Detailed view for PF3D7_1027600

Basic information

TDR Targets ID: 1485
Plasmodium falciparum, topoisomerase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.0731 | Length (AA): 336 | MW (Da): 39605 | Paralog Number: 1

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

PF04406   Type IIB DNA topoisomerase

Gene Ontology

Mouse over links to read term descriptions.
GO:0000737   DNA catabolic process, endonucleolytic  
GO:0005694   chromosome  
GO:0005524   ATP binding  
GO:0003824   catalytic activity  
GO:0003677   DNA binding  
GO:0006259   DNA metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
5 336 2zbk (A) 10 389 24.00 0 1 1.2089 0.27
51 335 1d3y (A) 72 368 22.00 0 1 1.07731 -0.48
122 193 4ja2 (A) 17 86 30.00 0.27 0.26 0.358186 1.33

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 Female Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, Sporozoite, Male Gametocyte. Otto TD Zanghi G Lasonder E
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, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Ring. 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.
  • 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.

Orthologs

Ortholog group members (OG5_127274)

Species Accession Gene Product
Arabidopsis thaliana AT5G02820   DNA topoisomerase 6 subunit A
Arabidopsis thaliana AT3G13170   meiotic recombination protein SPO11-1
Arabidopsis thaliana AT1G63990   meiotic recombination protein SPO11-2
Brugia malayi Bm1_31630   Type IIB DNA topoisomerase family protein
Candida albicans CaO19.11071   weak similarity to SPO11, catalytic subunit of topoisomerase-like transesterase involved in ds break formation step of meiotic r
Candida albicans CaO19.3589   catalytic subunit of meiotic double strand break transesterase
Caenorhabditis elegans CELE_T05E11.4   Protein SPO-11
Cryptosporidium hominis Chro.80160   SPO11 protein
Cryptosporidium parvum cgd8_1350   topoisomerase VIA/SpoII nuclease subunit, toprim domain
Cryptosporidium parvum cgd3_2720   putative topoisomerase VIA
Drosophila melanogaster Dmel_CG7753   meiotic W68
Echinococcus granulosus EgrG_000831500   meiotic recombination protein SPO11
Entamoeba histolytica EHI_194510   DNA topoisomerase, putative
Entamoeba histolytica EHI_125320   topoisomerase, putative
Echinococcus multilocularis EmuJ_000831500   meiotic recombination protein SPO11
Giardia lamblia GL50803_15279   Spo11 Type II DNA topoisomerase VI subunit A
Homo sapiens ENSG00000054796   SPO11 meiotic protein covalently bound to DSB
Leishmania braziliensis LbrM.16.0620   hypothetical protein, conserved
Leishmania donovani LdBPK_160630.1   meiotic recombination protein SPO11, putative
Leishmania infantum LinJ.16.0630   hypothetical protein, conserved
Loa Loa (eye worm) LOAG_10673   type IIB DNA topoisomerase
Mus musculus ENSMUSG00000005883   SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)
Oryza sativa 9267055   Os03g0752200
Oryza sativa 4344697   Os08g0156900
Oryza sativa 4332470   Os03g0284800
Oryza sativa 4352826   Os12g0622500
Plasmodium berghei PBANKA_0511700   topoisomerase, putative
Plasmodium berghei PBANKA_1432700   meiotic recombination protein SPO11, putative
Plasmodium falciparum PF3D7_1217100   meiotic recombination protein SPO11, putative
Plasmodium falciparum PF3D7_1027600   topoisomerase, putative
Plasmodium knowlesi PKNH_1436700   meiotic recombination protein SPO11, putative
Plasmodium knowlesi PKNH_0612000   topoisomerase, putative
Plasmodium vivax PVX_123530   meiotic recombination protein SPO11, putative
Plasmodium vivax PVX_111340   hypothetical protein, conserved
Plasmodium yoelii PY05879   putative topoisomerase VIA
Saccharomyces cerevisiae YHL022C   Spo11p
Schistosoma japonicum Sjp_0052550   ko:K03166 DNA topoisomerase VI subunit A, putative
Schistosoma mansoni Smp_131670   meiotic recombination protein spo11
Trypanosoma brucei gambiense Tbg972.5.5230   meiotic recombination protein spo11, putative
Trypanosoma brucei Tb927.5.3760   meiotic recombination protein SPO11, putative
Trypanosoma congolense TcIL3000_0_05590   meiotic recombination protein SPO11, putative
Trypanosoma cruzi TcCLB.511647.30   meiotic recombination protein SPO11, putative
Trypanosoma cruzi TcCLB.503619.10   meiotic recombination protein SPO11, putative
Toxoplasma gondii TGME49_240575   type iib dna topoisomerase
Theileria parva TP04_0401   hypothetical protein
Trichomonas vaginalis TVAG_258950   meiosis-specific transesterase Spo11-1

Essentiality

PF3D7_1027600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.5.3760 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.3760 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.3760 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.3760 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_T05E11.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_T05E11.4 Caenorhabditis elegans larval arrest wormbase
CELE_T05E11.4 Caenorhabditis elegans sterile wormbase
PBANKA_1432700 Plasmodium berghei Dispensable plasmo
TGME49_240575 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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)

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

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
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

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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User comments

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Gene identifier PF3D7_1027600 (Plasmodium falciparum), topoisomerase, putative
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