Detailed view for PF3D7_1363200

Basic information

TDR Targets ID: 2308
Plasmodium falciparum, bifunctional polynucleotide phosphatase/kinase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.3581 | Length (AA): 462 | MW (Da): 55334 | Paralog Number: 0

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

Druggability Group : DG3

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

PF00004   ATPase family associated with various cellular activities (AAA)
PF08645   Polynucleotide kinase 3 phosphatase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005524   ATP binding  
GO:0003684   damaged DNA binding  
GO:0006974   response to DNA damage stimulus  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 6 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
15 460 1yj5 (A) 145 519 26.00 0 1 1.11 -0.35
295 458 1knq (A) 3 172 12.00 0 0.26 0.27 -1.06
13 460 3zvl (A) 143 519 22.00 0 1 0.929497 0.34
15 460 3zvl (A) 145 519 27.00 0 1 1.04917 0.43
38 171 2gmw (A) 26 171 17.00 0 0.9 0.470843 -0.64
302 440 3a4m (A) 6 153 31.00 0.13 0.8 0.456066 0.04

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 intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, sporozoite, early ring. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, early trophozoite, late ring, late trophozoite, Ring, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 48 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite, Female Gametocyte. Zanghi G Lasonder E
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
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_128311)

Species Accession Gene Product
Arabidopsis thaliana AT3G14890   polynucleotide 3'-phosphatase ZDP
Babesia bovis BBOV_IV000690   polynucleotide kinase 3'-phosphatase, putative
Brugia malayi Bm1_40730   DNA 3'-phosphatase family protein
Candida albicans CaO19.9121   similar to S. pombe pnk1 (SPAC23C11.04c ) 5'kinase/DNA 3' phosphatase involved in DNA repair
Candida albicans CaO19.1547   similar to S. pombe pnk1 (SPAC23C11.04c ) 5'kinase/DNA 3' phosphatase involved in DNA repair
Caenorhabditis elegans CELE_F21D5.5   Protein F21D5.5
Dictyostelium discoideum DDB_G0281229   SAP DNA-binding domain-containing protein
Drosophila melanogaster Dmel_CG9601   CG9601 gene product from transcript CG9601-RA
Echinococcus granulosus EgrG_000166600   bifunctional polynucleotide
Entamoeba histolytica EHI_148430   polynucleotide kinase-3-phosphatase, putative
Echinococcus multilocularis EmuJ_000166600   bifunctional polynucleotide
Homo sapiens ENSG00000039650   polynucleotide kinase 3'-phosphatase
Leishmania donovani LdBPK_300180.1   hypothetical protein
Loa Loa (eye worm) LOAG_09075   hypothetical protein
Mus musculus ENSMUSG00000002963   polynucleotide kinase 3'- phosphatase
Neospora caninum NCLIV_003010   hypothetical protein
Oryza sativa 4327876   Os01g0737300
Onchocerca volvulus OVOC5322   Bifunctional polynucleotide phosphatase\/kinase homolog
Plasmodium berghei PBANKA_1139200   bifunctional polynucleotide phosphatase/kinase, putative
Plasmodium falciparum PF3D7_1363200   bifunctional polynucleotide phosphatase/kinase
Plasmodium knowlesi PKNH_1108100   bifunctional polynucleotide phosphatase/kinase, putative
Plasmodium vivax PVX_115115   bifunctional polynucleotide phosphatase/kinase, putative
Plasmodium yoelii PY05803   hypothetical protein
Saccharomyces cerevisiae YMR156C   Tpp1p
Schistosoma japonicum Sjp_0069760   ko:K08073 polynucleotide 5'-hydroxyl-kinase [EC2.7.1.78], putative
Schistosoma mansoni Smp_169740   polynucleotide kinase-3'-phosphatase
Schmidtea mediterranea mk4.000725.07   Bifunctional polynucleotide phosphatase/kinase
Trypanosoma brucei gambiense Tbg972.6.1250   polynucleotide kinase 3-phosphatase, putative
Trypanosoma brucei Tb927.6.1580   polynucleotide kinase 3'-phosphatase, putative
Trypanosoma congolense TcIL3000_6_1080   polynucleotide kinase 3'-phosphatase, putative
Trypanosoma congolense TcIL3000_0_16570   polynucleotide kinase 3'-phosphatase, putative
Trypanosoma cruzi TcCLB.505807.190   polynucleotide kinase 3'-phosphatase, putative
Trypanosoma cruzi TcCLB.507017.50   polynucleotide kinase 3'-phosphatase, putative
Theileria parva TP01_0091   hypothetical protein

Essentiality

PF3D7_1363200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.1580 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.1580 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.1580 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.1580 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_F21D5.5 Caenorhabditis elegans larval arrest wormbase
CELE_F21D5.5 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • 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.
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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

No literature references available for this target.

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Gene identifier PF3D7_1363200 (Plasmodium falciparum), bifunctional polynucleotide phosphatase/kinase
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