Detailed view for PF3D7_1406600

Basic information

TDR Targets ID: 2396
Plasmodium falciparum, ATP-dependent Clp protease regulatory subunit ClpC, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.7915 | Length (AA): 1341 | MW (Da): 156022 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 1

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

PF00004   ATPase family associated with various cellular activities (AAA)
PF07724   AAA domain (Cdc48 subfamily)
PF10431   C-terminal, D2-small domain, of ClpB protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0017111   nucleoside-triphosphatase activity  
GO:0005524   ATP binding  
GO:0005515   protein binding  
GO:0000166   nucleotide binding  
GO:0019538   protein metabolic process  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

Structural information

Modbase 3D models:

There are 15 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
337 475 1khy (A) 5 140 11.00 0.0000036 0.1 0.2 -0.89
506 695 1jbk (A) 161 351 47.00 0 1 0.84 -1.68
918 1185 1ny5 (A) 117 379 18.00 0 0.86 0.44 -0.37
942 1190 2bjv (A) 10 254 13.00 0 0.2 0.27 -0.47
495 1321 1qvr (A) 142 839 33.00 0 1 0.656604 0.86
507 1325 1r6b (X) 170 739 39.00 0 1 0.391638 1.85
517 686 2p65 (A) 16 187 47.00 0.0000000042 1 0.797671 -1.45
517 814 3pxg (A) 174 472 33.00 0 1 0.390122 0.98
913 1102 4l4u (A) 119 301 28.00 0.35 1 0.430285 -0.08
1135 1323 4uos (A) 1 183 17.00 0.15 0.65 0.43984 -1.58
59 179 3fh2 (A) 0 112 18.00 0.0000011 0.93 0.388837 -1.15
61 453 3s5m (A) 513 970 28.00 0.0044 0.22 0.226582 1.31
61 203 3fes (A) 1 135 16.00 0.000075 0.47 0.369316 -1.35
334 1326 3pxi (A) 5 806 22.00 0 1 0.28562 2.15
514 683 2p65 (A) 16 187 47.00 0.0000000025 1 0.800341 -1.45

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 sporozoite, early schizont, early trophozoite, late ring, late schizont, late trophozoite. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile gametocyte, merozoite, early ring. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Ring, Sporozoite, Female Gametocyte. Zanghi G Lasonder E
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • 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.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_133657)

Species Accession Gene Product
Babesia bovis BBOV_V000160   clpC
Escherichia coli b0882   ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease, chaperone activity
Plasmodium berghei PBANKA_1035600   ATP-dependent Clp protease regulatory subunit ClpC, putative
Plasmodium falciparum PF3D7_1406600   ATP-dependent Clp protease regulatory subunit ClpC, putative
Plasmodium knowlesi PKNH_1351500   ATP-dependent Clp protease regulatory subunit ClpC, putative
Plasmodium vivax PVX_086100   ATP-dependent Clp protease, putative
Plasmodium yoelii PY06430   ATP-dependent Clp protease, ATPase subunit-related
Schmidtea mediterranea mk4.035706.01  
Treponema pallidum TP0801   ATP-dependent Clp protease subunit A (clpA)
Theileria parva TP05_0023   ClpC molecular chaperone, putative

Essentiality

PF3D7_1406600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0882 Escherichia coli non-essential goodall
PBANKA_1035600 Plasmodium berghei Essential plasmo
Show/Hide essentiality data references
  • 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.
  • 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
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

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
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

  • Assay for Enterokinase (3.4.21.9 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

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.

User comments

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Gene identifier PF3D7_1406600 (Plasmodium falciparum), ATP-dependent Clp protease regulatory subunit ClpC, putative
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