Detailed view for PF3D7_1405600

Basic information

TDR Targets ID: 2386
Plasmodium falciparum, ribonucleoside-diphosphate reductase small chain, putative

Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 5.1988 | Length (AA): 349 | MW (Da): 40600 | 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

PF00268   Ribonucleotide reductase, small chain

Gene Ontology

Mouse over links to read term descriptions.
GO:0005575   cellular_component  
GO:0009263   deoxyribonucleotide biosynthetic process  
GO:0004748   ribonucleoside-diphosphate reductase activity  
GO:0046914   transition metal ion binding  
GO:0016491   oxidoreductase activity  
GO:0009186   deoxyribonucleoside diphosphate metabolic process  
GO:0006260   DNA replication  
GO:0055114   oxidation reduction  

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
15 312 1jk0 (A) 60 359 57.00 0 1 1.74 -2.23
30 307 1w68 (A) 70 348 62.00 0 1 1.78 -2.66
18 312 2o1z (A) 17 311 94.00 0 1 2.05487 -1.98

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:

  • 2O1Z:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 2P1I:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, early schizont, early trophozoite, late schizont, late trophozoite, Oocyst, Male Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile merozoite, sporozoite, late ring, Sporozoite, Female Gametocyte. PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, early ring, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 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.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB

Orthologs

Ortholog group members (OG5_126823)

