Detailed view for Rv0211

Basic information

TDR Targets ID: 6653
Mycobacterium tuberculosis, Probable iron-regulated phosphoenolpyruvate carboxykinase [GTP] PckA (phosphoenolpyruvate carboxylase) (PEPCK)(pep carboxykinase
Source Database / ID:  Tuberculist 

pI: 4.679 | Length (AA): 606 | MW (Da): 67253 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00821   Phosphoenolpyruvate carboxykinase C-terminal P-loop domain
PF17297   Phosphoenolpyruvate carboxykinase N-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004613   phosphoenolpyruvate carboxykinase (GTP) activity  
GO:0004611   phosphoenolpyruvate carboxykinase activity  
GO:0017076   purine nucleotide binding  
GO:0005525   GTP binding  
GO:0006094   gluconeogenesis  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 606 4wpt (A) 1 606 99.99 0 1 2.2472 -1.64

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:

PDB tag
  • 4R43:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4RCG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WIE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WIU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WL8:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WOU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WPT:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WPU:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4WPV:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5I67:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase, Dormant phase. hasan 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_129007)

Species Accession Gene Product
Brugia malayi Bm1_17155   phosphoenolpyruvate carboxykinase [GTP]
Brugia malayi Bm1_25195   phosphoenolpyruvate carboxykinase [GTP]
Caenorhabditis elegans CELE_R11A5.4   Protein PCK-2, isoform C
Caenorhabditis elegans CELE_W05G11.6   Protein PCK-1, isoform C
Chlamydia trachomatis CT_710   phosphoenolpyruvate carboxykinase
Dictyostelium discoideum DDB_G0271904   phosphoenolpyruvate carboxykinase
Drosophila melanogaster Dmel_CG10924   CG10924 gene product from transcript CG10924-RA
Drosophila melanogaster Dmel_CG17725   Phosphoenolpyruvate carboxykinase
Echinococcus granulosus EgrG_000292700   phosphoenolpyruvate carboxykinase
Echinococcus multilocularis EmuJ_000292700   phosphoenolpyruvate carboxykinase
Giardia lamblia GL50803_10623   Phosphoenolpyruvate carboxykinase
Homo sapiens 5105   phosphoenolpyruvate carboxykinase 1 (soluble)
Homo sapiens ENSG00000100889   phosphoenolpyruvate carboxykinase 2 (mitochondrial)
Loa Loa (eye worm) LOAG_01890   hypothetical protein
Loa Loa (eye worm) LOAG_07217   phosphoenolpyruvate carboxykinase
Loa Loa (eye worm) LOAG_10229   phosphoenolpyruvate carboxykinase cytosolic family member
Mycobacterium leprae ML2624   PROBABLE IRON-REGULATED PHOSPHOENOLPYRUVATE CARBOXYKINASE [GTP] PCKA (PHOSPHOENOLPYRUVATE CARBOXYLASE) (PEPCK)(PEP CARBOXYKINASE
Mus musculus ENSMUSG00000027513   phosphoenolpyruvate carboxykinase 1, cytosolic
Mus musculus ENSMUSG00000040618   phosphoenolpyruvate carboxykinase 2 (mitochondrial)
Mycobacterium tuberculosis Rv0211   Probable iron-regulated phosphoenolpyruvate carboxykinase [GTP] PckA (phosphoenolpyruvate carboxylase) (PEPCK)(pep carboxykinase
Mycobacterium ulcerans MUL_1101   phosphoenolpyruvate carboxykinase
Onchocerca volvulus OVOC1459  
Schistosoma japonicum Sjp_0202690   ko:K01596 phosphoenolpyruvate carboxykinase (GTP) [EC4.1.1.32], putative
Schistosoma mansoni Smp_005880   phosphoenolpyruvate carboxykinase
Schmidtea mediterranea mk4.001640.00  
Schmidtea mediterranea mk4.018802.00  
Schmidtea mediterranea mk4.000488.07  
Schmidtea mediterranea mk4.003158.00   Putative phosphoenolpyruvate carboxykinase
Schmidtea mediterranea mk4.000512.06  
Schmidtea mediterranea mk4.015910.00  
Schmidtea mediterranea mk4.000556.00  
Schmidtea mediterranea mk4.004453.00  
Schmidtea mediterranea mk4.000512.04  
Treponema pallidum TP0122   phosphoenolpyruvate carboxykinase
Trichomonas vaginalis TVAG_213710   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_420390   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_314840   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_310250   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_434120   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_139300   phosphoenolpyruvate carboxykinase, putative
Trichomonas vaginalis TVAG_479540   phosphoenolpyruvate carboxykinase, putative

Essentiality

Rv0211 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_W05G11.6 Caenorhabditis elegans larval lethal wormbase
Show/Hide essentiality data references
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.

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

Druggability index (range: 0 to 1): 0.5

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Rattus norvegicus Phosphoenolpyruvate carboxykinase, cytosolic [GTP] Compounds References
Homo sapiens phosphoenolpyruvate carboxykinase 1 (soluble) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0913 1 0.5
0.09 1 0.5
0.1082 0.284 0.5
0.0088 1 1
0.1096 1 0.5
0.0571 0.8578 0.5
0.109 1 0.5
0.0529 1 0.5
0.0306 1 0.5
0.0467 1 0.5
0.0548 0.7528 0.5
0.1157 1 1
0.0191 1 0.5
0.1089 1 0.5
0.0778 1 0.5
0.0768 1 0.5
0.1566 1 1
0.0191 1 0.5
0.0698 1 1
0.0888 1 0.5
0.1097 1 0.5
0.0191 1 0.5
0.1006 1 0.5
0.0992 1 0.5
0.0913 1 0.5
0.1113 0.621 1
0.0142 0.3268 0.5
0.0191 1 0.5
0.1566 1 1
0.0673 1 1
0.1157 0.4593 1
0.0895 1 0.5
0.0616 1 0.5
0.1083 1 0.5
0.1075 1 1
0.1566 1 1
0.0351 1 0.5
0.0454 1 0.5
0.0698 1 1
0.0672 1 0.5
0.2105 1 1
0.0971 1 0.5
0.1083 1 0.5
0.0159 0.9443 0.5
0.1064 1 0.5
0.018 1 0.5
0.0833 1 0.5
0.1481 1 0.5
0.0454 1 0.5
0.0678 1 1
0.1566 1 1
0.046 1 0.5
0.1082 0.284 0.5
0.1113 0.621 1
0.0531 0.7216 0.5
0.092 1 0.5
0.0191 1 0.5
0.1127 1 0.5
0.0191 1 0.5
0.109 1 0.5
0.099 1 0.5
0.0191 1 0.5
0.1413 1 0.5
0.1113 0.621 1
0.0809 0.9252 1
0.0715 1 0.5
0.0968 1 0.5
0.1089 1 0.5
0.0809 0.9252 1
0.1334 0.6033 1
0.0191 1 0.5

Assayability

Assay information

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium smegmatis ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv0211 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Mycobacterium smegmatis ( 1 )

Bibliographic References

No literature references available for this target.

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Gene identifier Rv0211 (Mycobacterium tuberculosis), Probable iron-regulated phosphoenolpyruvate carboxykinase [GTP] PckA (phosphoenolpyruvate carboxylase) (PEPCK)(pep carboxykinase
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