Detailed view for PF3D7_0202700

Basic information

TDR Targets ID: 3299
Plasmodium falciparum, octaprenyl pyrophosphate synthase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.8671 | Length (AA): 538 | MW (Da): 63046 | Paralog Number: 0

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

Druggability Group : DG4

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

PF00348   Polyprenyl synthetase

Gene Ontology

Mouse over links to read term descriptions.
GO:0005739   mitochondrion  
GO:0004659   prenyltransferase activity  
GO:0008299   isoprenoid biosynthetic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

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
153 536 1wy0 (A) 6 341 23.00 0 1 0.78 -0.81
212 490 1v4e (A) 12 276 26.00 0 1 0.93 -1.04
152 536 3apz (A) 8 347 29.00 0 1 0.781013 0.3
202 536 3aq0 (A) 25 347 33.00 0 1 0.999477 -0.44
210 459 4lfg (A) 1 261 24.00 0.00000073 0.9 0.735084 -0.05
259 413 2ftz (A) 52 202 37.00 0.000016 0.2 0.390904 1.2

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 60-80% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, early schizont, early trophozoite, late ring, late schizont, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, merozoite, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, Sporozoite, Female Gametocyte, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Ring. Zanghi G
Show/Hide expression data references
  • 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.
  • 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

Orthologs

Ortholog group members (OG5_126937)

Species Accession Gene Product
Arabidopsis thaliana AT1G17050   solanesyl diphosphate synthase 2
Arabidopsis thaliana AT1G78510   solanesyl diphosphate synthase 1
Arabidopsis thaliana AT2G34630   geranyl diphosphate synthase 1
Babesia bovis BBOV_IV007310   polyprenyl synthetase superfamily protein
Brugia malayi Bm1_35720   Polyprenyl synthetase family protein
Candida albicans CaO19.7478   trans-hexaprenyltranstransferase
Caenorhabditis elegans CELE_C24A11.9   Protein COQ-1
Cryptosporidium hominis Chro.70416   hypothetical protein
Cryptosporidium parvum cgd7_3730   long chain fatty acyl diphosphate synthase
Dictyostelium discoideum DDB_G0280293   hexaprenyl pyrophosphate synthetase
Drosophila melanogaster Dmel_CG31005   CG31005 gene product from transcript CG31005-RA
Escherichia coli b3187   octaprenyl diphosphate synthase
Echinococcus granulosus EgrG_000256100   decaprenyl diphosphate synthase subunit 1
Entamoeba histolytica EHI_028880   geranylgeranyl pyrophosphate synthetase, putative
Entamoeba histolytica EHI_105060   geranylgeranyl pyrophosphate synthase, putative
Echinococcus multilocularis EmuJ_000256100   decaprenyl diphosphate synthase subunit 1
Homo sapiens ENSG00000148459   prenyl (decaprenyl) diphosphate synthase, subunit 1
Leishmania braziliensis LbrM.15.1060   solanesyl-diphosphate synthase, putative
Leishmania donovani LdBPK_151080.1   solanesyl-diphosphate synthase, putative
Leishmania infantum LinJ.15.1080   solanesyl-diphosphate synthase, putative
Leishmania major LmjF.15.1020   solanesyl-diphosphate synthase, putative
Leishmania mexicana LmxM.15.1020   farnesyl synthetase, putative
Loa Loa (eye worm) LOAG_00347   polyprenyl synthetase
Mycobacterium leprae ML2277   PROBABLE POLYPRENYL-DIPHOSPHATE SYNTHASE GRCC1 (POLYPRENYL PYROPHOSPHATE SYNTHETASE)
Mus musculus ENSMUSG00000026784   prenyl (solanesyl) diphosphate synthase, subunit 1
Mycobacterium tuberculosis Rv0562   Probable polyprenyl-diphosphate synthase GrcC1 (polyprenyl pyrophosphate synthetase)
Mycobacterium ulcerans MUL_0664   polyprenyl diphosphate synthetase, GrcC1
Neospora caninum NCLIV_036980   hypothetical protein
Oryza sativa 9272514   Os08g0193100
Oryza sativa 4351957   Os12g0271700
Oryza sativa 4341844   Os06g0678200
Plasmodium berghei PBANKA_0300800   octaprenyl pyrophosphate synthase, putative
Plasmodium falciparum PF3D7_0202700   octaprenyl pyrophosphate synthase
Plasmodium knowlesi PKNH_0418400   octaprenyl pyrophosphate synthase, putative
Plasmodium vivax PVX_003575   octaprenyl pyrophosphate synthase, putative
Plasmodium yoelii PY00446   Polyprenyl synthetase, putative
Saccharomyces cerevisiae YBR003W   trans-hexaprenyltranstransferase
Schistosoma japonicum Sjp_0306360   Decaprenyl-diphosphate synthase subunit 1, putative
Schistosoma japonicum Sjp_0071520   ko:K00810 similar to prenyl diphosphate synthase, subunit 1 [EC:2.5.1.-], putative
Schistosoma mansoni Smp_059800   trans-prenyltransferase
Schmidtea mediterranea mk4.001177.03  
Schmidtea mediterranea mk4.001177.02   Prenyl transferase
Trypanosoma brucei gambiense Tbg972.9.3090   farnesyl pyrophosphate synthetase, putative
Trypanosoma brucei Tb927.9.5890   solanesyl-diphosphate synthase, putative
Trypanosoma cruzi TcCLB.509445.30   solanesyl-diphosphate synthase
Trypanosoma cruzi TcCLB.427091.10   solanesyl-diphosphate synthase, putative
Trypanosoma cruzi TcCLB.422031.10   solanesyl-diphosphate synthase, putative
Toxoplasma gondii TGME49_269430   polyprenyl synthetase superfamily protein
Theileria parva TP03_0238   prenyl transferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0532   geranylgeranyl pyrophosphate synthase

