Genome location: Pf3D7_09_v3:1,342,715..1,346,826(+)
Genome classification: Core
Product Description: TFIIH basal transcription factor complex helicase XPD subunit
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: 3.6.4.12 (DNA helicase)
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0005737 | cytoplasm |
| Component | GO:0005634 | nucleus |
| Function | GO:0043139 | 5'-3' DNA helicase activity |
| Function | GO:0003678 | DNA helicase activity |
| Function | GO:0003684 | damaged DNA binding |
| Function | GO:0005515 | protein binding |
| Function | GO:0017116 | single-stranded DNA helicase activity |
| Process | GO:0000717 | nucleotide-excision repair, DNA duplex unwinding |
| Process | GO:0033683 | nucleotide-excision repair, DNA incision |
| Process | GO:0045951 | positive regulation of mitotic recombination |
| Process | GO:0000019 | regulation of mitotic recombination |
| Process | GO:0009411 | response to UV |
| Process | GO:0006979 | response to oxidative stress |
| Process | GO:0006366 | transcription by RNA polymerase II |
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 | 0.30 | 0.85 |
| Trophozoite | expressed | 0.64 | 0.63 |
| Schizont | expressed | 0.19 | 0.88 |
| Gametocyte | expressed | 0.33 | 0.80 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_0934100
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: 0.136 | MFS: -2.803 | #Insertions: 0
PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_0834900)
RMgmDB ABS Phenotype: N/A
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8I2H7
"Best" AlphaFill ligand hit: FC6 (ferri(iii)hexacyanide, Local RMSD=2.19) with 3CRW (Global RMSD=4.50)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 3.6.4.12 | DNA helicase | No BRENDA inhibitors |
Orthology to BindingDB Entries:
| UniProt | Protein Name | Species | Homology Source | BindingDB Ligands |
|---|---|---|---|---|
| Q9BX63 | Fanconi anemia group J protein | OrthoDB | Telomestatin (TMS)Telomestatin (TMS)Telomestatin (TMS)TMPyP4... |
Ortholog Group (OrthoMCL): OG6_101742
Most Similar Human Ortholog: A8MX75
TM-align score: 0.96 | RMSD: 2.04
Seq Identity: 0.41 | Length: 699 / 1056
All Human Orthologs (OrthoMCL):
| Gene ID | Description |
|---|---|
| ENSG00000104884 | ERCC excision repair 2, TFIIH core complex helicase subunit |
Protein Length: 1056 | Molecular Weight (kDa): 122.839
UniProt ID(s): I6XGB8, I6XPP1, Q8I2H7, Q8WSK4, R4S3T7
PDB ID(s): None
Isoelectric Point: 6.23
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR001945 | RAD3/XPD family |
| InterPro | IPR006554 | Helicase-like, DEXD box c2 type |
| InterPro | IPR006555 | ATP-dependent helicase, C-terminal |
| InterPro | IPR006935 | Helicase/UvrB, N-terminal |
| InterPro | IPR010614 | DEAD2 |
| InterPro | IPR010643 | Helical and beta-bridge domain |
| InterPro | IPR013020 | ATP-dependent helicase Rad3/Chl1-like |
| InterPro | IPR027417 | P-loop containing nucleoside triphosphate hydrolase |
| PFam | PF04851 | Helicase/UvrB, N-terminal |
| PFam | PF06733 | DEAD2 |
| PFam | PF06777 | Helical and beta-bridge domain |
| PFam | PF13307 | ATP-dependent helicase, C-terminal |
| Superfamily | SSF52540 | P-loop containing nucleoside triphosphate hydrolase |
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 9 | 43 | 29 | 63 |
| disruptive | 61 | 99 | 59 | 113 |
| missense | 29 | 52 | 38 | 91 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 17 | 96 | 38 | 67 |
| disruptive | 94 | 185 | 76 | 180 |
| missense | 40 | 114 | 62 | 131 |
PlasmoDB Total SNPs: 156
Non-coding: 45 | Synonymous: 73 | Nonsynonymous: 38 | Stop Codon: 0
| 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 |
| 25708921 | Plasmodium falciparum XPD translocates in 5' to 3' direction, is expressedthroughout the blood stages, and interacts with p44. | Tajedin L, Tarique M, Tuteja R | 10.1007/s00709-015-0779-4 |