Detailed view for Rv3042c

Basic information

TDR Targets ID: 9890
Mycobacterium tuberculosis, Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase)
Source Database / ID:  Tuberculist 

pI: 4.5327 | Length (AA): 409 | MW (Da): 43059 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | Predicted trans-membrane segments: 0

Druggability Group : DG1

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF12710   haloacid dehalogenase-like hydrolase
PF13740   ACT domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016791   phosphoric monoester hydrolase activity  
GO:0016597   amino acid binding  
GO:0004647   phosphoserine phosphatase activity  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  
GO:0006564   L-serine biosynthetic process  

Structural information

Modbase 3D models:

There are 3 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
4 398 5is2 (A) 6 400 85.00 0 1 2.00997 -1.01
177 384 1l7m (A) 3 210 41.00 0 1 1.14356 -1.44
317 384 1nf2 (A) 190 258 32.00 0 0.66 0.500259 0.18

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Dormant phase. murphy
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_128110)

Species Accession Gene Product
Arabidopsis thaliana AT1G18640   phosphoserine phosphatase
Brugia malayi Bm1_49380   L-3-phosphoserine phosphatase
Candida albicans CaO19.5838   phosphoserine phosphohydrolase
Candida albicans CaO19.13260   phosphoserine phosphohydrolase
Caenorhabditis elegans CELE_Y62E10A.13   Protein Y62E10A.13, isoform D
Dictyostelium discoideum DDB_G0291368   phosphoserine phosphatase
Drosophila melanogaster Dmel_CG3705   astray
Escherichia coli b4388   3-phosphoserine phosphatase
Echinococcus granulosus EgrG_001063400   phosphoserine phosphatase
Echinococcus granulosus EgrG_001062900   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001063100   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001063400   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001062900   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001063200   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001063300   phosphoserine phosphatase
Echinococcus multilocularis EmuJ_001063000   phosphoserine phosphatase
Homo sapiens ENSG00000146733   phosphoserine phosphatase
Loa Loa (eye worm) LOAG_00707   L-3-phosphoserine phosphatase
Mycobacterium leprae ML1727c   PROBABLE PHOSPHOSERINE PHOSPHATASE SERB2 (PSP) (O-PHOSPHOSERINE PHOSPHOHYDROLASE) (PSPASE)
Mus musculus ENSMUSG00000029446   phosphoserine phosphatase
Mycobacterium tuberculosis Rv3042c   Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase)
Mycobacterium ulcerans MUL_1888   phosphoserine phosphatase SerB2
Neospora caninum NCLIV_005930   phosphoserine phosphatase, putative
Oryza sativa 4352281   Os12g0502400
Oryza sativa 4350964   Os11g0629500
Onchocerca volvulus OVOC793   Phosphoserine phosphatase homolog
Saccharomyces cerevisiae YGR208W   phosphoserine phosphatase
Schistosoma japonicum Sjp_0011450   expressed protein
Schistosoma mansoni Smp_063340   phosphoserine phosphatase
Schmidtea mediterranea mk4.002114.03   Phosphoserine phosphatase
Toxoplasma gondii TGME49_222900   phosphoserine phosphatase

Essentiality

Rv3042c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3095 this record Mycobacterium tuberculosis essential nmpdr
b4388 Escherichia coli non-essential goodall
TGME49_222900 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier Rv3042c (Mycobacterium tuberculosis), Probable phosphoserine phosphatase SerB2 (PSP) (O-phosphoserine phosphohydrolase) (pspase)
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