Detailed view for PF3D7_0623000

Basic information

TDR Targets ID: 4578
Plasmodium falciparum, chorismate synthase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.1159 | Length (AA): 527 | MW (Da): 59666 | 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

PF01264   Chorismate synthase

Gene Ontology

Mouse over links to read term descriptions.
GO:0009423   chorismate biosynthetic process  
GO:0004107   chorismate synthase activity  
GO:0009073   aromatic amino acid family biosynthetic process  

Structural information

Modbase 3D models:

There are 4 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
1 512 1um0 (A) 1 351 36.00 0 1 0.85 0.74
1 525 1sq1 (A) 1 357 37.00 0 1 0.422905 1.41
1 514 1r53 (A) 1 368 47.00 0 1 0.571032 1.63
1 525 1um0 (A) 1 360 34.00 0 1 0.746905 1.27

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 - 24 hs, intra-erythrocytic - 32 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Ring, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 8 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Female Gametocyte. 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_128304)

Species Accession Gene Product
Arabidopsis thaliana AT1G48850   chorismate synthase
Candida albicans CaO19.3489   chorismate synthase
Candida albicans CaO19.1986   Chorismate synthase
Chlamydia trachomatis CT_368   chorismate synthase
Escherichia coli b2329   chorismate synthase
Mycobacterium leprae ML0516   Chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase).
Mycobacterium tuberculosis Rv2540c   Probable chorismate synthase AroF (5-enolpyruvylshikimate-3-phosphate phospholyase)
Mycobacterium ulcerans MUL_1759   chorismate synthase
Neospora caninum NCLIV_023120   Chorismate synthase (EC 4.2.3.5), related
Oryza sativa 4332286   Os03g0254800
Plasmodium berghei PBANKA_1121900   chorismate synthase, putative
Plasmodium falciparum PF3D7_0623000   chorismate synthase
Plasmodium knowlesi PKNH_1127200   chorismate synthase, putative
Plasmodium vivax PVX_114265   chorismate synthase
Plasmodium yoelii PY04071   chorismate synthase, putative
Saccharomyces cerevisiae YGL148W   bifunctional chorismate synthase/riboflavin reductase [NAD(P)H] ARO2
Toxoplasma gondii TGME49_201380   chorismate synthase, putative

Essentiality

PF3D7_0623000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b2329 Escherichia coli non-essential goodall
PBANKA_1121900 Plasmodium berghei Dispensable plasmo
TGME49_201380 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) decreased time (PATO:0000716) multi-cellular organism (CARO:0000012) bloodstream stage (PLO:0040) inferred from RNAi experiment (ECO:0000019) Plasmodium falciparum No drug identifiers listed for this gene.
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 11814579

