Detailed view for PF3D7_1474300

Basic information

TDR Targets ID: 3041
Plasmodium falciparum, DNA repair metallo-beta-lactamase protein, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.9152 | Length (AA): 860 | MW (Da): 102350 | 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

PF07522   DNA repair metallo-beta-lactamase

Gene Ontology

Mouse over links to read term descriptions.
GO:0008150   biological_process  
GO:0005575   cellular_component  
GO:0003674   molecular_function  

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
2 200 1ycg (A) 35 224 17.00 0 1 0.22 -0.12
7 132 1ztc (A) 27 163 21.00 0.00000027 1 0.49 -1.33
6 54 1ztc (A) 26 75 22.00 0.25 0.22 0.223377 0.44
21 169 4b87 (A) 702 853 38.00 0 1 0.610056 -0.2
279 474 4uos (A) 1 183 20.00 0.096 0.28 0.424707 -0.82
437 792 4b87 (A) 696 1034 21.00 0 1 0.511353 0.61

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
Mid 40-60% percentile intra-erythrocytic - 24 hs, Female Gametocyte, Male Gametocyte. Otto TD 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 - 32 hs, intra-erythrocytic - 40 hs, Oocyst, Ring, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 48 hs. Otto TD
Show/Hide expression data references
  • 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.
  • 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_129094)

Species Accession Gene Product
Arabidopsis thaliana AT2G45700   sterile alpha motif (SAM) domain-containing protein
Arabidopsis thaliana AT3G26680   DNA cross-link repair protein SNM1
Candida albicans CaO19.2926   similar to S. cerevisiae interstrand crosslink repair protein PSO2 (YMR137C)
Candida albicans CaO19.10443   similar to S. cerevisiae interstrand crosslink repair protein PSO2 (YMR137C)
Dictyostelium discoideum DDB_G0277755   DNA repair metallo-beta-lactamase domain-containing protein
Drosophila melanogaster Dmel_CG10018   CG10018 gene product from transcript CG10018-RA
Echinococcus granulosus EgrG_001017300   DNA cross link repair 1A protein
Entamoeba histolytica EHI_200790   hypothetical protein, conserved
Echinococcus multilocularis EmuJ_001017300   DNA cross link repair 1A protein
Homo sapiens ENSG00000198924   DNA cross-link repair 1A
Mus musculus ENSMUSG00000025077   DNA cross-link repair 1A, PSO2 homolog (S. cerevisiae)
Neospora caninum NCLIV_041920   hypothetical protein
Oryza sativa 4335730   Os04g0401800
Oryza sativa 4347162   Os09g0439000
Plasmodium berghei PBANKA_1301900   DNA repair metallo-beta-lactamase protein, putative
Plasmodium falciparum PF3D7_1474300   DNA repair metallo-beta-lactamase protein, putative
Plasmodium knowlesi PKNH_1244600   DNA repair metallo-beta-lactamase protein, putative
Plasmodium vivax PVX_118595   DNA repair metallo-beta-lactamase protein, putative
Plasmodium yoelii PY02631   hypothetical protein
Saccharomyces cerevisiae YMR137C   Pso2p
Schistosoma japonicum Sjp_0205290   DNA cross-link repair 1A protein, putative
Schistosoma mansoni Smp_136360   DNA cross-link repair protein pso2/snm1
Toxoplasma gondii TGME49_289670   DNA repair metallo-beta-lactamase
Trichomonas vaginalis TVAG_536090   DNA cross-link repair protein pso2/snm1, putative
Trichomonas vaginalis TVAG_137960   DNA cross-link repair protein pso2/snm1, putative

Essentiality

PF3D7_1474300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
PBANKA_1301900 Plasmodium berghei Dispensable plasmo
TGME49_289670 Toxoplasma gondii Probably non-essential 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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
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.

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_1474300 (Plasmodium falciparum), DNA repair metallo-beta-lactamase protein, putative
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