Detailed view for PF3D7_0520500

Basic information

TDR Targets ID: 4237
Plasmodium falciparum, phosphomethylpyrimidine kinase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.5748 | Length (AA): 310 | MW (Da): 34975 | 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

PF08543   Phosphomethylpyrimidine kinase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008972   phosphomethylpyrimidine kinase activity  
GO:0016301   kinase activity  
GO:0009228   thiamin biosynthetic process  

Metabolic Pathways

Thiamine metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 5 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
3 294 1jxh (A) 2 264 28.00 0 1 1.1 -0.66
5 292 1ub0 (A) 2 257 28.00 0 1 1.15 -0.79
2 294 3rm5 (A) 21 296 27.00 0 1 1.10886 -0.5
5 309 4c5k (A) 4 276 23.00 0 1 1.21767 -0.4
8 276 4jjp (A) 9 244 43.00 0 1 1.14454 -0.16

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 80-100% percentile Sporozoite. Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early schizont, early trophozoite, late schizont, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 24 hs, gametocyte, late ring, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, Oocyst, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Male Gametocyte. 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_128612)

Species Accession Gene Product
Arabidopsis thaliana AT1G22940   thiamine biosynthetic bifunctional enzyme TH1
Candida albicans CaO19.889   thiamine biosynthesis
Candida albicans CaO19.8508   thiamine biosynthesis
Escherichia coli b2103   bifunctional hydroxy-methylpyrimidine kinase/hydroxy-phosphomethylpyrimidine kinase
Mycobacterium leprae ML0295   Probable phosphomethylpyrimidine kinase ThiD
Mycobacterium tuberculosis Rv0422c   Probable phosphomethylpyrimidine kinase ThiD (HMP-phosphate kinase) (HMP-P kinase)
Mycobacterium ulcerans MUL_3599   phosphomethylpyrimidine kinase
Plasmodium falciparum PF3D7_0520500   phosphomethylpyrimidine kinase, putative
Plasmodium knowlesi PKNH_1012600   phosphomethylpyrimidine kinase, putative
Plasmodium vivax PVX_080220   phosphomethylpyrimidine kinase, putative
Saccharomyces cerevisiae YPL258C   bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
Saccharomyces cerevisiae YOL055C   trifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase/thiaminase
Saccharomyces cerevisiae YPR121W   putative phosphomethylpyrimidine kinase
Schmidtea mediterranea mk4.050116.03  
Treponema pallidum TP0115   phosphomethypyrimidine kinase (thiD)

Essentiality

PF3D7_0520500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu425 Mycobacterium tuberculosis essential nmpdr
b2103 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

  • Pviv008494AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Pviv008494; Recombinant protein: full-length; Source: P vivax; phosphomethylpyrimidine kinase, putative homolog ; Identifier: Pv080220

Bibliographic References

No literature references available for this target.

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Gene identifier PF3D7_0520500 (Plasmodium falciparum), phosphomethylpyrimidine kinase, putative
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