Detailed view for PF3D7_1337200

Basic information

TDR Targets ID: 98
Plasmodium falciparum, 1-deoxy-D-xylulose 5-phosphate synthase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 9.1067 | Length (AA): 1205 | MW (Da): 140230 | Paralog Number: 0

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

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

PF02779   Transketolase, pyrimidine binding domain
PF02780   Transketolase, C-terminal domain
PF13292   1-deoxy-D-xylulose-5-phosphate synthase

Gene Ontology

Mouse over links to read term descriptions.
GO:0020011   apicoplast  
GO:0008661   1-deoxy-D-xylulose-5-phosphate synthase activity  
GO:0003824   catalytic activity  
GO:0016114   terpenoid biosynthetic process  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 17 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
314 381 2ctp (A) 7 70 8.00 0.0000012 0.01 0.12 -0.87
410 1204 2g28 (A) 56 860 12.00 0 1 0.38 0.24
816 1201 2bfd (B) 2 341 14.00 0 1 0.24 -0.71
29 806 3vuo (A) 320 1147 22.00 0.33 0.95 0.578443 1.84
36 158 4py6 (A) 1187 1314 14.00 0.71 0.02 0.231175 -0.74
108 293 2ab5 (A) 306 494 30.00 0.0019 0.67 0.231157 0.52
415 1018 2o1x (A) 8 508 35.00 0.00000000024 1 0.521045 0.76
417 1201 2o1s (A) 8 620 35.00 0 1 0.452252 1.45
417 1200 2o1s (A) 8 619 39.00 0 1 0.591422 0.61
864 1201 2ozl (B) 44 328 16.00 0.00033 0.98 0.187598 0.64
1056 1201 1w85 (B) 188 323 16.00 0.015 0.78 0.293262 -0.51
3 257 4u0r (A) 171 496 13.00 0.18 0.03 0.255018 -0.16
108 293 2ab5 (A) 306 494 30.00 0.0012 0.88 0.248557 0.56
417 1201 2o1s (A) 8 620 34.00 0.000000000039 1 0.449052 1.42
417 1200 2o1s (A) 8 619 39.00 0 1 0.586822 0.66
417 1035 2o1x (A) 10 525 33.00 0.000000058 1 0.502293 1.01
418 990 2o1x (A) 11 482 39.00 0 1 0.596719 0.21

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
Mid 40-60% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, Ring. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst. Otto TD Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Sporozoite, Female Gametocyte, Male Gametocyte. Zanghi G Lasonder E
Show/Hide expression data references
  • 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_129068)

Species Accession Gene Product
Arabidopsis thaliana AT5G11380   1-deoxy-D-xylulose 5-phosphate synthase 3
Arabidopsis thaliana AT4G15560   1-deoxy-D-xylulose-5-phosphate synthase
Arabidopsis thaliana AT3G21500   1-deoxy-D-xylulose 5-phosphate synthase 1
Babesia bovis BBOV_III002600   1-deoxy-D-xylulose-5-phosphate synthase family protein
Chlamydia trachomatis CT_331   1-deoxy-D-xylulose-5-phosphate synthase
Escherichia coli b0420   1-deoxyxylulose-5-phosphate synthase, thiamine triphosphate-binding, FAD-requiring
Mycobacterium leprae ML1038   PROBABLE 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE DXS1 (1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE) (DXP SYNTHASE) (DXPS)
Mycobacterium tuberculosis Rv2682c   Probable 1-deoxy-D-xylulose 5-phosphate synthase Dxs1 (1-deoxyxylulose-5-phosphate synthase) (DXP synthase) (DXPS)
Mycobacterium ulcerans MUL_3319   1-deoxy-D-xylulose-5-phosphate synthase
Neospora caninum NCLIV_003330   hypothetical protein
Oryza sativa 4338768   Os05g0408900
Oryza sativa 4342614   Os07g0190000
Oryza sativa 4340090   Os06g0142900
Plasmodium berghei PBANKA_1351000   1-deoxy-D-xylulose 5-phosphate synthase, putative
Plasmodium falciparum PF3D7_1337200   1-deoxy-D-xylulose 5-phosphate synthase
Plasmodium knowlesi PKNH_1264100   1-deoxy-D-xylulose 5-phosphate synthase, putative
Plasmodium vivax PVX_082790   1-deoxy-D-xylulose 5-phosphate synthase, putative
Plasmodium yoelii PY04970   unnamed protein product-related
Schmidtea mediterranea mk4.046580.01  
Toxoplasma gondii TGME49_208820   1-deoxy-D-xylulose-5-phosphate synthase
Treponema pallidum TP0824   1-deoxy-D-xylulose-5-phosphate synthase
Theileria parva TP01_0516   1-deoxy-D-xylulose 5-phosphate synthase, putative

