Rv0782 (ptrBb)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: oligopeptidase B
- REFSEQ: oligopeptidase B
- PATRIC: Protease II (EC 3.4.21.83)
- TUBERCULIST: Probable protease II PtrBb [second part] (oligopeptidase B)
- NCBI: Probable protease II PtrBb [second part] (oligopeptidase B)
- updated information (H37Rv4):
  - gene name: ptrBb
  - function:
  - reference:
Type: Not Target
Start: 874732
End: 876390
Operon:

Trans-membrane region:
Role: II.B.3 - Proteins, peptides and glycopeptides
GO terms:
- GO:0070008 - serine-type exopeptidase activity (Uniprot)
- GO:0008236 - serine-type peptidase activity (Uniprot)
- GO:0008233 - peptidase activity (Uniprot)
- GO:0006508 - proteolysis (Uniprot)
- GO:0004252 - serine-type endopeptidase 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
4BP9	43%	TRYPANOSOMA BRUCEI	Oligopeptidase B from Trypanosoma brucei with covalently bound antipain - closed form
4BP8	43%	TRYPANOSOMA BRUCEI	Oligopeptidase B from Trypanosoma brucei - open form
2XE4	40%	LEISHMANIA MAJOR	Structure of Oligopeptidase B from Leishmania major

Links to additional information on ptrBb:
- 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 = 1.207 (from Jeremy Rock's lab)

Amino Acid Sequence

VTNDIPCGSRIYAPENSTRTRSPGSERESPGQLTTTVYYTTVDAAWRPDTVWRYRLGSGESSERVYHEADDRFWLAVGRTRSNAYLLIAAGSSITSEVRY
AHAADPTAQFSVVLPRRDGVEYSVEHAVIAGQDRFLILHNDGAVNFTLVEAPVEDPARQRTLIAHRDDVRLDAVDALAGHLVVSYRREALPRVQLWPIGP
DGNYGEPEEISFDSELMSAGLGPNPNWDSPKLRVGAGSFVTPVRIYDIDLVTGERTLLKEQPVLGGYRREDYVERRDWAYGDDGTRIPVSIVHRADIEFP
APALIYGYGAYEICEDPRFSIARLSLLDRGMVFVVAHVRGGGEMGRLWYENGKLLDKKNTFTDFIAVARHLVDTGLTSQQQLVALGGSAGGLLMGAVANM
APDLFAGILAQVPFVDPLTTILDPSLPLTVTEWDEWGNPLNDSDVYAYVKSYSPYENVTAQKYPAILAMTSLNDTRVYYVEPAKWVAALRHAKTDGNSVL
LKTQMHAGHGGISGRYERWKETAFQYGWLLATADSDRYGGGQGNDLDGAAPA

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.881600; 11 non-insertions in a row out of 45 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000050; 7 non-insertions in a row out of 45 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000150; 7 non-insertions in a row out of 45 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.759450; 8 non-insertions in a row out of 37 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.742800; 8 non-insertions in a row out of 37 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: 0.46
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

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	PhysicalInteraction Rv0781	priti.priety	IGC		Gene Neighborhood (Functional linkage) authors,ML. Ribeiro-Guimares,MC. Pessolani Comparative genomics of mycobacterial proteases. Microb. Pathog. null
Interaction	PhysicalInteraction Rv0781	ashwinigbhat	IGC		Gene Neighborhood (Functional linkage) authors,ML. Ribeiro-Guimares,MC. Pessolani Comparative genomics of mycobacterial proteases. Microb. Pathog. null
Citation	Comparative genomics of mycobacterial proteases. authors,ML. Ribeiro-Guimares,MC. Pessolani Microb. Pathog. null	shahanup86	IGC	17611072	Gene Neighborhood (Functional linkage)
Interaction	PhysicalInteraction Rv0781	shahanup86	IGC		Gene Neighborhood (Functional linkage) authors,ML. Ribeiro-Guimares,MC. Pessolani Comparative genomics of mycobacterial proteases. Microb. Pathog. null
Citation	Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis. G. Rehren, S. Walters et al. Tuberculosis (Edinb) 2007	shahanup86	IGC	17433778	Gene Neighborhood (Functional linkage)
Interaction	PhysicalInteraction Rv0781	shahanup86	IGC		Gene Neighborhood (Functional linkage) G. Rehren, S. Walters et al. Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007
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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