Detailed view for PF3D7_1467300

Basic information

TDR Targets ID: 2971
Plasmodium falciparum, 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.7908 | Length (AA): 488 | MW (Da): 55757 | Paralog Number: 0

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

Druggability Group : DG4

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

PF02670   1-deoxy-D-xylulose 5-phosphate reductoisomerase
PF08436   1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal
PF13288   DXP reductoisomerase C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0070402   GO:NADPH binding  

GO:0020011   apicoplast  
GO:0019288   isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway  
GO:0046872   metal ion binding  
GO:0030604   1-deoxy-D-xylulose-5-phosphate reductoisomerase activity  
GO:0005515   protein binding  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0055114   oxidation reduction  
GO:0008299   isoprenoid biosynthetic process  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 2 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
78 487 1q0q (A) 2 398 36.00 0 1 1.44 -1.83
77 486 4y67 (A) 77 486 99.99 0 1 2.13576 -2.02

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
  • 3AU8:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3AU9:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3AUA:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3WQQ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3WQR:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3WQS:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4GAE:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4KP7:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4Y67:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4Y6P:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4Y6R:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 4Y6S:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JAZ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JBI:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JC1:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JMP:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JMW:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JNL:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 5JO0:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 32 hs. Otto TD
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, early schizont, early trophozoite, late schizont, late trophozoite. Otto TD PlasmoDB
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 8 hs, gametocyte, Oocyst, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite, Male 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_130462)

Species Accession Gene Product
Arabidopsis thaliana AT5G62790   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Babesia bovis BBOV_III010740   1-deoxy-D-xylulose 5-phosphate reductoisomerase family protein
Chlamydia trachomatis CT_071   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Escherichia coli b0173   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Mycobacterium leprae ML1583c   PROBABLE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE DXR (DXP REDUCTOISOMERASE) (1-DEOXYXYLULOSE-5-PHOSPHATE REDUCTOISOMERAS
Mycobacterium tuberculosis Rv2870c   Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomeras
Mycobacterium ulcerans MUL_2085   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Neospora caninum NCLIV_051900   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Oryza sativa 4326153   Os01g0106900
Plasmodium berghei PBANKA_1330600   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium falciparum PF3D7_1467300   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Plasmodium knowlesi PKNH_1214000   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium vivax PVX_117100   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Plasmodium yoelii PY05578   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Toxoplasma gondii TGME49_214850   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Treponema pallidum TP0601   1-deoxy-D-xylulose 5-phosphate reductoisomerase
Theileria parva TP02_0073   1-deoxy-D-xylulose 5-phosphate reductoisomerase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0179   1-deoxy-D-xylulose 5-phosphate reductoisomerase

Essentiality

PF3D7_1467300 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b0173 Escherichia coli essential goodall
PBANKA_1330600 Plasmodium berghei Essential plasmo
TGME49_214850 Toxoplasma gondii Probably essential 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) multi-cellular organism (CARO:0000012) bloodstream stage (PLO:0040) in vivo inhibition (TDR:00016) Plasmodium falciparum 326368   576648  
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 10477522 11277531 12183243 12937969 16711755

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): 0.6

Known modulators for this target

Compound Source Reference
Curated by TDRTargets References
Curated by TDRTargets References