Essentiality

PF3D7_1337200 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2728 Mycobacterium tuberculosis essential nmpdr
b0420 Escherichia coli essential goodall
TGME49_208820 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • 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.
  • 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.
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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

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
Mycobacterium tuberculosis Probable 1-deoxy-D-xylulose 5-phosphate synthase Dxs1 (1-deoxyxylulose-5-phosphate synthase) (DXP synthase) (DXPS) Compounds References
Haemophilus influenzae (strain 86-028NP) 1-deoxy-D-xylulose-5-phosphate synthase Compounds References
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 /LMG 4051 / NBRC 15346 / NCIMB 92 1-deoxy-D-xylulose-5-phosphate synthase Compounds References
Arabidopsis thaliana 1-deoxy-D-xylulose-5-phosphate synthase Compounds References
Escherichia coli 1-deoxyxylulose-5-phosphate synthase, thiamine triphosphate-binding, FAD-requiring 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
0.0292 0.3014 0
0.0055 0.5529 0.5529
0.0226 0.305 1
0.0052 0.553 0.553
0.057 0.7376 1
0.0946 0.928 1
0.0586 0.5094 0.6561
0.0226 1 1
0.0226 1 0.5
0.0594 0.5714 1
0.0366 0.3895 0
0.0413 1 1
0.0184 0.4027 1
0.1018 0.6991 1
0.0201 0.3326 1
0.0372 0.3596 1
0.0226 0.298 1
0.0603 0.5438 0.8593
0.031 0.4555 0.8232
0.1028 0.6379 1
0.1012 0.6571 1
0.0799 0.527 1
0.0747 1 1
0.039 0.3784 1
0.0078 0.3014 0
0.0194 0.3136 1
0.0366 0.6626 0.6516
0.0054 0.2543 0.5529
0.0226 1 1
0.0035 0.4707 0.6302
0.0042 0.6302 0.6302
0.077 1 1
0.045 1 1
0.0775 0.5761 1
0.0382 0.3721 1
0.1036 0.6559 0.9411
0.027 0.4515 0.8232
0.0054 0.3152 0
0.0383 0.3894 0.6432
0.0208 1 1
0.0453 1 1
0.041 1 1
0.0056 0.5952 0.5952
0.0035 0.6302 0.6302
0.0759 0.6012 0.7316
0.0954 1 1
0.0226 0.298 1
0.0453 0.312 1
0.0206 0.4405 1
0.0452 0.8993 1
0.0587 0.5464 1
0.1034 0.6861 1
0.0562 0.2839 0.3519
0.0463 1 1
0.0035 0.6302 0.6302
0.0035 0.3052 0.6302
0.0483 1 1
0.0465 1 1
0.0183 0.6349 1
0.0226 1 1
0.02 1 1
0.0053 0.5509 0.5531
0.0053 0.2736 0.5531
0.0238 0.4801 1
0.0383 0.5108 1
0.0991 0.8283 1
0.0443 1 1
0.0766 0.9711 1
0.0052 0.553 0.553
0.0763 0.5788 0.6868
0.0206 0.4405 1
0.0226 1 1
0.019 0.3807 1
0.0181 0.3565 0.577
0.0035 0.6302 0.6302
0.0797 0.5651 0.9776
0.0183 1 1
0.0758 1 1
0.0573 0.341 0.9049
0.0413 1 1
0.0238 0.4801 1
0.0796 0.5685 1
0.0036 0.6302 0.6302
0.0226 0.5224 1
0.0035 0.6302 0.6302
0.0233 0.7606 1
0.0626 0.3747 0.826
0.0035 0.6302 0.6302
0.0788 0.8947 1
0.0376 0.3394 1
0.0053 0.5529 0.5529
0.0206 0.4405 1
0.027 0.4515 0.8232
0.0463 1 1
0.0388 0.3915 0

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.

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier PF3D7_1337200 (Plasmodium falciparum), 1-deoxy-D-xylulose 5-phosphate synthase
Title for this comment
Comment