Genome location: Pf3D7_14_v3:2,036,761..2,042,148(-)
Genome classification: Core
Product Description: exosome complex exonuclease RRP6
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: 3.1.13.- (Exoribonucleases producing 5'-phosphomonoesters.)
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0005737 | cytoplasm |
| Component | GO:0000177 | cytoplasmic exosome (RNase complex) |
| Component | GO:0000178 | exosome (RNase complex) |
| Component | GO:0000176 | nuclear exosome (RNase complex) |
| Component | GO:0034399 | nuclear periphery |
| Component | GO:0005730 | nucleolus |
| Function | GO:0000175 | 3'-5'-exoribonuclease activity |
| Function | GO:0004527 | exonuclease activity |
| Function | GO:0004532 | exoribonuclease activity |
| Function | GO:0005515 | protein binding |
| Function | GO:0003727 | single-stranded RNA binding |
| Process | GO:0006401 | RNA catabolic process |
| Process | GO:0000467 | exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
| Process | GO:0016458 | gene silencing |
| Process | GO:0071044 | histone mRNA catabolic process |
| Process | GO:0071039 | nuclear polyadenylation-dependent CUT catabolic process |
| Process | GO:0071040 | nuclear polyadenylation-dependent antisense tra |
| Process | GO:0071035 | |
| Process | GO:0071037 | |
| Process | GO:0071036 | |
| Process | GO:0071038 | |
| Process | GO:0071048 | |
| Process | GO:0071051 |
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 | expressed | 0.94 | 0.58 |
| Trophozoite | expressed | 0.84 | 0.54 |
| Schizont | expressed | 0.23 | 0.87 |
| Gametocyte | expressed | 0.57 | 0.69 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_1449700
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: 0.119 | MFS: -3.009 | #Insertions: 0
PlasmoGEM Phenotype: N/A
RMgmDB ABS Phenotype: N/A
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8IKX8
"Best" AlphaFill ligand hit: AMP (adenosine monophosphate, Local RMSD=0.51) with 2HBL (Global RMSD=3.00)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 3.1.13.- | Ex: poly(A)-specific ribonuclease | SDSKClATPADPUDPGTPGDPUTPAMPCMPGMPNEM... |
No evidence of orthology to BindingDB entries
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 6 | 76 | 51 | 84 |
| disruptive | 28 | 232 | 142 | 300 |
| missense | 26 | 220 | 135 | 280 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 18 | 154 | 65 | 89 |
| disruptive | 69 | 521 | 205 | 404 |
| missense | 54 | 475 | 179 | 300 |
PlasmoDB Total SNPs: 231
Non-coding: 142 | Synonymous: 38 | Nonsynonymous: 51 | Stop Codon: 0
Protein Length: 1136 | Molecular Weight (kDa): 135.628
UniProt ID(s): Q8IKX8
PDB ID(s): None
Isoelectric Point: 6.72
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR002562 | 3'-5' exonuclease domain |
| InterPro | IPR010997 | HRDC-like superfamily |
| InterPro | IPR012337 | Ribonuclease H-like superfamily |
| PFam | N/A | N/A |
| Superfamily | SSF47819 | HRDC-like superfamily |
| Superfamily | SSF53098 | Ribonuclease H-like superfamily |
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 12368864 | Genome sequence of the human malaria parasite Plasmodium falciparum. | Gardner MJ, Hall N, ..., Barrell B | 10.1038/nature01097 |
| 25043062 | Exonuclease-mediated degradation of nascent RNA silences genes linked to severemalaria. | Zhang Q, Siegel TN, ..., Scherf A | 10.1038/nature13468 |
| 29664138 | Characterization of the Catalytic Subunits of the RNA Exosome-like Complex inPlasmodium falciparum. | Jiang N, Yu S, ..., Chen Q | 10.1111/jeu.12625 |
| 30235972 | Disruption of the RNA exosome reveals the hidden face of the malaria parasitetranscriptome. | Droll D, Wei G, ..., Zhang Q | 10.1080/15476286.2018.1517014 |
| 32487761 | Rrp6 Regulates Heterochromatic Gene Silencing via nc RNA R UF6 Decay in Malaria Parasites | Fan Y, Shen S, ..., Zhang Q | 10.1128/mBio.01110-20 |
| 37533322 | The Sequential Recruitments of Rab-GTPase Ypt1p and the NNS Complex onto pre-HAC1mRNA Promote Its Nuclear Degradation in Baker's Yeast | Paira S, Chakraborty A, Das B | 10.1080/10985549.2023.2227016 |
| 34705258 | Non-mitochondrial aconitase regulates the expression of iron-uptake genes bycontrolling the RNA turnover process in fission yeast | Cho SY, Jung SJ, Kim KD, Roe JH | 10.1007/s12275-021-1438-4 |
| 36436601 | LsrR-like protein responds to stress tolerance by regulating polysaccharidebiosynthesis in Lactiplantibacillus plantarum | Meng F, Lyu Y, ..., Lu Z | 10.1016/j.ijbiomac.2022.11.180 |
| 33782132 | Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome | Das M, Zattas D, ..., Lima CD | 10.1073/pnas.2024846118 |
| 34664673 | Nrd1p identifies aberrant and natural exosomal target messages during the nuclearmRNA surveillance in Saccharomyces cerevisiae | Singh P, Chaudhuri A, ..., Das B | 10.1093/nar/gkab930 |
| 34259554 | Interplay of the RNA Exosome Complex and RNA-Binding Protein Ssd1 in MaintainingCell Wall Stability in Yeast | Novacic A, Supljika N, ..., Stuparevic I | 10.1128/Spectrum.00295-21 |
| 33599082 | Regulation of the conserved 3'- 5' exoribonuclease EXOSC10/Rrp6 during celldivision, development and cancer | Stuparevic I, Novacic A, ..., Primig M | 10.1111/brv.12693 |
| 33439673 | Yeast RNA exosome activity is necessary for maintaining cell wall stabilitythrough proper protein glycosylation | Novacic A, Beauvais V, ..., Stuparevic I | 10.1091/mbc.E20-08-0544-T |
| 35650250 | Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observedin the yeast small subunit processome | Zhao Y, Rai J, ..., Li H | 10.1038/s42003-022-03500-y |
| 33971368 | Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled byalternative transcription, 14-3-3 and Spl2 | Crooijmans ME, Delzenne TO, ..., van Heusden GPH | 10.1016/j.bbagrm.2021.194714 |
| 34153074 | The leucine-NH4+ uptake regulator Any1 limits growth as part of a general aminoacid control response to loss of La protein by fission yeast | Cherkasova V, Iben JR, ..., Maraia RJ | 10.1371/journal.pone.0253494 |