Detailed view for PF3D7_1347100

Basic information

TDR Targets ID: 2230
Plasmodium falciparum, DNA topoisomerase 3, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.2613 | Length (AA): 710 | MW (Da): 84306 | Paralog Number: 0

Signal peptide: N | 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

PF01131   DNA topoisomerase
PF01751   Toprim domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0003918   DNA topoisomerase (ATP-hydrolyzing) activity  
GO:0005694   chromosome  
GO:0003676   nucleic acid binding  
GO:0003917   DNA topoisomerase type I activity  
GO:0003916   DNA topoisomerase activity  
GO:0003677   DNA binding  
GO:0006268   DNA unwinding during replication  
GO:0006265   DNA topological change  
GO:0006259   DNA metabolic process  

Metabolic Pathways

Homologous recombination (KEGG)

Structural information

Modbase 3D models:

There are 3 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
5 692 1mw9 (X) 3 584 23.00 0 1 0.84 0.7
5 710 4rul (A) 3 595 22.00 0 1 0.911466 1.26
5 703 4cgy (A) 35 637 41.00 0 1 1.29971 0.28

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 gametocyte, Female Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile early schizont, early trophozoite, late trophozoite, Male Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, late schizont, Oocyst. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, Ring, Sporozoite. Otto TD Zanghi G
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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
  • 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_126736)

Species Accession Gene Product
Arabidopsis thaliana AT5G63920   topoisomerase 3alpha
Arabidopsis thaliana AT4G31210   DNA topoisomerase, type IA, core
Babesia bovis BBOV_III001510   DNA topoisomerase family protein
Brugia malayi Bm1_56415   DNA topoisomerase III
Candida albicans CaO19.5934   likely DNA topoisomerase III similar to S. cerevisiae TOP3 (YLR234W) involved in recombination repair events
Candida albicans CaO19.13355   likely DNA topoisomerase III similar to S. cerevisiae TOP3 (YLR234W) involved in recombination repair events
Caenorhabditis elegans CELE_Y56A3A.27   Protein TOP-3
Cryptosporidium hominis Chro.50267   DNA topoisomerase III
Cryptosporidium parvum cgd5_1180   DNA topoisomerase III, putative
Chlamydia trachomatis CT_643   DNA topoisomerase I
Dictyostelium discoideum DDB_G0275257   DNA topoisomerase III
Drosophila melanogaster Dmel_CG10123   Topoisomerase 3alpha
Escherichia coli b1274   DNA topoisomerase I, omega subunit
Escherichia coli b1763   DNA topoisomerase III
Echinococcus granulosus EgrG_000163600   DNA topoisomerase 3 alpha
Entamoeba histolytica EHI_038920   DNA topoisomerase III, putative
Echinococcus multilocularis EmuJ_000163600   rho GTPase activating protein 20
Giardia lamblia GL50803_7615   DNA topoisomerase III
Homo sapiens ENSG00000177302   topoisomerase (DNA) III alpha
Leishmania braziliensis LbrM.35.3420   DNA topoisomerase III, putative
Leishmania braziliensis LbrM.21.0170   DNA topoisomerase 1A
Leishmania donovani LdBPK_363350.1   DNA topoisomerase III, putative
Leishmania donovani LdBPK_210180.1   DNA topoisomerase 1A
Leishmania infantum LinJ.21.0180   DNA topoisomerase 1A
Leishmania infantum LinJ.36.3350   DNA topoisomerase III, putative
Leishmania major LmjF.21.0125   DNA topoisomerase 1A
Leishmania major LmjF.36.3200   DNA topoisomerase III, putative
Leishmania mexicana LmxM.21.0125   DNA topoisomerase 1A
Leishmania mexicana LmxM.36.3200   DNA topoisomerase III, putative
Loa Loa (eye worm) LOAG_03396   DNA topoisomerase III
Mycobacterium leprae ML0200   Probable DNA topoisomerase I TopA (omega-protein) (relaxing enzyme) (untwisting enzyme) (swivelase) (type I DNA topoisomerase) (
Mus musculus ENSMUSG00000002814   topoisomerase (DNA) III alpha
Mycobacterium tuberculosis Rv3646c   DNA topoisomerase I TopA (omega-protein) (relaxing enzyme) (untwisting enzyme) (swivelase) (type I DNA topoisomerase) (nicking-c
Mycobacterium ulcerans MUL_4222   DNA topoisomerase I
Neospora caninum NCLIV_046480   DNA topoisomerase III alpha, putative
Oryza sativa 9271035   Os06g0281400
Oryza sativa 9269718   Os03g0165000
Plasmodium berghei PBANKA_1360000   DNA topoisomerase 3, putative
Plasmodium falciparum PF3D7_1347100   DNA topoisomerase 3, putative
Plasmodium knowlesi PKNH_1253800   DNA topoisomerase 3, putative
Plasmodium vivax PVX_083255   DNA topoisomerase 3, putative
Plasmodium yoelii PY01134   DNA topoisomerase iii
Saccharomyces cerevisiae YLR234W   DNA topoisomerase 3
Schistosoma japonicum Sjp_0109870   DNA topoisomerase 3-alpha, putative
Schistosoma japonicum Sjp_0113590   DNA topoisomerase 3-alpha, putative
Schistosoma japonicum Sjp_0049450   ko:K03165 DNA topoisomerase III, putative
Schistosoma mansoni Smp_158140   prokaryotic DNA topoisomerase
Schmidtea mediterranea mk4.000689.04  
Schmidtea mediterranea mk4.008541.03   DNA topoisomerase 3-alpha
Schmidtea mediterranea mk4.017870.00   Putative prokaryotic DNA topoisomerase
Schmidtea mediterranea mk4.000689.00   DNA topoisomerase 3
Schmidtea mediterranea mk4.000306.07   Putative prokaryotic DNA topoisomerase
Schmidtea mediterranea mk4.000689.01   Putative prokaryotic DNA topoisomerase
Schmidtea mediterranea mk4.059086.00  
Schmidtea mediterranea mk4.008541.01   Putative prokaryotic DNA topoisomerase
Schmidtea mediterranea mk4.000306.05   DNA topoisomerase 3-alpha
Trypanosoma brucei gambiense Tbg972.11.10690   DNA topoisomerase III, putative
Trypanosoma brucei gambiense Tbg972.10.2290   DNA topoisomerase IA, putative
Trypanosoma brucei Tb927.10.1900   DNA topoisomerase IA, putative
Trypanosoma brucei Tb927.11.9520   DNA topoisomerase III, putative
Trypanosoma congolense TcIL3000.11.9990   DNA topoisomerase III, putative
Trypanosoma congolense TcIL3000_10_1610   DNA topoisomerase IA, putative
Trypanosoma cruzi TcCLB.510121.160   DNA topoisomerase IA, putative
Trypanosoma cruzi TcCLB.508851.170   DNA topoisomerase III, putative
Trypanosoma cruzi TcCLB.511589.120   DNA topoisomerase III, putative
Trypanosoma cruzi TcCLB.506493.80   DNA topoisomerase IA, putative
Toxoplasma gondii TGME49_226480   DNA topoisomerase family protein
Treponema pallidum TP0394   DNA topoisomerase I (topA)
Theileria parva TP03_0692   DNA topoisomerase III, putative
Trichomonas vaginalis TVAG_306650   prokaryotic DNA topoisomerase, putative
Trichomonas vaginalis TVAG_033330   prokaryotic DNA topoisomerase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0037   topoisomerase IA, TopA

