Detailed view for PF3D7_0616000

Basic information

TDR Targets ID: 4511
Plasmodium falciparum, pyridoxal kinase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.049 | Length (AA): 497 | MW (Da): 57189 | 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:0009443   pyridoxal 5'-phosphate salvage  
GO:0008614   pyridoxine metabolic process  
GO:0008478   pyridoxal kinase activity  

Metabolic Pathways

Vitamin B6 metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 8 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
240 495 2ajp (A) 34 312 21.00 0 1 0.69 -1
308 482 1vi9 (A) 104 278 17.00 0.00000000073 1 0.73 -1.62
259 465 2f7k (A) 55 271 30.00 0 1 0.689399 -0.12
302 385 4jjp (A) 90 176 35.00 0.25 0.98 0.580914 -0.03
310 465 1lhp (A) 105 271 33.00 0 1 0.749783 -0.65
126 202 1hcd (A) 25 106 25.00 0.32 0.02 0.42129 -1.3
219 425 2f7k (A) 55 271 30.00 0 1 0.726754 -0.13
301 346 4xda (A) 175 220 41.00 0.016 1 0.692456 -0.91

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 - 16 hs, intra-erythrocytic - 24 hs, Oocyst, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Female Gametocyte, Male Gametocyte. Otto TD Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% 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.
  • 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_127394)

Species Accession Gene Product
Arabidopsis thaliana AT5G37850   Pyridoxal kinase
Brugia malayi Bm1_07835   pyridoxal kinase
Candida albicans CaO19.3411   same as N terminus of cosmid orf Ca20C1.16
Candida albicans CaO19.9387   similar to BUD17-like CaP19.3411
Candida albicans CaO19.1828   similar to BUD17-like CaP19.3411
Candida albicans CaO19.10914   similar to N terminus of S. cerevisiae BUD17 (YNR027W)
Caenorhabditis elegans CELE_F57C9.1   Protein F57C9.1, isoform A
Dictyostelium discoideum DDB_G0268628   pyridoxal kinase
Drosophila melanogaster Dmel_CG34455   Pyridoxal kinase
Escherichia coli b1636   pyridoxamine kinase
Escherichia coli b2418   pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase
Echinococcus granulosus EgrG_000600600   pyridoxal kinase
Entamoeba histolytica EHI_126090   pyridoxal kinase, putative
Echinococcus multilocularis EmuJ_000600600   pyridoxal kinase
Homo sapiens ENSG00000160209   pyridoxal (pyridoxine, vitamin B6) kinase
Leishmania braziliensis LbrM.30.1370   Pyridoxal kinase, putative
Leishmania donovani LdBPK_301310.1   pyridoxal kinase, putative
Leishmania infantum LinJ.30.1310   Pyridoxal kinase, putative
Leishmania major LmjF.30.1250   Pyridoxal kinase, putative
Leishmania mexicana LmxM.29.1250   Pyridoxal kinase, putative
Loa Loa (eye worm) LOAG_01254   hypothetical protein
Mus musculus 102641556   mucin-1-like
Mus musculus ENSMUSG00000032788   pyridoxal (pyridoxine, vitamin B6) kinase
Oryza sativa 4352717   Os12g0600400
Onchocerca volvulus OVOC280   Putative pyridoxal kinase
Plasmodium berghei PBANKA_1230800   pyridoxal kinase, putative
Plasmodium falciparum PF3D7_0616000   pyridoxal kinase
Plasmodium knowlesi PKNH_1134000   pyridoxal kinase, putative
Plasmodium vivax PVX_113935   pyridoxal kinase, putative
Plasmodium yoelii PY01633   putative pyridoxine kinase
Saccharomyces cerevisiae YEL029C   putative pyridoxal kinase BUD16
Saccharomyces cerevisiae YNR027W   putative pyridoxal kinase BUD17
Schistosoma japonicum Sjp_0098930   ko:K00868 pyridoxine kinase [EC2.7.1.35], putative
Schistosoma mansoni Smp_164250.1   pyridoxine kinase
Schistosoma mansoni Smp_164250.2   pyridoxine kinase
Schmidtea mediterranea mk4.008081.02  
Schmidtea mediterranea mk4.000800.10  
Schmidtea mediterranea mk4.004639.00   Putative pyridoxal kinase
Schmidtea mediterranea mk4.010590.00  
Schmidtea mediterranea mk4.010030.00  
Trypanosoma brucei gambiense Tbg972.6.2510   pyridoxal kinase
Trypanosoma brucei Tb927.6.2740   pyridoxal kinase
Trypanosoma congolense TcIL3000_0_21240   pyridoxal kinase
Trypanosoma cruzi TcCLB.509059.50   pyridoxal kinase, putative
Trypanosoma cruzi TcCLB.507925.40   pyridoxal kinase, putative
Trichomonas vaginalis TVAG_493290   phosphomethylpyrimidine kinase, putative
Trichomonas vaginalis TVAG_425810   phosphomethylpyrimidine kinase, putative
Trichomonas vaginalis TVAG_132920   pyridoxine kinase, putative

Essentiality

PF3D7_0616000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.6.2740 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.6.2740 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.6.2740 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.6.2740 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b1636 Escherichia coli non-essential goodall
b2418 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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.
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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
Species Known druggable target Linked compounds Reference
Homo sapiens pyridoxal (pyridoxine, vitamin B6) kinase Compounds References
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

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

Reagent availability

  • Reagent:
  • Target Type Source Notes
    PF3D7_0616000 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Plasmodium falciparum ( 1 )

Bibliographic References

2 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PF3D7_0616000 (Plasmodium falciparum), pyridoxal kinase
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