Detailed view for PF3D7_0623500

Basic information

TDR Targets ID: 4583
Plasmodium falciparum, superoxide dismutase [Fe]
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.7393 | Length (AA): 266 | MW (Da): 31293 | Paralog Number: 0

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

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

PF00081   Iron/manganese superoxide dismutases, alpha-hairpin domain
PF02777   Iron/manganese superoxide dismutases, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0046872   metal ion binding  
GO:0004784   superoxide dismutase activity  
GO:0055114   oxidation reduction  
GO:0019430   removal of superoxide radicals  
GO:0006979   response to oxidative stress  
GO:0006801   superoxide metabolic process  

Metabolic Pathways

Peroxisome (KEGG)

Structural information

Modbase 3D models:

There are 10 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
66 257 1gv3 (A) 31 237 34.00 0 1 1.25 -1.57
75 254 2awp (A) 5 192 54.00 0 1 1.53 -2.36
67 265 1unf (X) 14 233 38.00 0 1 1.32102 -1.58
71 265 2a03 (A) 1 195 50.00 0 1 1.50498 -1.87
73 265 4yet (A) 3 195 48.00 0 1 1.44106 -2.12
73 265 2ce4 (A) 2 209 35.00 0 1 1.24796 -1.61
64 265 4h3e (A) 27 231 34.00 0 1 1.2772 -1.36
71 265 2a03 (A) 1 195 50.00 0 1 1.50268 -1.88
72 265 2ce4 (A) 1 209 35.00 0 1 1.24892 -1.58
73 263 2w7w (A) 3 193 42.00 0 1 1.42315 -2.03

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

Orthologs

Ortholog group members (OG5_158563)

Species Accession Gene Product
Plasmodium berghei PBANKA_1122400   superoxide dismutase [Fe], putative
Plasmodium falciparum PF3D7_0623500   superoxide dismutase [Fe]
Plasmodium knowlesi PKNH_1126700   superoxide dismutase [Fe], putative
Plasmodium vivax PVX_114290   superoxide dismutase [Fe], putative
Plasmodium yoelii PY04892   superoxide dismutase, C-terminal domain, putative
Theileria parva TP04_0025   Fe-superoxide dismutase, putative

Essentiality

PF3D7_0623500 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1122400 Plasmodium berghei Dispensable plasmo
Show/Hide essentiality data references
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) multi-cellular organism (CARO:0000012) bloodstream stage (PLO:0040) in vivo inhibition (TDR:00016) Plasmodium falciparum 368268   532179   532180   532181   532182   532183   532184   532185   532186  
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 14604655 14962361 2666151

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

Compound Source Reference
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References
Curated by TDRTargets References

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Leishmania major iron superoxide dismutase, putative 208 aa 46.4% 194 aa Compounds References
Leishmania major iron superoxide dismutase, putative 195 aa 46.4% 196 aa Compounds References
Plasmodium falciparum superoxide dismutase [Fe] 198 aa 52.4% 191 aa Compounds References
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.028 0.2716 1
0.0256 0.3131 1
0.0863 0.9101 1
0.0271 0.3078 1

Assayability

Assay information

  • Assay for Superoxide Dismutase (1.15.1.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

78 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_0623500 (Plasmodium falciparum), superoxide dismutase [Fe]
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