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Mycobacterium tuberculosis Probable 1-deoxy-D-xylulose 5-phosphate reductoisomerase Dxr (DXP reductoisomerase) (1-deoxyxylulose-5-phosphate reductoisomeras Compounds References
Synechocystis sp. (strain PCC 6803 / Kazusa) 1-deoxyxylulose-5-phosphate reductoisomerase Compounds References
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
Escherichia coli 1-deoxy-D-xylulose 5-phosphate reductoisomerase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0519737 1 0.5
0.0366 0.3554 1
0.052 1 1
0.0983 1 0.5
0.1299 1 0.5
0.0833 0.5 0.5
0.104 0.3216 1
0.224 1 0.5
0.1719 1 1
0.1739 1 1
0.0845 0.5 0.5
0.0888 1 0.5
0.1118 1 1
0.05 0.2984 1
0.1768 0.6008 1
0.3528 0.5 0.5
0.395036 1 1
0.4514 1 1
0.6563 0.5 0.5
0.0923 0.5 0.5
1.9715 0.9097 1
0.05 0.3578 1
0.2804 0.3922 1
0.052 0.2747 1
0.5095 0.5 0.5
0.266 1 1
0.0519737 1 1
0.7907 1 1
0.083 0.5 0.5
0.2655 0.5 0.5
0.4379 1 0.5
0.0449 0.6488 1
0.3788 1 1
0.102 1 1
0.1424 0.9627 1
0.102 1 1
0.1011 0.7261 1
0.2743 1 1
0.0428 1 1
0.2641 0.2763 1
0.0519737 0.5 0.5
0.5352 1 0.5
0.4514 1 1
0.101974 0.5 0.5
0.052 0.6122 1
0.0662 1 1
2.1901 1 1
0.052 0.3955 1
0.101974 1 0.5
0.5352 0.8174 1
0.1782 1 0.5
0.089 0.9067 0.5
0.0431 0.6187 1
0.052 0.5513 1
0.5352 0.8174 1
0.0821 0.5 0.5
0.2159 0.5 0.5
2.3657 1 1
0.1467 0.788 0.5
0.1462 1 1
0.0416 1 1
0.052 0.2578 1
0.1007 0.5 0.5
0.05 1 0.5
0.1861 0.6465 1
0.0446 0.6447 1
0.0902 1 0.5
0.0456 0.6515 1
0.0971 1 1
0.05 1 0.5
0.0971 1 1
0.052 1 0.5
0.1746 0.7634 1
0.052 1 0.5
0.101974 0.5 0.5
0.052 1 1
0.086 1 1
0.102 0.5 0.5
0.0971 1 1
0.0249 0.972 0.5
0.1265 1 0.5
0.0698 0.5801 1
0.1373 1 0.5
0.0519737 0.5 0.5
0.3165 1 0.5
0.0443 0.5404 1
0.1467 0.3483 1
0.052 1 1
0.0906 1 0.5
0.4093 1 1
0.2496 1 1
0.052 0.5037 1
0.052 0.6082 1
0.1292 0.5 0.5
0.052 0.6401 1
0.2795 0.5 0.5
0.042 0.2719 1
0.1738 1 0.5
0.0487 0.3203 1
0.052 0.5037 1
0.0606 0.3545 1
0.0168 0.4528 1
0.4566 0.5874 1
0.225 1 1
0.05 1 1
0.045 0.3051 1
0.0971 1 1
0.052 0.4287 1
0.3099 1 0.5
0.0426543 0.5 0.5
0.3723 1 1
0.0519821 1 0.5
0.101974 0.5 0.5
0.0425 0.573 0.5
0.052 0.4287 1
0.0519737 1 0.5
0.4514 1 1
0.0496 1 1
0.2276 1 1
0.052 0.3004 1
0.4514 1 1
0.052 0.3794 1
0.0519737 1 0.5
0.3534 0.5 0.5
0.1539 1 1
0.052 1 1
0.101974 0.5 0.5
0.4517 1 0.5
0.1394 1 1
0.0476 1 1
0.1778 0.5 0.5
0.2286 1 1
0.089 0.9069 0.5
0.052 0.6122 1
0.1351 0.5 0.5
0.052 0.3815 0.5
0.052 1 1
0.5352 0.8174 1
0.1394 1 1
0.052 0.6082 1
0.1265 1 0.5
0.102 0.5 0.5
0.1796 0.5 0.5
1.0988 0.517 0.9832
0.052 1 1
0.2304 1 1
0.3866 1 0.5
1.0606 0.6346 1
0.0364 1 1
0.7907 1 1
0.052 0.2966 1
0.052 0.5513 1
0.0519737 1 1
0.2743 1 1
0.1008 1 1
0.5352 0.8174 1
0.3723 1 1
0.101974 0.5 0.5
0.5258 1 1
0.1177 0.2895 1
0.0983 1 0.5
0.052 0.4726 1
0.0923 0.5 0.5
0.101974 1 1
0.0427 0.6236 1
0.1739 1 1
0.1762 0.5 0.5
0.052 0.6077 1