Essentiality

PF3D7_1347100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.1280 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb11.01.1280 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb11.01.1280 Trypanosoma brucei significant gain of fitness in procyclic forms alsford
Tb11.01.1280 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
Tb927.10.1900 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.1900 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.1900 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.1900 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b1274 Escherichia coli essential goodall
b1763 Escherichia coli non-essential goodall
PBANKA_1360000 Plasmodium berghei Slow plasmo
TGME49_226480 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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

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): 0.3

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
Yersinia pestis DNA topoisomerase Compounds References
Trypanosoma cruzi DNA topoisomerase IA, putative Compounds References
Bos taurus DNA topoisomerase Compounds References
Trypanosoma brucei DNA topoisomerase IA, putative Compounds References
Trypanosoma cruzi DNA topoisomerase IA, 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
0.0651 0.3626 0.361
0.0402 0.281 0.3126
0.0395 0.4322 0.8368
0.0351 0.4035 1
0.0082 0.3617 1
0.0044 0.4319 1
0.0354 0.393 1
0.0042 0.4949 1
0.0402 0.281 0.3126
0.0431 0.4727 1
0.0192 0.4236 1
0.0354 0.393 1
0.0393 0.4427 1
0.0245 0.5258 1
0.0048 0.4319 1
0.0314 0.4837 1
0.035 0.5396 1
0.0351 0.4035 1
0.0656 0.5612 1
0.0624 0.5596 1
0.007 0.4372 1
0.0351 0.4035 1
0.0539 0.4822 1
0.0431 0.4727 1
0.0103 0.2872 0.5
0.0395 0.4322 0.8368
0.0634 0.3573 1
0.0402 0.281 0.3126
0.0044 0.4319 1
0.0402 0.281 0.3126
0.0283 0.5579 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

29 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_1347100 (Plasmodium falciparum), DNA topoisomerase 3, putative
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