Rv1028c (kdpD)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: sensor protein kdpD
- REFSEQ: sensor protein KDPD
- PATRIC: Osmosensitive K+ channel histidine kinase KdpD (EC 2.7.3.-)
- TUBERCULIST: Probable sensor protein KdpD
- NCBI: Probable sensor protein KdpD
- updated information (H37Rv4):
  - gene name: kdpD
  - function:
  - reference:
Type: Not Target
Start: 1149104
End: 1151686
Operon:

Trans-membrane region:
Role: I.J.2 - Two component systems
GO terms:
- GO:0023014 - signal transduction by protein phosphorylation (Uniprot)
- GO:0018106 - peptidyl-histidine phosphorylation (Uniprot)
- GO:0016772 - transferase activity, transferring phosphorus-containing groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0016310 - phosphorylation (Uniprot)
- GO:0016301 - kinase activity (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0007165 - signal transduction (Uniprot)
- GO:0006950 - response to stress (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005737 - cytoplasm (Uniprot)
- GO:0005524 - ATP binding (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0004673 - protein histidine kinase activity (Uniprot)
- GO:0000166 - nucleotide binding (Uniprot)
- GO:0000160 - phosphorelay signal transduction system (Uniprot)
- GO:0000155 - phosphorelay sensor kinase 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):

PDB aa ident species PDB title

2R8R 52% Pseudomonas syringae pv. tomato Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000
Links to additional information on kdpD:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.103 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
2R8R	52%	Pseudomonas syringae pv. tomato	Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000

Amino Acid Sequence

VTLLFADLCAIFTPYRWMIEHVTTKRGQLRIYLGAAPGVGKTYAMLGEAHRRLERGTDVVAAVVETHGRNKTAKLLEGIEMIPPRYVEYRGARFPELDVE
AVLRRHPQVVLVDELAHTNTPGSKNPKRWQDVQEILDAGITVISTVNIQHLEGLNDVVEQITGIEQKEKIPDEIVRAADQVELVDITPEALRRRLAHGNV
YAAERVDAALSNYFRTGNLTALREIALLWLADQVDAALEKYRADKKITATWEARERVVVAVTGGPESETLVRRASRIASKSSAELMVVHVIRGDGLAGVS
APQLGRVRELATSLGATMHTVVGDDVPTALLDFAREMNATQLVVGTSRRSRWARLFDEGIGARTVQEPGGIDVHMVTHPAASRASGWSRVSPRERHIASW
LAALVVPSVICAITVAWLDRFMGIGGESALFFIGVLIVALLGGVAPAALSALLSGMLLNYFLTEPRYTWTIAEPDAAVTEFVLLAMAVAVAVLVDGAASR
TREARRASQEAELLALFAGSVLRGADLATLLQRVRETYSQRAVTMLRVRQGASTGETVACVGTNPCRDVDSADTAIEVGDDEFWMLMAGRKLAARDRRVL
TAVATQAAGLVKQRELAEEAGQAEAIARADELRRSLLSAVSHDLRTPLAAAKVAVSSLRTEDVAFSPEDTAELLATIEESIDQLTALVANLLDSSRLAAG
VIRPQLRRAYLEEAVQRALVSIGKGATGFYRSGIDRVKVDVGDAVAMADAGLLERVLANLIDNALRYAPDCVVRVNAGRVRERVLINVIDEGPGVPRGTE
EQLFAPFQRPGDHDNTTGVGLGMSVARGFVEAMGGTISATDTPGGGLTVVIDLAAPEDRP

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

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)	2.27 (0.66)	1.88 (0.98)
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"

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv1028c/kdpD, gene len: 2582 bp, num TA sites: 28

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	non-essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	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	non-essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.08)	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	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=-0.153)	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, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=-1.4)	YM rich vs minimal medium	resampling

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:
- No bindings to other targets were found.

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 Rv1368	swetha.r	IPI		Yeast three-hybrid (Physical interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Interaction	Regulatory Rv1368	swetha.r	IPI		Yeast two-hybrid (Physical interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Citation	Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. T. Parish, DA. Smith et al. Infect. Immun. 2003	darhngu	IPI	12595424	Yeast Two- Three Hybrid(Physical Interaction)
Interaction	Signaling Rv1368	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) T. Parish, DA. Smith et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect. Immun. 2003
Interaction	Signaling Rv1690	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) T. Parish, DA. Smith et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect. Immun. 2003
Citation	Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. A. Singh, D. Mai et al. Proc. Natl. Acad. Sci. U.S.A. 2006	darhngu	IPI	16844784	Yeast Two- Three Hybrid(Physical Interaction)
Interaction	Signaling Rv1368	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) A. Singh, D. Mai et al. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2006
Interaction	Signaling Rv1690	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) A. Singh, D. Mai et al. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2006
Citation	Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. T. Parish, DA. Smith et al. Infect. Immun. 2003	akankshajain.21	IPI	12595424	Protein fragment complementation
Interaction	Regulatory Rv1027c	akankshajain.21	IPI		Protein fragment complementation T. Parish, DA. Smith et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect. Immun. 2003
Citation	Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. A. Singh, D. Mai et al. Proc. Natl. Acad. Sci. U.S.A. 2006	akankshajain.21	IPI	16844784	Protein fragment complementation
Interaction	Regulatory Rv1027c	akankshajain.21	IPI		Protein fragment complementation A. Singh, D. Mai et al. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2006
Citation	Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. AJ. Steyn, J. Joseph et al. Mol. Microbiol. 2003	darhngu	IPI	12581360	Yeast Two- Three Hybrid(Physical Interaction)
Interaction	Signaling Rv1368	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Interaction	Signaling Rv1690	darhngu	IPI		Yeast Two- Three Hybrid(Physical Interaction) AJ. Steyn, J. Joseph et al. Interaction of the sensor module of Mycobacterium tuberculosis H37Rv KdpD with members of the Lpr family. Mol. Microbiol. 2003
Interaction	Regulatory Rv1027c	darhngu	IPI		Protein fragment complementation T. Parish, DA. Smith et al. Deletion of two-component regulatory systems increases the virulence of Mycobacterium tuberculosis. Infect. Immun. 2003
Interaction	Regulatory Rv1027c	darhngu	IPI		Protein fragment complementation A. Singh, D. Mai et al. Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association. Proc. Natl. Acad. Sci. U.S.A. 2006

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