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): 0.6

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
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) Chorismate synthase 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
0.5344 0.4401 1
0.106 1 1
0.4385 1 1
0.3715 0.4208 0.4678
0.3663 1 0.5
0.2998 0.9417 1
0.1425 0.3375 1
0.1064 0.313 1
0.324 0.4358 1
0.1604 0.4869 1
0.2182 1 1
0.2331 0.3449 1
0.106 0.2602 1
0.3715 0.4208 0.4678
0.199 0.3352 1
0.0347 1 0.5
0.3678 1 1
0.0216 0.4649 0.5
0.1797 0.261 1
0.0795 0.3231 1
0.5001 0.6671 1
0.1999 0.256 1
0.0523 1 0.5
0.0552 0.8898 1
0.1797 0.261 1
0.1829 1 1
0.0216 1 0.5
0.0204 0.6944 1
0.4596 1 1
0.0216 1 0.5
0.3663 1 0.5
0.218 0.3172 1
0.1435 1 1
0.3452 0.4187 1
0.18 0.4584 1
0.1062 0.4273 1
0.4997 0.7237 1
0.4997 0.7237 1
0.1798 1 1
0.106 0.2602 1
0.4997 0.7237 1
0.0216 0.4649 0.5
0.1236 0.4887 1
0.4244 0.4276 1
0.0216 1 0.5
0.3715 0.4208 0.4678
0.0179 0.3155 1
0.1604 0.4869 1
0.3222 1 1
0.4138 1 1
0.4047 1 1
0.4138 1 1
0.2749 0.4911 1
0.0216 0.3256 0.5
0.2314 0.6929 1
0.1069 1 1
0.3457 1 1
0.0698 0.2667 1
0.2168 0.2771 1
0.0174 0.2731 1
0.4766 0.7953 1
0.4809 1 1
0.4997 0.7237 1
0.2493 0.4382 1
0.0178 0.4339 0.5
0.0744 0.3514 1
0.3715 0.4208 0.4678
0.071 1 0.5
0.0705 1 1
0.2168 0.3171 1
0.3533 1 1
0.4972 0.8659 1
0.1993 0.3846 1
0.4809 1 1
0.3758 1 1
0.1435 1 1
0.3715 0.4208 0.4678
0.1786 0.5428 1
0.1959 0.5528 0.5
0.3008 0.9689 1
0.4997 0.7237 1
0.2372 0.3439 1
0.1818 0.2665 1
0.4663 1 1
0.3347 1 0.5
0.0534 0.3131 0.7592
0.0351 0.3474 1
0.0192 0.2642 1
0.1991 0.2547 1
0.0204 0.3559 1
0.4049 1 1
0.0795 0.3231 1
0.4265 1 1
0.324 0.4358 1
0.2304 0.4753 1
0.5898 1 1
0.1807 0.4344 1
0.4831 0.7295 1
0.3256 0.4372 1
0.1988 1 1
0.0527 0.3285 0.7944
0.3008 0.9689 1
0.29 0.3912 1
0.0699 0.7081 1
0.18 0.4584 1
0.0191 0.47 1
0.3031 0.5641 1
0.0744 0.3514 1
0.0723 0.3614 1
0.218 0.539 1
0.324 0.4358 1
0.0216 0.5 0.5
0.3482 0.4602 1
0.3426 1 0.5
0.1439 0.3381 1
0.4049 1 1
0.324 0.4358 1
0.3715 0.4208 0.4678
0.4809 1 1
0.1079 0.2528 0.7813
0.218 0.3172 1
0.1061 0.4224 1
0.094 0.2945 1
0.2378 0.2987 1
0.5001 0.6671 1
0.4244 0.4276 1
0.1062 0.4273 1
0.288 0.3905 1
0.1973 0.5837 1
0.0175 0.5345 0.5
0.2331 0.3449 1
0.3296 0.4411 1
0.1054 0.3288 1
0.5001 0.6673 1
0.5729 0.8248 1
0.1097 0.2734 1
0.2683 0.3596 1
0.4997 0.7237 1
0.3469 0.8059 1
0.4445 1 1
0.0347 1 0.5
0.4361 1 1
0.4809 1 1
0.1062 0.4273 1
0.2182 0.3188 1
0.324 0.4358 1
0.0204 0.3559 1
0.0699 0.8805 1
0.272 0.5114 0.5
0.3715 0.4208 0.4678
0.324 0.4358 1
0.2166 1 1
0.2643 0.9857 1
0.1246 0.404 1
0.324 0.4358 1
0.1055 0.2615 1
0.1072 0.4132 1
0.0216 1 0.5
0.2381 0.2773 1
0.0216 0.5 0.5
0.107 0.2511 1
0.0204 0.3559 1
0.324 0.4358 1
0.3715 0.4208 0.4678
0.0192 0.2642 1
0.286 0.378 1
0.0216 0.444 0.5
0.0795 0.3231 1
0.2899 0.3658 1
0.2388 0.3518 1
0.0795 0.3231 1
0.0884 0.3457 1
0.1614 0.3123 1
0.2362 0.3 1
0.107 0.2511 1
0.1246 0.404 1
0.2166 1 1
0.3715 0.4208 0.4678
0.2392 0.3483 1
0.2623 1 1
0.3715 0.4208 0.4678
0.0682 0.2752 1
0.0877 0.3512 1
0.2188 0.2821 1
0.4997 0.7237 1
0.0182 0.3084 1
0.0176 0.434 0.5
0.3715 0.4208 0.4678
0.2869 0.5022 1
0.3415 1 1
0.4766 0.7953 1
0.4871 1 1
0.2373 0.2986 1
0.2175 0.5313 1
0.407 1 1
0.0698 0.2721 1
0.4709 1 1
0.1972 0.3857 1
0.0216 0.536 1
0.2571 0.3718 1
0.1236 0.4887 1
0.1057 0.4208 1
0.0663 0.7852 1
0.1999 0.2932 1
0.1764 1 1
0.0663 0.7852 1
0.29 0.3912 1
0.3715 0.4208 0.4678
0.1068 0.4301 1
0.1798 1 1
0.3173 1 0.5
0.0888 1 1

Assayability

Assay information

No assay information for this target.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    PF3D7_0623000 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Plasmodium falciparum ( 1 )

Bibliographic References

4 literature references were collected for this gene.

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Gene identifier PF3D7_0623000 (Plasmodium falciparum), chorismate synthase
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