,WW. Mohn,LD. Eltis Proc. Natl. Acad. Sci. U.S.A. 2007	nsampson		17264217	Assay of unpurified protein expressed in a heterlogous host
Term	EC:3.7.1.- Hydrolases. Acting on carbon-carbon bonds. In ketonic substances. - NR	nsampson	NR		Assay of unpurified protein expressed in a heterlogous host authors,R. Van der Geize,K. Yam,T. Heuser,MH. Wilbrink,H. Hara,MC. Anderton,E. Sim,L. Dijkhuizen,JE. Davies,WW. Mohn,LD. Eltis A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. U.S.A. 2007
Citation	Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. authors,NA. Lack,KC. Yam,ED. Lowe,GP. Horsman,RL. Owen,E. Sim,LD. Eltis J. Biol. Chem. 2010	nsampson		19875455	Assay of protein purified to homogeneity from a heterlogous host
Term	EC:3.7.1.- Hydrolases. Acting on carbon-carbon bonds. In ketonic substances. - NR	nsampson	NR		Assay of protein purified to homogeneity from a heterlogous host authors,NA. Lack,KC. Yam,ED. Lowe,GP. Horsman,RL. Owen,E. Sim,LD. Eltis Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 2010
Citation	Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. authors,NA. Lack,KC. Yam,ED. Lowe,GP. Horsman,RL. Owen,E. Sim,LD. Eltis J. Biol. Chem. 2010	extern:JZUCKER		19875455	Assay of protein purified to homogeneity from a heterlogous host
Term	EC:4.1.2.37 Acetone-cyanohydrin lyase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from a heterlogous host authors,NA. Lack,KC. Yam,ED. Lowe,GP. Horsman,RL. Owen,E. Sim,LD. Eltis Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 2010
Other	EC:4.1.2.46	extern:JZUCKER			Assay of protein purified to homogeneity from a heterlogous host authors,NA. Lack,KC. Yam,ED. Lowe,GP. Horsman,RL. Owen,E. Sim,LD. Eltis Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 2010

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