Detailed view for PF3D7_0621200

Basic information

TDR Targets ID: 4562
Plasmodium falciparum, pyridoxine biosynthesis protein PDX1
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.164 | Length (AA): 301 | MW (Da): 33013 | 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

PF01680   SOR/SNZ family

Gene Ontology

Mouse over links to read term descriptions.
GO:0042823   pyridoxal phosphate biosynthetic process  
GO:0042819   vitamin B6 biosynthetic process  
GO:0003824   catalytic activity  
GO:0008615   pyridoxine biosynthetic process  
GO:0008152   metabolic process  

Metabolic Pathways

Vitamin B6 metabolism (KEGG)

Structural information

Modbase 3D models:

There are 2 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
20 273 1znn (A) 18 271 61.00 0 1 1.66 -1.49
6 283 4adt (A) 7 283 79.00 0 1 1.68219 -0.22

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 intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Ring, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, Oocyst, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • 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.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_128957)

Species Accession Gene Product
Arabidopsis thaliana AT5G01410   Pyridoxal biosynthesis protein PDX1.3
Arabidopsis thaliana AT2G38230   Pyridoxal biosynthesis protein PDX1.1
Candida albicans CaO19.2947   stationary-phase-induced
Candida albicans CaO19.10464   stationary-phase-induced
Dictyostelium discoideum DDB_G0288299   vitamin B6 biosynthesis family protein
Mycobacterium leprae ML0450c   Possible pyridoxine biosynthesis protein SnzP
Mycobacterium tuberculosis Rv2606c   Possible pyridoxine biosynthesis protein SnzP
Mycobacterium ulcerans MUL_3250   pyridoxal biosynthesis lyase PdxS
Neospora caninum NCLIV_051000   Ethylene-inducible protein hever, related
Oryza sativa 4347937   Os10g0100700
Oryza sativa 4351233   Os11g0708500
Oryza sativa 4342162   Os07g0100200
Plasmodium berghei PBANKA_1120200   pyridoxine biosynthesis protein PDX1, putative
Plasmodium falciparum PF3D7_0621200   pyridoxine biosynthesis protein PDX1
Plasmodium knowlesi PKNH_1129000   pyridoxine biosynthesis protein PDX1, putative
Plasmodium vivax PVX_114180   pyridoxine biosynthesis protein PDX1, putative
Plasmodium yoelii PY04475   ethylene-inducible protein hever
Saccharomyces cerevisiae YNL333W   pyridoxine biosynthesis protein SNZ2
Saccharomyces cerevisiae YMR096W   pyridoxine biosynthesis protein SNZ1
Saccharomyces cerevisiae YFL059W   pyridoxine biosynthesis protein SNZ3
Schmidtea mediterranea mk4.000858.13  
Toxoplasma gondii TGME49_237140   ethylene inducible protein, putative

Essentiality

PF3D7_0621200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1120200 Plasmodium berghei Dispensable plasmo
TGME49_237140 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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

Druggability index (range: 0 to 1): 0.2

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

3 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_0621200 (Plasmodium falciparum), pyridoxine biosynthesis protein PDX1
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