Detailed view for PF3D7_0104400

Basic information

TDR Targets ID: 3167
Plasmodium falciparum, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.7895 | Length (AA): 535 | MW (Da): 62470 | 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

PF02401   LytB protein

Gene Ontology

Mouse over links to read term descriptions.
GO:0051745   4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity  
GO:0050992   dimethylallyl diphosphate biosynthetic process  
GO:0020011   apicoplast  
GO:0019288   isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway  
GO:0046872   metal ion binding  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
218 535 4n7b (A) 1 318 99.99 0 1 1.84769 -1.62

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
  • 4N7B:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile gametocyte, merozoite, sporozoite, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Female Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs, early ring, Oocyst, Sporozoite. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 40 hs, Ring, Male Gametocyte. Otto TD 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.
  • 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.
  • 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_130373)

Species Accession Gene Product
Arabidopsis thaliana AT4G34350   4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Babesia bovis BBOV_III001660   LytB protein, putative
Chlamydia trachomatis CT_859   4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Escherichia coli b0029   4-hydroxy-3-methylbut-2-enyl diphosphate reductase, 4Fe-4S protein
Mycobacterium leprae ML1938c   PROBABLE LYTB-RELATED PROTEIN LYTB2
Mycobacterium tuberculosis Rv3382c   Probable LYTB-related protein LytB1
Mycobacterium tuberculosis Rv1110   Probable LYTB-related protein LytB2
Mycobacterium ulcerans MUL_0168   4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Neospora caninum NCLIV_045740   lytB domain-containing protein, putative
Oryza sativa 4334003   Os03g0731900
Oryza sativa 4334004   Os03g0732000
Plasmodium berghei PBANKA_0208700   4-hydroxy-3-methylbut-2-enyl diphosphate reductase, putative
Plasmodium falciparum PF3D7_0104400   4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Plasmodium knowlesi PKNH_0209100   4-hydroxy-3-methylbut-2-enyl diphosphate reductase, putative
Plasmodium vivax PVX_081535   4-hydroxy-3-methylbut-2-enyl diphosphate reductase, putative
Plasmodium yoelii PY01243   LytB protein, putative
Schmidtea mediterranea mk4.031738.05  
Toxoplasma gondii TGME49_227420   4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Treponema pallidum TP0547   penicillin tolerance protein (lytB)
Theileria parva TP03_0674   LytB protein, putative
Wolbachia endosymbiont of Brugia malayi Wbm0046   4-hydroxy-3-methylbut-2-enyl diphosphate reductase

Essentiality

PF3D7_0104400 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3442 Mycobacterium tuberculosis non-essential nmpdr
b0029 Escherichia coli essential goodall
TGME49_227420 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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
  • 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
  • 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
  • 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)

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
Aquifex aeolicus (strain VF5) 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 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

2 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.

User comments

2010-03-17 18:59:08 user Fernan Aguero added growth inhibition after knockdown

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Gene identifier PF3D7_0104400 (Plasmodium falciparum), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
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