Detailed view for PF3D7_0306400

Basic information

TDR Targets ID: 3565
Plasmodium falciparum, FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.6648 | Length (AA): 653 | MW (Da): 74688 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF01266   FAD dependent oxidoreductase
PF16901   C-terminal domain of alpha-glycerophosphate oxidase

Gene Ontology

Mouse over links to read term descriptions.
GO:0006127   glycerophosphate shuttle  
GO:0009331   glycerol-3-phosphate dehydrogenase complex  
GO:0005739   mitochondrion  
GO:0016491   oxidoreductase activity  
GO:0004368   glycerol-3-phosphate dehydrogenase activity  
GO:0055114   oxidation reduction  
GO:0006072   glycerol-3-phosphate metabolic process  

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
54 348 1trb () 2 315 13.00 0.0000005 0.08 0.5 -0.11
55 458 1el5 (A) 1 382 10.00 0 1 0.56 0.23
46 651 2rgh (A) 7 602 33.00 0 1 1.10912 0.21
56 115 2qae (A) 1 65 40.00 0.61 0.4 0.368984 0.75
58 95 3urh (A) 3 40 47.00 0.97 0.65 0.523293 0.62
400 464 3ult (A) 8 75 34.00 0.23 0.12 0.438641 -0.35

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 - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, gametocyte, sporozoite, late schizont, late trophozoite, Female Gametocyte. Otto TD PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, early trophozoite, Ring, Sporozoite, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 24 hs. Otto TD
Show/Hide expression data references
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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_127215)

Species Accession Gene Product
Arabidopsis thaliana AT3G10370   glycerol-3-phosphate dehydrogenase SDP6
Babesia bovis BBOV_III000930   FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Candida albicans CaO19.10645   glycerol-3-phosphate dehydrogenase, mitochondrial
Candida albicans CaO19.3133   glycerol-3-phosphate dehydrogenase, mitochondrial
Caenorhabditis elegans CELE_T25G3.4   Protein T25G3.4
Dictyostelium discoideum DDB_G0283951   hypothetical protein
Drosophila melanogaster Dmel_CG8256   Glycerophosphate oxidase-1
Drosophila melanogaster Dmel_CG2137   CG2137 gene product from transcript CG2137-RA
Escherichia coli b3426   sn-glycerol-3-phosphate dehydrogenase, aerobic, FAD/NAD(P)-binding
Escherichia coli b2241   sn-glycerol-3-phosphate dehydrogenase (anaerobic), large subunit, FAD/NAD(P)-binding
Echinococcus granulosus EgrG_000964600   glycerol 3 phosphate dehydrogenase
Echinococcus multilocularis EmuJ_000964600   glycerol 3 phosphate dehydrogenase
Homo sapiens ENSG00000115159   glycerol-3-phosphate dehydrogenase 2 (mitochondrial)
Leishmania braziliensis LbrM.28.0250   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Leishmania donovani LdBPK_280240.1   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Leishmania infantum LinJ.28.0240   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Leishmania mexicana LmxM.28.0240   glycerol-3-phosphate dehydrogenase, putative
Loa Loa (eye worm) LOAG_11054   glycerol-3-phosphate dehydrogenase
Loa Loa (eye worm) LOAG_08286   hypothetical protein
Mycobacterium leprae ML0713   Probable glycerol-3-phosphate dehydrogenase GlpD
Mus musculus ENSMUSG00000026827   glycerol phosphate dehydrogenase 2, mitochondrial
Mycobacterium tuberculosis Rv3302c   Probable glycerol-3-phosphate dehydrogenase GlpD2
Mycobacterium tuberculosis Rv2249c   Probable glycerol-3-phosphate dehydrogenase GlpD1
Mycobacterium ulcerans MUL_2667   glycerol-3-phosphate dehydrogenase GlpD2
Mycobacterium ulcerans MUL_1300   glycerol-3-phosphate dehydrogenase
Neospora caninum NCLIV_024220   glycerol-3-phosphate dehydrogenase, putative
Oryza sativa 4335210   Os04g0224900
Plasmodium berghei PBANKA_0404800   FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Plasmodium falciparum PF3D7_0306400   FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Plasmodium knowlesi PKNH_0836300   FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Plasmodium vivax PVX_119445   FAD-dependent glycerol-3-phosphate dehydrogenase, putative
Plasmodium yoelii PY05303   putative FAD-dependent glycerol-3-phosphate dehydrogenase
Saccharomyces cerevisiae YIL155C   glycerol-3-phosphate dehydrogenase
Schistosoma japonicum Sjp_0104060   Probable glycerol-3-phosphate dehydrogenase, mitochondrial precursor, putative
Schistosoma japonicum Sjp_0303310   ko:K00111 glycerol-3-phosphate dehydrogenase [EC1.1.99.5A], putative
Schistosoma mansoni Smp_121990   glycerol-3-phosphate dehydrogenase
Schmidtea mediterranea mk4.017466.00  
Schmidtea mediterranea mk4.018679.00   Glycerol-3-phosphate dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.011430.03   Glycerol-3-phosphate dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.016770.00   Glycerol-3-phosphate dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.011430.04   Glycerol-3-phosphate dehydrogenase, mitochondrial
Schmidtea mediterranea mk4.020831.00   Glycerol-3-phosphate dehydrogenase, mitochondrial
Trypanosoma brucei gambiense Tbg972.11.8440   glycerol-3-phosphate dehydrogenase, putative
Trypanosoma brucei Tb927.11.7380   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Trypanosoma congolense TcIL3000.11.7960   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Trypanosoma congolense TcIL3000_0_58760   glycerol-3-phosphate dehydrogenase (FAD-dependent), mitochondrial
Trypanosoma cruzi TcCLB.511151.90   glycerol-3-phosphate dehydrogenase, putative
Toxoplasma gondii TGME49_263730   FAD-dependent glycerol-3-phosphate dehydrogenase
Theileria parva TP03_0730   glycerol-3-phosphate dehydrogenase, putative

Essentiality

PF3D7_0306400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.02.5280 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.5280 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5280 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.5280 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b2241 Escherichia coli non-essential goodall
b3426 Escherichia coli non-essential goodall
PBANKA_0404800 Plasmodium berghei Slow plasmo
TGME49_263730 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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

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

12 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_0306400 (Plasmodium falciparum), FAD-dependent glycerol-3-phosphate dehydrogenase, putative
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