Rv2289 (cdh)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: cdp-diacylglycerol pyrophosphatase cdh
- REFSEQ: CDP-diacylglycerol pyrophosphatase
- PATRIC: CDP-diacylglycerol pyrophosphatase (EC 3.6.1.26)
- TUBERCULIST: Probable CDP-diacylglycerol pyrophosphatase Cdh (CDP-diacylglycerol diphosphatase) (CDP-diacylglycerol phosphatidylhydrolase)
- NCBI: Probable CDP-diacylglycerol pyrophosphatase Cdh (CDP-diacylglycerol diphosphatase) (CDP-diacylglycerol phosphatidylhydrolase)
- updated information (H37Rv4):
  - gene name: cdh
  - function:
  - reference:
Type: Not Target
Start: 2561675
End: 2562457
Operon:

Trans-membrane region:
Role: I.H.3 - Acyltransferases, Mycoloyltransferases, and phospholipid synthesis
GO terms:
- GO:0046342 - CDP-diacylglycerol catabolic process (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0008715 - CDP-diacylglycerol diphosphatase activity (Uniprot)
- GO:0008654 - phospholipid biosynthetic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- CDPDG[c] -> 2 H[c] + CMP[c] + PA[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): (none with >35% aa id)
Links to additional information on cdh:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.83 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VPKSRRAVSLSVLIGAVIAALAGALIAVTVPARPNRPEADREALWKIVHDRCEFGYRRTGAYAPCTFVDEQSGTALYKADFDPYQFLLIPLARITGIEDP
ALRESAGRNYLYDAWAARFLVTARLNNSLPESDVVLTINPKNARTQDQLHIHISCSSPTTSAALRNVDTSEYVGWKQLPIDLGGRRFQGLAVDTKAFESR
NLFRDIYLKVTADGKKMENASIAVANVAQDQFLLLLAEGTEDQPVAAETLQDHDCSITKS

(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; 5 non-insertions in a row out of 22 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 5 non-insertions in a row out of 22 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 5 non-insertions in a row out of 22 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 21 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 21 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: 1.31
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 (-) (Direct binding)
- Rv0757 (phoP) (Direct binding)
- Rv3681c (whiB4) (Direct binding)
- Rv0691c (-) (Upstream of operon)
- Rv2250c (-) (Upstream of operon)
- Rv3133c (devR) (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:

Property	Value	Creator	Evidence	PMID	Comment
Citation	Genes required for mycobacterial growth defined by high density mutagenesis. authors,CM. Sassetti,DH. Boyd,EJ. Rubin Mol. Microbiol. 2003	njamshidi	IPI	12657046	Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046
Term	EC:3.6.1.26 CDP-diacylglycerol diphosphatase. - IPI	njamshidi	IPI		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Term	TBRXN:CDAPPA160 CDP-Diacylglycerol pyrophostatase (n-C16:0) - IPI	njamshidi	IPI		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Citation	Phosphatidylinositol is an essential phospholipid of mycobacteria. M. Jackson,DC. Crick,PJ. Brennan J. Biol. Chem. 2000	njamshidi	ISS	10889206	Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046
Term	EC:3.6.1.26 CDP-diacylglycerol diphosphatase. - ISS	njamshidi	ISS		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 M. Jackson,DC. Crick,PJ. Brennan Phosphatidylinositol is an essential phospholipid of mycobacteria. J. Biol. Chem. 2000
Term	TBRXN:CDAPPA160 CDP-Diacylglycerol pyrophostatase (n-C16:0) - ISS	njamshidi	ISS		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 M. Jackson,DC. Crick,PJ. Brennan Phosphatidylinositol is an essential phospholipid of mycobacteria. J. Biol. Chem. 2000
Citation	Genes required for mycobacterial growth defined by high density mutagenesis. authors,CM. Sassetti,DH. Boyd,EJ. Rubin Mol. Microbiol. 2003	njamshidi	ISS	12657046	Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046
Term	EC:3.6.1.26 CDP-diacylglycerol diphosphatase. - ISS	njamshidi	ISS		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Term	TBRXN:CDAPPA160 CDP-Diacylglycerol pyrophostatase (n-C16:0) - ISS	njamshidi	ISS		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Citation	Phosphatidylinositol is an essential phospholipid of mycobacteria. M. Jackson,DC. Crick,PJ. Brennan J. Biol. Chem. 2000	njamshidi	IPI	10889206	Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046
Term	EC:3.6.1.26 CDP-diacylglycerol diphosphatase. - IPI	njamshidi	IPI		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 M. Jackson,DC. Crick,PJ. Brennan Phosphatidylinositol is an essential phospholipid of mycobacteria. J. Biol. Chem. 2000
Term	TBRXN:CDAPPA160 CDP-Diacylglycerol pyrophostatase (n-C16:0) - IPI	njamshidi	IPI		Phosphatidylinositol is required for mtb growth - see: 10889206 and 12657046 M. Jackson,DC. Crick,PJ. Brennan Phosphatidylinositol is an essential phospholipid of mycobacteria. J. Biol. Chem. 2000
Interaction	RegulatedBy Rv0757	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. SB. Walters, E. Dubnau et al. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 2006

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