Detailed view for PF3D7_0623900

Basic information

TDR Targets ID: 4587
Plasmodium falciparum, ribonuclease H2 subunit A, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.9559 | Length (AA): 288 | MW (Da): 33095 | 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

PF01351   Ribonuclease HII

Gene Ontology

Mouse over links to read term descriptions.
GO:0004523   ribonuclease H activity  
GO:0003723   RNA binding  
GO:0003676   nucleic acid binding  
GO:0016070   RNA metabolic process  
GO:0006401   RNA catabolic process  

Metabolic Pathways

DNA replication (KEGG)

Structural information

Modbase 3D models:

There are 7 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
17 239 1eke (A) 2 224 34.00 0 1 1.18 -0.98
18 242 1io2 (A) 3 213 36.00 0 1 1.17 -1.05
18 244 1io2 (A) 3 211 39.00 0 1 1.14 0.01
2 246 3kio (A) 13 258 47.00 0 1 1.41009 -0.58
6 288 3p56 (D) 20 299 45.00 0 1 1.04504 1.11
6 288 3puf (A) 20 299 49.00 0 1 1.40104 -0.15
19 235 1eke (A) 4 220 36.00 0 1 1.13177 -0.69

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 Male Gametocyte. Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, Oocyst, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Ring, Sporozoite. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 8 hs. Otto TD
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_126908)

Species Accession Gene Product
Arabidopsis thaliana AT2G25100   ribonuclease H2 subunit A
Babesia bovis BBOV_I000890   ribonuclease H, putative
Brugia malayi Bm1_42230   ribonuclease HI large subunit
Candida albicans CaO19.13915   likely Ribonuclease HII similar to S. pombe SPAC4G9.02 and to S. cerevisiae RNH35 (YNL072W)
Candida albicans CaO19.6562   likely Ribonuclease HII similar to S. pombe SPAC4G9.02 and to S. cerevisiae RNH35 (YNL072W)
Candida albicans CaO19_6562   hypothetical protein
Caenorhabditis elegans CELE_T13H5.7   Protein RNH-2
Cryptosporidium hominis Chro.40245   similar to ribonuclease HI large subunit (RNase HI large subunit)
Cryptosporidium parvum cgd4_2160   conserved hypothetical protein
Chlamydia trachomatis CT_029   ribonuclease HII
Dictyostelium discoideum DDB_G0277705   hypothetical protein
Dictyostelium discoideum DDB_G0292584   RNase H2 subunit A
Drosophila melanogaster Dmel_CG13690   CG13690 gene product from transcript CG13690-RA
Escherichia coli b0183   ribonuclease HII, degrades RNA of DNA-RNA hybrids
Echinococcus granulosus EgrG_000899800   ribonuclease hi large subunit
Entamoeba histolytica EHI_134360   ribonuclease H2 subunit A, putative
Entamoeba histolytica EHI_084700   RNase HI large subunit, putative
Echinococcus multilocularis EmuJ_000899800   ribonuclease hi large subunit
Giardia lamblia GL50803_6483   Ribonuclease HI, large sub
Homo sapiens ENSG00000104889   ribonuclease H2, subunit A
Leishmania braziliensis LbrM.13.0050   ribonuclease HII, putative
Leishmania braziliensis LbrM.35.0760   ribonuclease H, putative
Leishmania donovani LdBPK_130050.1   ribonuclease HII, putative
Leishmania donovani LdBPK_360700.1   ribonuclease H, putative
Leishmania infantum LinJ.36.0700   ribonuclease H, putative
Leishmania infantum LinJ.13.0050   ribonuclease HII, putative
Leishmania major LmjF.13.0050   ribonuclease HII, putative
Leishmania major LmjF.36.0640   ribonuclease H, putative
Leishmania mexicana LmxM.13.0050   ribonuclease HII, putative
Leishmania mexicana LmxM.36.0640   ribonuclease H, putative
Loa Loa (eye worm) LOAG_01088   ribonuclease HI large subunit
Mycobacterium leprae ML1611c   PROBABLE RIBONUCLEASE HII PROTEIN RNHB (RNASE HII)
Mus musculus ENSMUSG00000052926   ribonuclease H2, large subunit
Mycobacterium tuberculosis Rv2902c   Probable ribonuclease HII protein RnhB (RNase HII)
Mycobacterium ulcerans MUL_2054   ribonuclease HII
Neospora caninum NCLIV_023470   Ribonuclease (EC 3.1.26.-), related
Oryza sativa 4349811   Os11g0153900
Plasmodium berghei PBANKA_1122800   ribonuclease H2 subunit A, putative
Plasmodium falciparum PF3D7_0623900   ribonuclease H2 subunit A, putative
Plasmodium knowlesi PKNH_1126300   ribonuclease H2 subunit A, putative
Plasmodium vivax PVX_114310   ribonuclease H2 subunit A, putative
Plasmodium yoelii PY06561   ribonuclease HII, putative
Saccharomyces cerevisiae YNL072W   Rnh201p
Schistosoma japonicum Sjp_0000830   ko:K10743 ribonuclease H2 subunit A, putative
Schistosoma mansoni Smp_041890.2   ribonuclease hi large subunit
Schistosoma mansoni Smp_041890.1   ribonuclease hi large subunit
Schmidtea mediterranea mk4.036732.02  
Trypanosoma brucei gambiense Tbg972.10.6130   ribonuclease H, putative
Trypanosoma brucei Tb927.10.5070   ribonuclease H, putative
Trypanosoma brucei Tb11.v5.0340   ribonuclease HII, putative
Trypanosoma congolense TcIL3000_10_4240   ribonuclease H, putative
Trypanosoma cruzi TcCLB.510293.70   ribonuclease H, putative
Trypanosoma cruzi TcCLB.508661.50   ribonuclease H, putative
Toxoplasma gondii TGME49_281510   ribonuclease H1 large subunit, putative
Theileria parva TP01_0041   ribonuclease H1 large subunit, putative
Trichomonas vaginalis TVAG_262310   ribonuclease hi large subunit, putative
Wolbachia endosymbiont of Brugia malayi Wbm0642   ribonuclease HII

Essentiality

PF3D7_0623900 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2949 Mycobacterium tuberculosis non-essential nmpdr
Tb927.10.5070 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.5070 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.5070 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.5070 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0183 Escherichia coli non-essential goodall
PBANKA_1122800 Plasmodium berghei Slow plasmo
TGME49_281510 Toxoplasma gondii Essentiality uncertain sidik
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

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

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.

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Gene identifier PF3D7_0623900 (Plasmodium falciparum), ribonuclease H2 subunit A, putative
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