Detailed view for PF3D7_1219900

Basic information

TDR Targets ID: 5242
Plasmodium falciparum, ribulose-phosphate 3-epimerase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.4926 | Length (AA): 227 | MW (Da): 25549 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF00834   Ribulose-phosphate 3 epimerase family

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0016857   racemase and epimerase activity, acting on carbohydrates and derivatives  
GO:0009052   pentose-phosphate shunt, non-oxidative branch  
GO:0004750   ribulose-phosphate 3-epimerase activity  
GO:0003824   catalytic activity  
GO:0005975   carbohydrate metabolic process  
GO:0008152   metabolic process  
GO:0006098   pentose-phosphate shunt  

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
2 227 1rd5 (A) 14 260 16.00 0 1 1.11 -1.14
5 224 1tqx (A) 5 224 99.99 0 1 2.32 -2.74
4 224 1tqx (A) 4 224 99.99 0 1 2.27887 -2.11

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
  • 1TQX:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 16 hs, sporozoite, early ring, early schizont, early trophozoite, late ring, late trophozoite, Oocyst, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile late schizont. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 0 hs. Otto TD
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_127027)

Species Accession Gene Product
Arabidopsis thaliana AT1G63290   putative D-ribulose-5-phosphate 3-epimerase
Arabidopsis thaliana AT5G61410   D-ribulose-5-phosphate-3-epimerase
Arabidopsis thaliana AT3G01850   ribulose-phosphate 3-epimerase
Brugia malayi Bm1_10935   hypothetical protein
Candida albicans CaO19.7108   D-ribulose-5-Phosphate 3-epimerase
Candida albicans CaO19_7108   hypothetical protein
Caenorhabditis elegans CELE_F08F8.7   Protein F08F8.7
Chlamydia trachomatis CT_121   ribulose-phosphate 3-epimerase
Dictyostelium discoideum DDB_G0278275   ribulose phosphate 3-epimerase
Drosophila melanogaster Dmel_CG30499   CG30499 gene product from transcript CG30499-RA
Escherichia coli b3386   D-ribulose-5-phosphate 3-epimerase
Echinococcus granulosus EgrG_000781900   ribulose phosphate 3 epimerase
Entamoeba histolytica EHI_006900   ribulose-phosphate 3-epimerase, putative
Echinococcus multilocularis EmuJ_000781900   ribulose phosphate 3 epimerase
Giardia lamblia GL50803_10324   Ribulose-phosphate 3-epimerase
Homo sapiens ENSG00000235376   ribulose-5-phosphate-3-epimerase-like 1
Homo sapiens ENSG00000197713   ribulose-5-phosphate-3-epimerase
Leishmania braziliensis LbrM.33.1830   ribulose-5-phosphate 3-epimerase, putative
Leishmania donovani LdBPK_331660.1   ribulose-5-phosphate 3-epimerase, putative
Leishmania infantum LinJ.33.1660   ribulose-5-phosphate 3-epimerase, putative
Leishmania major LmjF.33.1570   ribulose-5-phosphate 3-epimerase, putative
Leishmania mexicana LmxM.32.1570   ribulose-5-phosphate 3-epimerase, putative
Loa Loa (eye worm) LOAG_05451   rpe protein
Mycobacterium leprae ML0554   Probable ribulose-phosphate 3-epimerase Rpe
Mus musculus ENSMUSG00000026005   ribulose-5-phosphate-3-epimerase
Mycobacterium tuberculosis Rv1408   Probable ribulose-phosphate 3-epimerase Rpe (PPE) (R5P3E) (pentose-5-phosphate 3-epimerase)
Mycobacterium ulcerans MUL_1804   ribulose-phosphate 3-epimerase
Neospora caninum NCLIV_065340   hypothetical protein
Oryza sativa 4331761   Os03g0169100
Oryza sativa 4347508   Os09g0505700
Plasmodium berghei PBANKA_1435100   ribulose-phosphate 3-epimerase, putative
Plasmodium falciparum PF3D7_1219900   ribulose-phosphate 3-epimerase, putative
Plasmodium knowlesi PKNH_1439100   ribulose-phosphate 3-epimerase, putative
Plasmodium vivax PVX_123635   D-ribulose-5-phosphate 3-epimerase, putative
Plasmodium yoelii PY01807   putative D-ribulose-5-phosphate 3-epimerase
Saccharomyces cerevisiae YJL121C   ribulose-phosphate 3-epimerase RPE1
Schistosoma japonicum Sjp_0015540   ko:K01783 ribulose-phosphate 3-epimerase [EC5.1.3.1], putative
Schistosoma mansoni Smp_104580   ribulose-phosphate 3-epimerase
Schmidtea mediterranea mk4.006062.02  
Schmidtea mediterranea mk4.041404.02  
Schmidtea mediterranea mk4.000523.05   Ribulose-phosphate 3-epimerase
Trypanosoma brucei gambiense Tbg972.10.14730   ribulose-5-phosphate 3-epimerase, putative
Trypanosoma brucei Tb927.10.12210   ribulose-5-phosphate 3-epimerase, putative
Trypanosoma congolense TcIL3000_10_10440   ribulose-5-phosphate 3-epimerase, putative
Trypanosoma cruzi TcCLB.510257.30   ribulose-5-phosphate 3-epimerase, putative
Trypanosoma cruzi TcCLB.509213.70   ribulose-5-phosphate 3-epimerase, putative
Toxoplasma gondii TGME49_247670   ribulose-phosphate 3 epimerase family protein
Treponema pallidum TP0945   ribulose-phosphate 3-epimerase (cfxE)
Trichomonas vaginalis TVAG_158280   ribulose-5-phosphate-3-epimerase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0236   Pentose-5-phosphate-3-epimerase

Essentiality

PF3D7_1219900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.12210 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.12210 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.12210 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.12210 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3386 Escherichia coli essential goodall
TGME49_247670 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource

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

  • Assay for D-Ribulose 5-Phosphate 3-Epimerase (5.1.3.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Pfal009167AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Pfal009167; Recombinant protein: full-length; Source: P falciparum; D-ribulose-5-phosphate 3-epimerase, putative ;

Bibliographic References

2 literature references were collected for this gene.

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Gene identifier PF3D7_1219900 (Plasmodium falciparum), ribulose-phosphate 3-epimerase, putative
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