Detailed view for PBANKA_0608000

Basic information

TDR Targets ID: 826659
Plasmodium berghei, porphobilinogen deaminase
Source Database / ID: 

pI: 10.4289 | Length (AA): 438 | MW (Da): 50129 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG

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

PF01379   Porphobilinogen deaminase, dipyromethane cofactor binding domain
PF03900   Porphobilinogen deaminase, C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0004418   hydroxymethylbilane synthase activity  
GO:0033014   tetrapyrrole biosynthetic process  

Metabolic Pathways

Porphyrin and chlorophyll metabolism (KEGG)

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
71 436 3ecr (A) 22 352 28.00 0 1 0.826416 0.54
73 419 4htg (A) 13 311 35.00 0 1 1.04004 0.17
184 354 5izt (A) 226 400 14.00 0 0.09 0.442011 -0.18

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 Ookinete. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Gametocyte, 22 hs Schizont, Male gametocyte. Otto TD Yeoh LM
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile 4 hs Ring, 16 hs Trophozoite, Erthyrocytic stages, Female gametocyte. Otto TD Yeoh LM
Show/Hide expression data references
  • Otto TD A comprehensive evaluation of rodent malaria parasite genomes and gene expression.
  • Yeoh LM Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates.

Orthologs

Ortholog group members (OG5_127395)

Species Accession Gene Product
Arabidopsis thaliana AT5G08280   Porphobilinogen deaminase
Candida albicans CaO19.9309   Phorphobilinogen deaminase similar to S. cerevisiae HEM3 (YDL205C) involved in heme biosynthesis
Candida albicans CaO19.1742   Phorphobilinogen deaminase similar to S. cerevisiae HEM3 (YDL205C) involved in heme biosynthesis
Chlamydia trachomatis CT_299   porphobilinogen deaminase
Dictyostelium discoideum DDB_G0284697   hydroxymethylbilane synthase
Drosophila melanogaster Dmel_CG9165   lethal (3) 02640
Escherichia coli b3805   hydroxymethylbilane synthase
Echinococcus multilocularis EmuJ_000490600   porphobilinogen deaminase
Homo sapiens ENSG00000256269   hydroxymethylbilane synthase
Mycobacterium leprae ML2421c   PROBABLE PORPHOBILINOGEN DEAMINASE HEMC (PBG) (HYDROXYMETHYLBILANE SYNTHASE) (HMBS) (PRE-UROPORPHYRINOGEN SYNTHASE)
Mus musculus ENSMUSG00000032126   hydroxymethylbilane synthase
Mycobacterium tuberculosis Rv0510   Probable porphobilinogen deaminase HemC (PBG) (hydroxymethylbilane synthase) (HMBS) (pre-uroporphyrinogen synthase)
Mycobacterium ulcerans MUL_4599   porphobilinogen deaminase
Neospora caninum NCLIV_035490   porphobilinogen deaminase, putative
Oryza sativa 4328432   Os02g0168800
Plasmodium berghei PBANKA_0608000   porphobilinogen deaminase
Plasmodium falciparum PF3D7_1209600   porphobilinogen deaminase
Plasmodium knowlesi PKNH_1309500   porphobilinogen deaminase, putative
Plasmodium vivax PVX_084510   porphobilinogen deaminase, putative
Plasmodium yoelii PY01828   porphobilinogen deaminase, putative
Saccharomyces cerevisiae YDL205C   hydroxymethylbilane synthase
Schistosoma japonicum Sjp_0302440   ko:K01749 hydroxymethylbilane synthase [EC2.5.1.61], putative
Schistosoma mansoni Smp_095130   porphobilinogen deaminase
Schmidtea mediterranea mk4.021284.00   Porphobilinogen deaminase
Schmidtea mediterranea mk4.006075.09  
Schmidtea mediterranea mk4.021132.00   Porphobilinogen deaminase
Schmidtea mediterranea mk4.001955.01   Porphobilinogen deaminase
Schmidtea mediterranea mk4.006075.10   Porphobilinogen deaminase
Toxoplasma gondii TGME49_271420   porphobilinogen deaminase
Wolbachia endosymbiont of Brugia malayi Wbm0777   porphobilinogen deaminase

Essentiality

PBANKA_0608000 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
b3805 Escherichia coli essential goodall
YDL205C Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0608000 this record Plasmodium berghei Dispensable plasmo
TGME49_271420 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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

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 hydroxymethylbilane synthase Compounds References
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 PBANKA_0608000 (Plasmodium berghei), porphobilinogen deaminase
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