Rv3923c (rnpA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ribonuclease P protein component
- REFSEQ: ribonuclease P
- PATRIC: Ribonuclease P protein component (EC 3.1.26.5)
- TUBERCULIST: Ribonuclease P protein component RnpA (RNaseP protein) (RNase P protein) (protein C5)
- NCBI: Ribonuclease P protein component RnpA (RNaseP protein) (RNase P protein) (protein C5)
- updated information (H37Rv4):
  - gene name: rnpA
  - function: RNase P
  - reference:
Type: Not Target
Start: 4410412
End: 4410789
Operon:

Trans-membrane region:
Role: II.B.1 - RNA
GO terms:
- GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic (Uniprot)
- GO:0090501 - RNA phosphodiester bond hydrolysis (Uniprot)
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0008033 - tRNA processing (Uniprot)
- GO:0004526 - ribonuclease P activity (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0003723 - RNA binding (Uniprot)
- GO:0000049 - tRNA binding (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): (none with >35% aa id)
Links to additional information on rnpA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -9.104 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

LIATPGLFAVLRARNRMRRSADFETTVKHGMRTVRSDMVVYWWRGSGGGPRVGLIIAKSVGSAVERHRVARRLRHVAGSIVKELHPSDHVVIRALPSSRH
VSSARLEQQLRCGLRRAVELAGSDR

(Nucleotide sequence available on KEGG)

Additional Information

RNase P, rnpA

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; 3 non-insertions in a row out of 4 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.986150; 4 non-insertions in a row out of 4 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.985000; 4 non-insertions in a row out of 4 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 4 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 4 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.17
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:
- Rv2034 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv2034 (-) (Direct binding)
- Rv3133c (devR) (Direct binding)

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:
- Rv2034 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv0352	shahanup86	IEP		Co-expression (Functional linkage) GR. Stewart, BD. Robertson et al. Analysis of the function of mycobacterial DnaJ proteins by overexpression and microarray profiling. Tuberculosis (Edinburgh, Scotland) 2004
Citation	Analysis of the function of mycobacterial DnaJ proteins by overexpression and microarray profiling. GR. Stewart, BD. Robertson et al. Tuberculosis (Edinburgh, Scotland) 2004	shahanup86	IEP	15207487	Co-expression (Functional linkage)
Interaction	RegulatedBy Rv0348	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.. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009

TB Genome Annotation Portal