Detailed view for PF3D7_1216200

Basic information

TDR Targets ID: 5206
Plasmodium falciparum, glycerol-3-phosphate dehydrogenase, putative

Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.2705 | Length (AA): 367 | MW (Da): 41234 | Paralog Number: 1

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

Druggability Group : DG2

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

PF01210   NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
PF07479   NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus

Gene Ontology

Mouse over links to read term descriptions.
GO:0016616   oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor  
GO:0004367   glycerol-3-phosphate dehydrogenase (NAD+) activity  
GO:0009331   glycerol-3-phosphate dehydrogenase complex  
GO:0005737   cytoplasm  
GO:0050662   coenzyme binding  
GO:0042803   protein homodimerization activity  
GO:0016491   oxidoreductase activity  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0051287   NAD binding  
GO:0046168   glycerol-3-phosphate catabolic process  
GO:0008152   metabolic process  
GO:0006072   glycerol-3-phosphate metabolic process  
GO:0005975   carbohydrate metabolic process  
GO:0055114   oxidation reduction  

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
2 364 1yj8 (A) 10 372 99.99 0 1 2.25 -2.56
2 364 1yj8 (A) 10 372 99.99 0 1 2.2593 -1.88

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:

  • 1YJ8:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, gametocyte, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, merozoite, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Male Gametocyte. Lasonder E
Show/Hide expression data references
  • 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.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_126704)