Essentiality

PF3D7_0202700 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb09.160.4300 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb09.160.4300 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb09.160.4300 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb09.160.4300 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3187 Escherichia coli essential goodall
CELE_C24A11.9 Caenorhabditis elegans slow growth wormbase
PBANKA_0300800 Plasmodium berghei Essential plasmo
TGME49_269430 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.

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): 0.1

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 cruzi solanesyl-diphosphate synthase Compounds References
Trypanosoma cruzi solanesyl-diphosphate synthase, putative Compounds References
Trypanosoma cruzi solanesyl-diphosphate synthase, putative Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0679 0.2583 0.2569
0.1685 0.2666 0.2639
0.0157 0.5529 0.5529
0.0189 0.4012 0.3977
0.0157 0.5396 0
0.1486 0.3458 0.4428
0.0411 0.2525 0.2757
0.0679 0.2583 0.2569
0.0704 0.3928 0.3913
0.047 0.2506 0
0.1054 0.4087 0.4852
0.0824 0.358 0.358
0.1059 0.5002 0
0.1054 0.4087 0.4852
0.8288 0.3209 0.3209
0.0377 0.2905 0.2134
0.0663 0.273 0.2727
0.0519 0.2681 0.2661
0.1054 0.4087 0.4852
0.9267 0.3083 0.3083
0.0157 0.3438 0
0.0398 0.2674 0.2044
0.061 0.2693 0
0.0706 0.2737 0.272
0.0425 0.2773 0.2104
0.1054 0.4087 0.4852
0.0332 0.2653 0.2653
0.0433 0.267 0
0.0545 0.2666 0
0.0667 0.4405 0.4403
0.0788 0.2789 0.228
0.9267 0.3083 0.3083
0.3926 0.2756 0.2756
0.0157 0.3438 0
0.0411 0.2525 0.2757
0.0191 0.3456 0.4101
0.0774 0.2668 0
0.0679 0.2583 0.2569
0.0824 0.358 0.358
0.3926 0.2756 0.2756
0.0433 0.267 0
0.0667 0.4405 0.4403
0.0447 0.2832 0.2829
0.2036 0.3184 0
0.05 0.2528 0.2478
0.1054 0.4087 0.4852
0.1374 0.2627 0.2627
0.0416 0.3269 0.3303
0.0953 0.2702 0.2697
0.1063 0.2647 0.2647
0.0824 0.358 0.358
0.0157 0.3438 0
0.0411 0.2525 0.2757
0.1648 0.4301 0.427
0.0494 0.29 0.264
0.0517 0.2702 0
0.4054 0.2847 0.2847
0.0583 0.3069 0.3067
0.0448 0.2646 0.2161
0.4173 0.2761 0.276
0.1059 0.5002 0
0.0635 0.2606 0.2606
0.0425 0.2773 0.2104
0.0254 0.2727 0.2717
0.1059 0.5002 0
0.0261 0.2812 0.2877
0.0189 0.4012 0.3977
0.1054 0.4087 0.4852
0.0679 0.2583 0.2569
0.0824 0.358 0.358
0.0327 0.2716 0.2714
0.1063 0.2647 0.2647
0.026 0.2585 0.2565
0.0445 0.2829 0.2829
0.9267 0.3083 0.3083
0.1171 0.3221 0
0.0436 0.3099 0.3034
0.1054 0.4087 0.4852
0.1054 0.4087 0.4852
0.0128 0.288 0.0188
0.026 0.2585 0.2565
0.0169 0.3173 0.2603
0.084 0.2579 0.255
0.0157 0.3438 0
0.0667 0.4405 0.4403
0.0425 0.2654 0.2112
0.1821 0.2575 0.257
0.0679 0.2583 0.2569
0.0096429 0.366433 0
0.1059 0.5002 0
0.0157 0.3438 0
0.0429 0.451 0
0.0663 0.273 0.2727
0.1059 0.5002 0
0.0673 0.2639 0.2619
0.0118 0.3145 0.4648
0.084 0.2579 0.255

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

No literature references available for this target.

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Gene identifier PF3D7_0202700 (Plasmodium falciparum), octaprenyl pyrophosphate synthase
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