Detailed view for PF3D7_1344800

Basic information

TDR Targets ID: 133
Plasmodium falciparum, aspartate carbamoyltransferase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.6072 | Length (AA): 375 | MW (Da): 43252 | Paralog Number: 0

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

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

PF00185   Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
PF02729   Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0016743   carboxyl- or carbamoyltransferase activity  
GO:0016597   amino acid binding  
GO:0004070   aspartate carbamoyltransferase activity  
GO:0006520   amino acid metabolic process  
GO:0006207   'de novo' pyrimidine base biosynthetic process  

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
49 371 1vlv (A) 0 312 25.00 0 1 1.2 -1.6
55 372 1ml4 (A) 3 306 40.00 0 1 1.48 -1.84
47 372 4iv5 (A) 3 327 31.00 0 1 1.21843 -0.99
52 374 2be7 (A) 2 307 41.00 0 1 1.42143 -1.19
54 372 1ml4 (A) 2 306 40.00 0 1 1.36877 -1.34
58 373 2be9 (A) 2 299 39.00 0 1 1.33027 -1
58 375 4ekn (B) 2 304 43.00 0 1 1.3651 -1.13

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:

PDB tag
  • 5ILN:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5ILQ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 6FBA:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, sporozoite, Ring, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Female Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, Male Gametocyte. Otto TD Lasonder E
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • 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.

Orthologs

Ortholog group members (OG5_128535)

Species Accession Gene Product
Arabidopsis thaliana AT3G20330   aspartate carbamoyltransferase
Babesia bovis BBOV_I003660   aspartate transcarbamoylase, putative
Escherichia coli b4245   aspartate carbamoyltransferase, catalytic subunit
Leishmania braziliensis LbrM.16.0560   aspartate carbamoyltransferase, putative
Leishmania donovani LdBPK_160550.1   aspartate carbamoyltransferase, putative
Leishmania infantum LinJ.16.0550   aspartate carbamoyltransferase, putative
Leishmania major LmjF.16.0540   aspartate carbamoyltransferase, putative
Leishmania mexicana LmxM.16.0540   aspartate carbamoyltransferase, putative
Mycobacterium leprae ML0532   Probable aspartate carbamoyltransferase PyrB (Aspartate transcarbamylase) (ATCase)
Mycobacterium tuberculosis Rv1380   Probable aspartate carbamoyltransferase PyrB (ATCase) (aspartate transcarbamylase)
Mycobacterium ulcerans MUL_1780   aspartate carbamoyltransferase catalytic subunit
Neospora caninum NCLIV_043140   aspartate carbamoyltransferase, putative
Oryza sativa 4345071   Os08g0248800
Plasmodium berghei PBANKA_1357700   aspartate carbamoyltransferase, putative
Plasmodium falciparum PF3D7_1344800   aspartate carbamoyltransferase
Plasmodium knowlesi PKNH_1256500   aspartate carbamoyltransferase, putative
Plasmodium vivax PVX_083135   aspartate carbamoyltransferase, putative
Plasmodium yoelii PY06210   aspartate carbamoyltransferase
Trypanosoma brucei gambiense Tbg972.5.5310   aspartate carbamoyltransferase, putative
Trypanosoma brucei Tb927.5.3820   aspartate carbamoyltransferase, putative
Trypanosoma congolense TcIL3000_5_4290   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.511643.30   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.508375.30   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.511923.110   aspartate carbamoyltransferase, putative
Trypanosoma cruzi TcCLB.507091.50   aspartate carbamoyltransferase, putative
Toxoplasma gondii TGME49_291640   aspartate carbamoyltransferase
Theileria parva TP01_0476   aspartate carbamoyltransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0385   aspartate carbamoyltransferase

Essentiality

PF3D7_1344800 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu1403 Mycobacterium tuberculosis essential nmpdr
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.5.3820 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.5.3820 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b4245 Escherichia coli non-essential goodall
PBANKA_1357700 Plasmodium berghei Essential plasmo
TGME49_291640 Toxoplasma gondii Essentiality uncertain 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.
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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

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 Aspartate Transcarbamylase (2.1.3.2 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

No reagent availability information for this target.

Bibliographic References

4 literature references were 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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