Species Accession Gene Product
Arabidopsis thaliana AT5G40610   glycerol-3-phosphate dehydrogenase [NAD+]
Arabidopsis thaliana AT2G40690   glycerol-3-phosphate dehydrogenase [NAD(+)] 2
Babesia bovis BBOV_IV004480   glycerol-3-phosphate dehydrogenase, putative
Brugia malayi Bm1_45570   Probable glycerol-3-phosphate dehydrogenase, cytoplasmic
Candida albicans CaO19.8310   one of two genes similar to S. cerevisiae GPD1 (YDL022W) and GPD2 (YOL059W) glycerol-3-phosphate dehydrogenase
Candida albicans CaO19.9325   one of two genes similar to S. cerevisiae GPD1 (YDL022W) and GPD2 (YOL059W) glycerol-3-phosphate dehydrogenase
Candida albicans CaO19.691   one of two genes similar to S. cerevisiae GPD1 (YDL022W) and GPD2 (YOL059W) glycerol-3-phosphate dehydrogenase
Candida albicans CaO19.1756   one of two genes similar to S. cerevisiae GPD1 (YDL022W) and GPD2 (YOL059W) glycerol-3-phosphate dehydrogenase
Caenorhabditis elegans CELE_F47G4.3   Protein GPDH-1
Caenorhabditis elegans CELE_K11H3.1   Protein GPDH-2, isoform C
Cryptosporidium hominis Chro.20028   glycerol-3-phosphate dehydrogenase
Cryptosporidium parvum cgd2_210   glycerol-3-phosphate dehydrogenase
Chlamydia trachomatis CT_714   glycerol-3-phosphate dehydrogenase
Drosophila melanogaster Dmel_CG3215   CG3215 gene product from transcript CG3215-RA
Drosophila melanogaster Dmel_CG9042   Glycerol 3 phosphate dehydrogenase
Escherichia coli b3608   glycerol-3-phosphate dehydrogenase (NAD+)
Echinococcus granulosus EgrG_000686100   glycerol 3 phosphate dehydrogenase NAD
Echinococcus multilocularis EmuJ_000686100   glycerol 3 phosphate dehydrogenase (NAD+)
Homo sapiens ENSG00000152642   glycerol-3-phosphate dehydrogenase 1-like
Homo sapiens ENSG00000167588   glycerol-3-phosphate dehydrogenase 1 (soluble)
Leishmania braziliensis LbrM.10.0640   glycerol-3-phosphate dehydrogenase [NAD ], glycosomal
Leishmania donovani LdBPK_100560.1   glycerol-3-phosphate dehydrogenase [NAD+], glycosomal
Leishmania infantum LinJ.10.0560   glycerol-3-phosphate dehydrogenase [NAD ], glycosomal
Leishmania major LmjF.10.0510   glycerol-3-phosphate dehydrogenase [NAD ], glycosomal
Leishmania mexicana LmxM.10.0510   glycerol-3-phosphate dehydrogenase [NAD ], glycosomal/mitochondrial
Loa Loa (eye worm) LOAG_00716   glycerol-3-Phosphate DeHydrogenase family member
Loa Loa (eye worm) LOAG_11450   glycerol 3 phosphate dehydrogenase
Loa Loa (eye worm) LOAG_09844   hypothetical protein
Mycobacterium leprae ML1679c   PROBABLE GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(P)+] GPDA (NAD(P)H- DEPENDENT GLYCEROL-3-PHOSPHATE DEHYDROGENASE)
Mus musculus ENSMUSG00000023019   glycerol-3-phosphate dehydrogenase 1 (soluble)
Mus musculus ENSMUSG00000050627   glycerol-3-phosphate dehydrogenase 1-like
Mycobacterium tuberculosis Rv0564c   Probable glycerol-3-phosphate dehydrogenase [NAD(P)+] GpdA1 (NAD(P)H-dependent glycerol-3-phosphate dehydrogenase) (NAD(P)H-depe
Mycobacterium tuberculosis Rv2982c   Probable glycerol-3-phosphate dehydrogenase [NAD(P)+] GpdA2 (NAD(P)H- dependent glycerol-3-phosphate dehydrogenase)
Mycobacterium ulcerans MUL_1975   NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
Mycobacterium ulcerans MUL_0667   NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
Neospora caninum NCLIV_043550   Glycerol-3-phosphate dehydrogenase, related
Neospora caninum NCLIV_001180   CBR-GPDH-1 protein, related
Oryza sativa 4342770   Os07g0229800
Onchocerca volvulus OVOC3115  
Onchocerca volvulus OVOC8373  
Plasmodium berghei PBANKA_0932900   glycerol-3-phosphate dehydrogenase, putative
Plasmodium berghei PBANKA_1431900   glycerol-3-phosphate dehydrogenase, putative
Plasmodium falciparum PF3D7_1216200   glycerol-3-phosphate dehydrogenase, putative
Plasmodium falciparum PF3D7_1114800   glycerol-3-phosphate dehydrogenase, putative
Plasmodium knowlesi PKNH_0912300   glycerol-3-phosphate dehydrogenase, putative
Plasmodium knowlesi PKNH_1435700   glycerol-3-phosphate dehydrogenase, putative
Plasmodium vivax PVX_091380   glycerol-3-phosphate dehydrogenase, putative
Plasmodium vivax PVX_123490   glycerol-3-phosphate dehydrogenase, putative
Plasmodium yoelii PY02925   Unknown-related
Plasmodium yoelii PY00789   NAD-dependent glycerol-3-phosphate dehydrogenase
Plasmodium yoelii PY05585   glycerol-3-phosphate dehydrogenase
Saccharomyces cerevisiae YDL022W   glycerol-3-phosphate dehydrogenase (NAD(+)) GPD1
Saccharomyces cerevisiae YOL059W   glycerol-3-phosphate dehydrogenase (NAD(+)) GPD2
Schistosoma japonicum Sjp_0005480   ko:K00006 glycerol-3-phosphate dehydrogenase (NAD+) [EC1.1.1.8], putative
Schistosoma japonicum Sjp_0117170   Glycerol-3-phosphate dehydrogenase [NAD+], putative
Schistosoma mansoni Smp_030500.1   glycerol-3-phosphate dehydrogenase
Schistosoma mansoni Smp_030500.2   glycerol-3-phosphate dehydrogenase
Schmidtea mediterranea mk4.008015.01   Glycerol-3-phosphate dehydrogenase, putative
Schmidtea mediterranea mk4.001050.01  
Schmidtea mediterranea mk4.001797.04  
Schmidtea mediterranea mk4.001020.06  
Schmidtea mediterranea mk4.000878.05  
Schmidtea mediterranea mk4.011976.00  
Schmidtea mediterranea mk4.001612.07  
Schmidtea mediterranea mk4.003385.00  
Schmidtea mediterranea mk4.002551.01  
Schmidtea mediterranea mk4.000946.04  
Schmidtea mediterranea mk4.007040.01  
Schmidtea mediterranea mk4.014739.01  
Schmidtea mediterranea mk4.003527.01  
Schmidtea mediterranea mk4.002903.00  
Schmidtea mediterranea mk4.009142.03  
Schmidtea mediterranea mk4.025464.00  
Schmidtea mediterranea mk4.006553.00   Glycerol-3-phosphate dehydrogenase, putative
Trypanosoma brucei gambiense Tbg972.8.3210   glycerol-3-phosphate dehydrogenase [NAD ], glycosomal, putative
Trypanosoma brucei Tb927.8.3530   glycerol-3-phosphate dehydrogenase [NAD+], glycosomal
Trypanosoma congolense TcIL3000_8_3450   glycerol-3-phosphate dehydrogenase [NAD+], glycosomal, putative
Toxoplasma gondii TGME49_307570   glycerol-3-phosphate dehydrogenase (gpdh), putative
Toxoplasma gondii TGME49_210260   NAD-dependent glycerol-3-phosphate dehydrogenase
Treponema pallidum TP1009   NAD(P)H-dependent glycerol-3-phosphate dehydrogenase
Theileria parva TP01_0302   NAD-dependent glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_586980   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_601920   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_230610   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_525580   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_382880   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_361130   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_304500   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_512070   glycerol-3-phosphate dehydrogenase, putative
Trichomonas vaginalis TVAG_386800   glycerol-3-phosphate dehydrogenase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0597   NAD(P)H-dependent glycerol-3-phosphate dehydrogenase

Essentiality

PF3D7_1216200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu572 Mycobacterium tuberculosis non-essential nmpdr
mtu3032 Mycobacterium tuberculosis non-essential nmpdr
Tb927.8.3530 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.8.3530 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.8.3530 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.8.3530 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3608 Escherichia coli essential goodall
PBANKA_0932900 Plasmodium berghei Dispensable plasmo
PBANKA_1431900 Plasmodium berghei Dispensable plasmo
TGME49_307570 Toxoplasma gondii Essentiality uncertain sidik
TGME49_210260 Toxoplasma gondii Essentiality uncertain sidik
TGME49_307570 Toxoplasma gondii Probably essential sidik
TGME49_210260 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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
Species Known druggable target Linked compounds Reference
Trypanosoma brucei glycerol-3-phosphate dehydrogenase [NAD+], glycosomal 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

  • Assay for α-Glycerophosphate Dehydrogenase (1.1.1.8 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Pfal009132AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Pfal009132; Recombinant protein: full-length; Source: P falciparum; glycerol-3-phosphate dehydrogenase, putative ;

Bibliographic References

No literature references available for this target.

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Gene identifier PF3D7_1216200 (Plasmodium falciparum), glycerol-3-phosphate dehydrogenase, putative
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