Genome location: Pf3D7_08_v3:1,167,240..1,171,585(-)
Genome classification: Core
Product Description: ATP-dependent RNA helicase DBP10, putative
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: 3.6.4.13 (RNA helicase)
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0005730 | nucleolus |
| Function | GO:0005524 | ATP binding |
| Function | GO:0003723 | RNA binding |
| Process | GO:1902626 | assembly of large subunit precursor of preribosome |
Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):
| Stage | LR class | MCA mean | MCA prop. zeros |
|---|---|---|---|
| Sporozoite | expressed | N/A | N/A |
| Ring | expressed | 0.96 | 0.57 |
| Trophozoite | expressed | 0.91 | 0.52 |
| Schizont | expressed | 0.22 | 0.87 |
| Gametocyte | expressed | 0.61 | 0.66 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_0827000
Resistome Missense Mutations: E566D
Resistome Compounds with Missense Mutations: BI-2536
Resistome # Samples with Disruptive Mutations: 1 (1 missense, 0 "interesting" missense)
Zhang Phenotype: Non - Mutable in CDS
MIS: 0.158 | MFS: -2.814 | #Insertions: 0
PlasmoGEM Phenotype: Slow (Pb ortholog: PBANKA_0703700)
RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_0703700)
Modification: Disrupted | RMgm-2180
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8IBA2
"Best" AlphaFill ligand hit: 08T ([[[(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium, Local RMSD=0.66) with 7LIU (Global RMSD=4.24)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 3.6.4.13 | RNA helicase | ATPADPUDPAMPGTPGDPUTPKClNEMCDPITPTDP... |
No evidence of orthology to BindingDB entries
Ortholog Group (OrthoMCL): OG6_101760
Most Similar Human Ortholog: F8VRX4
TM-align score: 0.92 | RMSD: 1.29
Seq Identity: 0.37 | Length: 199 / 1289
All Human Orthologs (OrthoMCL):
| Gene ID | Description |
|---|---|
| ENSG00000123064 | DEAD-box helicase 54 |
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 12 | 89 | 59 | 95 |
| disruptive | 76 | 264 | 136 | 327 |
| missense | 39 | 211 | 115 | 270 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 25 | 178 | 65 | 114 |
| disruptive | 138 | 513 | 215 | 397 |
| missense | 71 | 411 | 171 | 285 |
PlasmoDB Total SNPs: 183
Non-coding: 11 | Synonymous: 91 | Nonsynonymous: 81 | Stop Codon: 0
Protein Length: 1289 | Molecular Weight (kDa): 151.105
UniProt ID(s): Q8IBA2
PDB ID(s): None
Isoelectric Point: 9.89
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR000629 | ATP-dependent RNA helicase DEAD-box, conserved site |
| InterPro | IPR001650 | Helicase, C-terminal |
| InterPro | IPR011545 | DEAD/DEAH box helicase domain |
| InterPro | IPR014001 | Helicase superfamily 1/2, ATP-binding domain |
| InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| PFam | PF00270 | DEAD/DEAH box helicase domain |
| PFam | PF00271 | Helicase, C-terminal |
| Superfamily | SSF52540 | P-loop containing nucleoside triphosphate hydrolase |
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 37961218 | The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis | Cruz VE, Weirich CS, Peddada N, Erzberger JP | 10.1101/2023.11.01.565222 |
| 10871363 | Dbp10p, a putative RNA helicase from Saccharomyces cerevisiae, is required for ribosome biogenesis | Burger F, Daugeron MC, Linder P | 10.1093/nar/28.12.2315 |
| 26823502 | The K(+)-dependent GTPase Nug1 is implicated in the association of the helicase Dbp10 to the immature peptidyl transferase centre during ribosome maturation | Manikas RG, Thomson E, Thoms M, Hurt E | 10.1093/nar/gkw045 |
| 37129998 | Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis | Lau B, Huang Z, ..., Cheng J | 10.15252/embr.202356910 |
| 22735702 | Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae | Talkish J, Zhang J, ..., Woolford JL Jr | 10.1093/nar/gks609 |
| 38113283 | The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis | Mitterer V, Hamze H, ..., Hurt E | 10.1093/nar/gkad1206 |
| 17409062 | Suppression of the Schizosaccharomyces pombe cut12.1 cell-cycle defect bymutations in cdc25 and genes involved in transcriptional and translational control | Tallada VA, Bridge AJ, Emery PA, Hagan IM | 10.1534/genetics.107.072090 |
| 35139378 | A comprehensive landscape of 60S ribosome biogenesis factors | Sailer C, Jansen J, ..., Stengel F | 10.1016/j.celrep.2022.110353 |
| 16449635 | Comprehensive mutational analysis of yeast DEXD/H box RNA helicases involved inlarge ribosomal subunit biogenesis | Bernstein KA, Granneman S, ..., Baserga SJ | 10.1128/MCB.26.4.1195-1208.2006 |