Genome location: Pf3D7_05_v3:1,026,705..1,030,943(+)
Genome classification: Core
Product Description: S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase, putative
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: 4.1.3.44 (tRNA 4-demethylwyosine synthase (AdoMet-dependent))
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Process | GO:0031591 | wybutosine biosynthetic process |
Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):
| Stage | LR class | MCA mean | MCA prop. zeros |
|---|---|---|---|
| Sporozoite | possibly expressed | N/A | N/A |
| Ring | expressed | 0.34 | 0.83 |
| Trophozoite | expressed | 0.34 | 0.81 |
| Schizont | expressed | 0.07 | 0.96 |
| Gametocyte | expressed | 0.37 | 0.79 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_0524900
Resistome Missense Mutations: None
Resistome Compounds with Missense Mutations: None
Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)
Zhang Phenotype: Mutable in CDS
MIS: 0.989 | MFS: -2.918 | #Insertions: 1
PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1239700)
RMgmDB ABS Phenotype: N/A
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8I3L6
"Best" AlphaFill ligand hit: FMN (flavin mononucleotide, Local RMSD=1.52) with 2BPO (Global RMSD=4.33)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 4.1.3.44 | tRNA 4-demethylwyosine synthase (AdoMet-dependent) | No BRENDA inhibitors |
No evidence of orthology to BindingDB entries
Ortholog Group (OrthoMCL): OG6_101841
Most Similar Human Ortholog: A0A087WWV6
TM-align score: 0.65 | RMSD: 3.62
Seq Identity: 0.46 | Length: 339 / 988
All Human Orthologs (OrthoMCL):
| Gene ID | Description |
|---|---|
| ENSG00000198874 | tRNA-yW synthesizing protein 1 homolog |
| ENSG00000277149 | tRNA-yW synthesizing protein 1 homolog B |
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 10 | 50 | 24 | 51 |
| disruptive | 13 | 108 | 61 | 160 |
| missense | 9 | 103 | 51 | 137 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 17 | 93 | 40 | 68 |
| disruptive | 43 | 237 | 129 | 274 |
| missense | 25 | 191 | 108 | 160 |
PlasmoDB Total SNPs: 255
Non-coding: 154 | Synonymous: 67 | Nonsynonymous: 34 | Stop Codon: 0
Protein Length: 988 | Molecular Weight (kDa): 116.754
UniProt ID(s): Q8I3L6
PDB ID(s): None
Isoelectric Point: 7.67
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR007197 | Radical SAM |
| InterPro | IPR008254 | Flavodoxin/nitric oxide synthase |
| InterPro | IPR013917 | tRNA wybutosine-synthesis |
| InterPro | IPR029039 | Flavoprotein-like superfamily |
| InterPro | IPR034556 | S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase |
| PFam | PF00258 | Flavodoxin/nitric oxide synthase |
| PFam | PF04055 | Radical SAM |
| PFam | PF08608 | tRNA wybutosine-synthesis |
| Superfamily | SSF102114 | Flavoprotein-like superfamily |
| Superfamily | SSF52218 |
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 12368867 | Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. | Hall N, Pain A, ..., Barrell BG | 10.1038/nature01095 |
| 35693892 | Biochemical and structural characterization of the flavodoxin-like domain of theSchizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1in complex with FMN | Sjekloca L, Ferre-D'Amare AR | 10.17912/micropub.biology.000570 |
| 21917924 | Yap5 protein-regulated transcription of the TYW1 gene protects yeast from highiron toxicity | Li L, Jia X, Ward DM, Kaplan J | 10.1074/jbc.M111.286666 |