Detailed view for Rv1127c

Basic information

TDR Targets ID: 6839
Mycobacterium tuberculosis, Probable pyruvate, phosphate dikinase PpdK
Source Database / ID:  Tuberculist 

pI: 4.7149 | Length (AA): 490 | MW (Da): 52005 | 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

PF00391   PEP-utilising enzyme, mobile domain
PF01326   Pyruvate phosphate dikinase, PEP/pyruvate binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0050242   pyruvate, phosphate dikinase activity  
GO:0016772   transferase activity, transferring phosphorus-containing groups  
GO:0016301   kinase activity  
GO:0005524   ATP binding  
GO:0003824   catalytic activity  
GO:0016310   phosphorylation  
GO:0006090   pyruvate metabolic 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
17 489 1kbl (A) 3 535 40.00 0 1 1.34911 -0.32
23 489 1vbg (A) 14 538 39.00 0 1 1.30586 -0.11
369 463 3t05 (A) 487 580 30.00 0.98 0.99 0.609678 -0.37

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
Mid 40-60% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. hasan
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_127082)

Species Accession Gene Product
Arabidopsis thaliana AT4G15530   pyruvate, phosphate dikinase 1
Caenorhabditis elegans CELE_T21C9.6   Protein T21C9.6
Chlamydia trachomatis CT_336   PTS system PEP phosphotransferase
Escherichia coli b2416   PEP-protein phosphotransferase of PTS system (enzyme I)
Escherichia coli b1702   phosphoenolpyruvate synthase
Escherichia coli b2829   fused PTS enzyme: PEP-protein phosphotransferase (enzyme I)/GAF domain containing protein
Entamoeba histolytica EHI_009530   pyruvate phosphate dikinase
Giardia lamblia GL50803_9909   Pyruvate, phosphate dikinase
Leishmania braziliensis LbrM.11.0800   pyruvate phosphate dikinase, putative
Leishmania donovani LdBPK_111000.1   pyruvate phosphate dikinase, putative
Leishmania infantum LinJ.11.1000   pyruvate phosphate dikinase, putative
Leishmania major LmjF.11.1000   pyruvate phosphate dikinase, putative
Leishmania mexicana LmxM.11.1000   pyruvate phosphate dikinase, putative
Mycobacterium leprae ML0955c   PROBABLE PYRUVATE, PHOSPHATE DIKINASE PPDK
Mycobacterium tuberculosis Rv1127c   Probable pyruvate, phosphate dikinase PpdK
Mycobacterium ulcerans MUL_0141   pyruvate phosphate dikinase
Oryza sativa 4333181   Os03g0432100
Oryza sativa 4338750   Os05g0405000
Schistosoma mansoni Smp_113420   pyruvate phosphate dikinase chloroplast
Schmidtea mediterranea mk4.000245.11  
Schmidtea mediterranea mk4.034972.02  
Trypanosoma brucei gambiense Tbg972.11.7080   pyruvate phosphate dikinase, putative
Trypanosoma brucei Tb927.11.6280   pyruvate phosphate dikinase
Trypanosoma congolense TcIL3000.11.6820   pyruvate phosphate dikinase
Trypanosoma cruzi TcCLB.506297.190   pyruvate phosphate dikinase, putative
Trypanosoma cruzi TcCLB.510101.140   pyruvate phosphate dikinase, putative
Treponema pallidum TP0746   pyruvate phosphate dikinase
Trichomonas vaginalis TVAG_585300   conserved hypothetical protein
Trichomonas vaginalis TVAG_437410   phosphoenolpyruvate-protein phosphotransferase, putative
Trichomonas vaginalis TVAG_073860   phosphoenolpyruvate-protein phosphotransferase, putative
Trichomonas vaginalis TVAG_394650   phosphoenolpyruvate-protein phosphotransferase, putative
Trichomonas vaginalis TVAG_178140   phosphoenolpyruvate-protein phosphotransferase, putative
Trichomonas vaginalis TVAG_161270   pyruvate, phosphate dikinase, chloroplast, putative
Trichomonas vaginalis TVAG_527480   pyruvate, phosphate dikinase, chloroplast, putative
Wolbachia endosymbiont of Brugia malayi Wbm0209   pyruvate phosphate dikinase

Essentiality

Rv1127c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1147 this record Mycobacterium tuberculosis non-essential nmpdr
Tb11.02.4150 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.4150 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.02.4150 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.4150 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b1702 Escherichia coli non-essential goodall
b2416 Escherichia coli essential goodall
b2829 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170

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

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0416 0.3267 0.4062
0.0422 0.4141 0.4141
0.0185 0.3099 0.3099
0.0304 0.4126 0.4126
0.0358 0.4134 0.4134
0.0302 0.3708 0.4053
0.0185 0.3099 0.3099
0.0206 0.3621 0.3421
0.0406 0.4104 0.4139
0.0188 0.3948 0
0.036 0.4139 0.4136
0.0313 0.315 0.4127
0.0199 0.3947 0.4093
0.0255 0.3205 0.4117
0.0315 0.4128 0.4128
0.0046 0.263 0
0.0247 0.4075 0
0.0259 0.4136 0
0.0209 0.2706 0.3983
0.0332 0.413 0.4107
0.026 0.3825 0
0.0301 0.3492 0.3988
0.0421 0.4147 0.4147
0.0269 0.2606 0.4
0.0243 0.3182 0.4001
0.0382 0.3555 0.4103
0.0269 0.2606 0.4
0.0332 0.413 0.4107
0.0298 0.3515 0.4113
0.0349 0.4098 0.4068
0.0349 0.4085 0.4085
0.0302 0.4133 0.4133
0.0332 0.3918 0.4054
0.0293 0.3444 0.4051
0.0324 0.4139 0.4139

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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Gene identifier Rv1127c (Mycobacterium tuberculosis), Probable pyruvate, phosphate dikinase PpdK
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