About Gene List

PF3D7_1307000 (RRP40)

Genome location: Pf3D7_13_v3:324,598..326,786(-)

Genome classification: Core

Function and Localization

Product Description: exosome complex component RRP40, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: None

Curated GO (PlasmoDB):

Type GO Term Name
Component GO:0000177 cytoplasmic exosome (RNase complex)
Component GO:0000178 exosome (RNase complex)
Component GO:0000176 nuclear exosome (RNase complex)
Function GO:0003723 RNA binding
Process GO:0071034 CUT catabolic process
Process GO:0034475 U4 snRNA 3'-end processing
Process GO:0043928 exonucleolytic catabolism of deadenylated mRNA
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:0071035 nuclear polyadenylation-dependent rRNA catabolic process
Process GO:0071038 nuclear polyadenyl
Process GO:0071049
Process GO:0034427
Process GO:0071051
Process GO:0006364

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 0.28 0.86
Trophozoite expressed 0.42 0.75
Schizont expressed 0.12 0.93
Gametocyte expressed 0.34 0.81

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1307000

Resistome Missense Mutations: None

Resistome Compounds with Missense Mutations: None

Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)

Essentiality (ABS)

Zhang Phenotype: Mutable in CDS

MIS: 0.957 | MFS: -2.896 | #Insertions: 1

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1405500)

  • Relative Growth Rate: 0.10 ± 0.13
  • Confidence: 1.00

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IEP5

"Best" AlphaFill ligand hit: ANP (phosphoaminophosphonic acid-adenylate ester, Local RMSD=1.08) with 1KQM (Global RMSD=11.77)

No associated EC numbers

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_102463

Most Similar Human Ortholog: Q9NQT5

TM-align score: 0.81 | RMSD: 2.59

Seq Identity: 0.24 | Length: 222 / 245

All Human Orthologs (OrthoMCL):

Gene ID Description
ENSG00000107371 exosome component 3

Genetic Variation

MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:

Homozygous genotype calls only

variant type common rare doubleton singleton
synonymous 2 9 8 22
disruptive 1 18 20 38
missense 1 18 20 37

Any inclusion in genotype call

variant type common rare doubleton singleton
synonymous 4 22 18 14
disruptive 4 46 42 58
missense 4 40 36 50

PlasmoDB Total SNPs: 63

Non-coding: 48 | Synonymous: 12 | Nonsynonymous: 2 | Stop Codon: 1

Protein Information

Protein Length: 245 | Molecular Weight (kDa): 28.292

UniProt ID(s): Q8IEP5

PDB ID(s): None

Isoelectric Point: 6.93

Protein Domain Annotations:

Source Family ID Description
InterPro IPR004088 K Homology domain, type 1
InterPro IPR012340 Nucleic acid-binding, OB-fold
InterPro IPR026699 Exosome complex RNA-binding protein 1/RRP40/RRP4
InterPro IPR036612 K Homology domain, type 1 superfamily
PFam PF15985 K Homology domain, type 1
Superfamily SSF50249 Nucleic acid-binding, OB-fold
Superfamily SSF54791 K Homology domain, type 1 superfamily

Associated Publications

PMID Title Authors DOI/Link
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
37904946 Comparative analyses of disease-linked missense mutations in the RNA exosomemodeled in budding yeast reveal distinct functional consequences in translation Sterrett MC, Cureton LA, ..., Ghalei H 10.18.562946
17159918 Structural and biochemical characterization of the yeast exosome component Rrp40 Oddone A, Lorentzen E, ..., Sattler M 10.1038/sj.embor.7400856
15116429 Screening for novel essential genes of Saccharomyces cerevisiae involved inprotein secretion Davydenko SG, Juselius JK, ..., Keranen S 10.1002/yea.1063
17391830 Analysis of the Saccharomyces cerevisiae exosome architecture and of the RNAbinding activity of Rrp40p Luz JS, Tavares JR, ..., Oliveira CC 10.1016/j.biochi.2007.01.011
27777260 Insight into the RNA Exosome Complex Through Modeling Pontocerebellar HypoplasiaType 1b Disease Mutations in Yeast Fasken MB, Losh JS, ..., van Hoof A 10.1534/genetics.116.195917