Genome location: Pf3D7_13_v3:1,497,877..1,501,494(+)
Genome classification: Core
Product Description: 1-deoxy-D-xylulose 5-phosphate synthase
SignalP Peptide: N/A
# Transmembrane Domains: 1
EC Numbers: 2.2.1.7 (1-deoxy-D-xylulose-5-phosphate synthase)
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0020011 | apicoplast |
| Function | GO:0016744 | transketolase or transaldolase activity |
Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):
| Stage | LR class | MCA mean | MCA prop. zeros |
|---|---|---|---|
| Sporozoite | not expressed | N/A | N/A |
| Ring | not expressed | 0.18 | 0.91 |
| Trophozoite | not expressed | 0.65 | 0.64 |
| Schizont | not expressed | 0.13 | 0.92 |
| Gametocyte | not expressed | 0.25 | 0.86 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_1337200
Resistome Missense Mutations: None
Resistome Compounds with Missense Mutations: None
Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)
Zhang Phenotype: Non - Mutable in CDS
MIS: 0.123 | MFS: -2.89 | #Insertions: 0
PlasmoGEM Phenotype: N/A
RMgmDB ABS Phenotype: N/A
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8IDW0
"Best" AlphaFill ligand hit: HTL (2-acetyl-thiamine diphosphate, Local RMSD=0.19) with 8A45 (Global RMSD=1.22)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 2.2.1.7 | 1-deoxy-D-xylulose-5-phosphate synthase | EDTApyruvateketoclomazoneFluoropyruvatenitrosobenzeneD-glyceraldehyde3-Fluoropyruvatebeta-fluoropyruvatebeta-Glycerophosphatebutylacetylphosphonateisopentenyl diphosphateMethylacetylphosphonate... |
Orthology to BindingDB Entries:
| UniProt | Protein Name | Species | Homology Source | BindingDB Ligands |
|---|---|---|---|---|
| Q38854 | 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic | OrthoDB, OrthoMCL, OrthoMCL BLAST | KETOCLOMAZONE | |
| P9WNS3 | 1-deoxy-D-xylulose-5-phosphate synthase | Mycobacterium tuberculosis | OrthoMCL, OrthoMCL BLAST | CHEMBL3305928 |
| P77488 | 1-deoxy-D-xylulose-5-phosphate synthase | OrthoMCL, OrthoMCL BLAST | CHEMBL3220784CHEMBL3220783CHEMBL3220785 | |
| B7UJP3 | 1-deoxy-D-xylulose-5-phosphate synthase | OrthoMCL BLAST | CHEMBL3306297CHEMBL3305928 | |
| Q4QKG6 | 1-deoxy-D-xylulose-5-phosphate synthase | OrthoMCL BLAST | CHEMBL3359031CHEMBL3359032 |
Protein Length: 1205 | Molecular Weight (kDa): 140.23
PDB ID(s): None
Isoelectric Point: 9.11
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR005475 | Transketolase-like, pyrimidine-binding domain |
| InterPro | IPR005477 | Deoxyxylulose-5-phosphate synthase |
| InterPro | IPR009014 | Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II |
| InterPro | IPR020826 | Transketolase binding site |
| InterPro | IPR029061 | Thiamin diphosphate-binding fold |
| InterPro | IPR033248 | Transketolase, C-terminal domain |
| PFam | PF02779 | Transketolase-like, pyrimidine-binding domain |
| PFam | PF02780 | Transketolase, C-terminal domain |
| PFam | PF13292 | Deoxyxylulose-5-phosphate synthase |
| Superfamily | SSF52518 | Thiamin diphosphate-binding fold |
| Superfamily | SSF52922 | Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II |
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 10 | 52 | 31 | 60 |
| disruptive | 37 | 171 | 85 | 218 |
| missense | 32 | 164 | 79 | 192 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 15 | 106 | 43 | 81 |
| disruptive | 69 | 339 | 146 | 339 |
| missense | 54 | 315 | 130 | 242 |
PlasmoDB Total SNPs: 86
Non-coding: 0 | Synonymous: 42 | Nonsynonymous: 43 | Stop Codon: 1
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 26699947 | Mechanistic binding insights for 1-deoxy-D-Xylulose-5-Phosphate synthase, theenzyme catalyzing the first reaction of isoprenoid biosynthesis in themalaria-causing protists, Plasmodium falciparum and Plasmodium vivax. | Battistini MR, Shoji C, ..., Merkler DJ | 10.1016/j.pep.2015.12.003 |
| 30212465 | Integrative proteomics and bioinformatic prediction enable a high-confidenceapicoplast proteome in malaria parasites. | Boucher MJ, Ghosh S, ..., Yeh E | 10.1371/journal.pbio.2005895 |