1.1192 1 1
0.052 0.312 1
0.0446 0.4753 1
0.4514 1 1
0.0469 0.3191 1
0.0444 1 0.5
2.0201 1 1
0.179 0.8522 1
0.8376 0.8305 1
0.052 0.3076 1
0.1287 0.9357 1
0.2641 0.2763 1
0.052 0.3955 1
0.4058 1 1
0.0267 1 1
0.0837 1 0.5
0.044 0.5339 1
0.052 1 1
0.052 1 1
0.052 0.5843 1
0.05 0.3076 1
0.089 0.9067 0.5
0.1807 0.5 0.5
0.05 0.3803 0.5495
0.0375 1 0.5
0.052 0.3076 1
0.05 1 1
0.6464 1 1
0.0971 1 1
0.3092 1 0.5
0.0938918 1 0.5
2.5678 1 1
0.0416 0.4235 1
0.1385 1 1
0.3165 1 0.5
0.1118 1 1
0.1682 1 0.5
0.3099 1 0.5
0.3579 1 1
0.0907 1 1
0.1818 1 0.5
0.5352 0.8174 1
0.0836 0.3741 1
1.4565 1 1
0.1242 0.8096 1
0.0452 0.652 1
0.1242 0.8096 1
0.0416 0.4235 1
0.4514 1 1
0.0896 1 0.5
0.0519737 1 1
0.05 1 0.5
2.5678 1 1
0.0519737 0.5 0.5
0.044 0.2958 1
0.3125 0.5 0.5
0.1394 1 1
1.8917 1 1
0.2641 0.2763 1
0.052 1 1
0.089 0.9067 0.5
1.0505 1 1
0.0437 0.5571 1
1.5763 0.8325 1
0.4035 1 1
0.0445 0.2608 1
0.1351 0.4753 0.5
0.0953 0.5 0.5
0.1907 1 1
0.0449 0.2706 1
1.5123 1 1
0.0971 1 1
0.2679 1 0.5
0.1541 1 1
0.0418 0.518 1
0.0331 0.3487 0.3376
0.5268 0.5 0.5
0.8128 0.8305 1
0.101974 1 0.5
0.2743 1 1
0.05 1 1
0.134 1 0.5
0.052 0.4747 1
0.7882 1 1
0.2743 1 1
0.172 0.5 0.5
0.2521 1 0.5
0.052 0.5843 1
0.4514 1 1
0.0899 0.3021 0.4972
0.5225 1 0.5
0.052 0.6082 1
0.6842 1 0.5
0.052 1 1
2.5678 1 1
0.052 0.312 1
0.0452 0.3063 1
2.5678 1 1
0.7481 1 1
0.0899 0.3021 0.4972
0.086 0.5 0.5
0.3515 0.5 0.5
0.0885 0.5698 0.5
0.052 0.6077 1
0.1676 0.5 0.5
0.052 0.2966 1
0.102 0.5 0.5
0.0449 0.6488 1
0.052 0.3004 1
0.1746 0.7634 1
0.2215 1 1
0.4517 1 0.5
0.1467 1 1
0.5352 1 0.5
0.0857 0.2887 1
1.0606 0.6346 1
0.0846 0.616 1
0.0886 1 0.5
0.0488 0.2967 1
0.3019 1 1
0.4385 1 1
0.1279 1 1
0.6418 0.5 0.5
0.0449 0.6488 1
0.2496 1 1
0.052 0.6453 1
0.101974 0.5 0.5
0.3579 1 1
0.2563 1 0.5
2.3657 1 1
0.225729 0.5 0.5
0.2803 1 1
0.052 0.2747 1
0.0431 0.3109 1
1.5763 0.8325 1
0.05 1 0.5
0.2199 1 0.5
0.0421 1 0.5
0.143 1 0.5
0.102 0.5 0.5
1.5123 1 1
0.6464 1 1
0.0519737 1 1
0.135 1 1
0.052 0.3076 1
0.0433 0.4316 1
0.5352 0.8174 1
0.4514 1 1
1.5763 0.8325 1
0.0873 1 0.5
0.2988 1 1
2.1901 1 1
0.052 0.6453 1
0.1279 1 1
0.2423 1 0.5
0.052 1 0.5
0.052 0.6401 1
0.0448 0.4496 1
0.052 0.3794 1
0.052 0.2578 1
0.312 0.3795 1
2.3657 1 1
1.7089 1 1

Assayability

Assay information

  • Assay for Glyoxylate Reductase (1.1.1.26 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.

Reagent availability

  • Reagent:
  • Target Type Source Notes
    PF3D7_1467300 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Plasmodium falciparum ( 1 )

Bibliographic References

5 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

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Gene identifier PF3D7_1467300 (Plasmodium falciparum), 1-deoxy-D-xylulose 5-phosphate reductoisomerase
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