Species Accession Gene Product
Arabidopsis thaliana AT3G23580   ribonucleoside-diphosphate reductase small chain A
Arabidopsis thaliana AT3G27060   ribonucleoside-diphosphate reductase small chain C
Babesia bovis BBOV_IV010610   ribonucleoside-diphosphate reductase small subunit, putative
Brugia malayi Bm1_34225   ribonucleotide reductase 2
Candida albicans CaO19.1868   small subunit of ribonucleotide reductase
Candida albicans CaO19.9424   small subunit of ribonucleotide reductase
Candida albicans CaO19.5801   subunit of ribonucleotide reductase
Candida albicans CaO19.13223   subunit of ribonucleotide reductase
Caenorhabditis elegans CELE_F58F9.1   Protein F58F9.1
Caenorhabditis elegans CELE_C03C10.3   Protein RNR-2
Cryptosporidium hominis Chro.60090   ribonucleotide reductase R2 subunit
Cryptosporidium parvum cgd6_690   ribonucleotide reductase small subunit, duplicated adjacent gene
Chlamydia trachomatis CT_828   ribonucleoside-diphosphate reductase subunit beta
Dictyostelium discoideum DDB_G0274021   ribonucleoside-diphosphate reductase
Dictyostelium discoideum DDB_G0272616   ribonucleoside-diphosphate reductase
Drosophila melanogaster Dmel_CG8975   Ribonucleoside diphosphate reductase small subunit
Escherichia coli b2235   ribonucleoside-diphosphate reductase 1, beta subunit, ferritin-like protein
Echinococcus granulosus EgrG_000437000   ribonucleoside diphosphate reductase subunit
Echinococcus multilocularis EmuJ_000437000   ribonucleoside diphosphate reductase subunit
Homo sapiens ENSG00000171848   ribonucleotide reductase M2
Homo sapiens ENSG00000048392   ribonucleotide reductase M2 B (TP53 inducible)
Leishmania braziliensis LbrM.27.2230   ribonucleoside-diphosphate reductase small chain, putative
Leishmania braziliensis LbrM.22.1170   ribonucleoside-diphosphate reductase small chain, putative
Leishmania infantum LinJ.27.1970   ribonucleoside-diphosphate reductase small chain, putative
Leishmania infantum LinJ.22.1110   ribonucleoside-diphosphate reductase small chain, putative
Leishmania major LmjF.22.1290   ribonucleoside-diphosphate reductase small chain, putative
Leishmania major LmjF.27.2050   ribonucleoside-diphosphate reductase small chain, putative
Leishmania mexicana LmxM.22.1290   ribonucleoside-diphosphate reductase small chain, putative
Leishmania mexicana LmxM.27.2050   ribonucleoside-diphosphate reductase small chain, putative
Loa Loa (eye worm) LOAG_04964   ribonucleotide reductase M2 B
Mus musculus ENSMUSG00000022292   ribonucleotide reductase M2 B (TP53 inducible)
Mus musculus ENSMUSG00000020649   ribonucleotide reductase M2
Mycobacterium tuberculosis Rv0233   Ribonucleoside-diphosphate reductase (beta chain) NrdB (ribonucleotide reductase small chain)
Mycobacterium tuberculosis Rv1981c   Ribonucleoside-diphosphate reductase (beta chain) NrdF1 (ribonucleotide reductase small subunit) (R2F protein)
Neospora caninum NCLIV_052980   hypothetical protein
Oryza sativa 4339981   Os06g0127900
Oryza sativa 9266846   Os06g0257450
Plasmodium berghei PBANKA_1036600   ribonucleoside-diphosphate reductase small chain, putative
Plasmodium falciparum PF3D7_1405600   ribonucleoside-diphosphate reductase small chain, putative
Plasmodium knowlesi PKNH_1352500   ribonucleoside-diphosphate reductase small chain, putative
Plasmodium vivax PVX_086155   ribonucleoside-diphosphate reductase small chain, putative
Plasmodium yoelii PY03671   Ribonucleotide reductase, small chain
Saccharomyces cerevisiae YJL026W   ribonucleotide-diphosphate reductase subunit RNR2
Schistosoma japonicum Sjp_0071060   ko:K00526 ribonucleoside-diphosphate reductase beta chain [EC1.17.4.1B], putative
Schistosoma mansoni Smp_055890   ribonucleoside-diphosphate reductase small chain
Schmidtea mediterranea mk4.022157.01   Ribonucleoside-diphosphate reductase subunit M2
Schmidtea mediterranea mk4.014717.02   Ribonucleoside-diphosphate reductase subunit M2
Schmidtea mediterranea mk4.003858.03  
Schmidtea mediterranea mk4.036403.00   Ribonucleoside diphosphate reductase subunit M2-2
Schmidtea mediterranea mk4.001969.00   Ribonucleoside-diphosphate reductase subunit M2
Schmidtea mediterranea mk4.036428.00   Ribonucleoside diphosphate reductase subunit M2-2
Schmidtea mediterranea mk4.023330.00   Ribonucleoside diphosphate reductase subunit M2
Schmidtea mediterranea mk4.034835.01   Ribonucleoside-diphosphate reductase subunit M2
Schmidtea mediterranea mk4.005023.00  
Schmidtea mediterranea mk4.019490.00   Ribonucleoside-diphosphate reductase subunit M2
Trypanosoma brucei gambiense Tbg972.11.14280   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei gambiense Tbg972.11.14290   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei gambiense Tbg972.11.14270   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei Tb927.11.12800   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei Tb927.11.12810   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei Tb927.11.12820   ribonucleoside-diphosphate reductase small chain
Trypanosoma brucei Tb11.v5.0288   ribonucleoside-diphosphate reductase small chain, putative
Trypanosoma congolense TcIL3000_0_15160   ribonucleoside-diphosphate reductase small chain
Trypanosoma congolense TcIL3000_0_35830   ribonucleoside-diphosphate reductase small chain
Trypanosoma cruzi TcCLB.506621.30   ribonucleoside-diphosphate reductase small chain, putative
Trypanosoma cruzi TcCLB.511555.80   ribonucleoside-diphosphate reductase small chain, putative
Toxoplasma gondii TGME49_207060   ribonucleoside-diphosphate reductase small subunit
Treponema pallidum TP0053   ribonucleotide-diphosphate reductase subunit beta
Theileria parva TP01_0725   ribonucleotide-diphosphate reductase small subunit, putative
Wolbachia endosymbiont of Brugia malayi Wbm0267   ribonucleotide-diphosphate reductase subunit beta

Essentiality

PF3D7_1405600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu235 Mycobacterium tuberculosis non-essential nmpdr
Tb11.v4.0004 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.v4.0004 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.v4.0004 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.v4.0004 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2235 Escherichia coli essential goodall
CELE_C03C10.3 Caenorhabditis elegans adult lethal wormbase
CELE_C03C10.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_C03C10.3 Caenorhabditis elegans slow growth wormbase
CELE_C03C10.3 Caenorhabditis elegans sterile wormbase
YJL026W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_1036600 Plasmodium berghei Essential plasmo
TGME49_207060 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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 anti-sense experiment (ECO:0000018) Plasmodium falciparum No drug identifiers listed for this gene.
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 8552672

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): 1


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
Homo sapiens ribonucleotide reductase M2 B (TP53 inducible) Compounds References
Homo sapiens ribonucleotide reductase M2 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
0.0237 0.4526 1
0.0315747 0.311388 0.311388
0.0105 1 1
0.0102 1 1
0.032 1 1
0.0078 0.2869 0.2552

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

User comments

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Gene identifier PF3D7_1405600 (Plasmodium falciparum), ribonucleoside-diphosphate reductase small chain, putative
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