About Gene List

PF3D7_1105700 (RTCB)

Genome location: Pf3D7_11_v3:246,768..249,431(+)

Genome classification: Core

Function and Localization

Product Description: tRNA-splicing ligase RtcB, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 6.5.1.8 (3'-phosphate/5'-hydroxy nucleic acid ligase)

Curated GO (PlasmoDB):

Type GO Term Name
Component GO:0005634 nucleus
Component GO:0072669 tRNA-splicing ligase complex
Function GO:0003972 RNA ligase (ATP) activity
Process GO:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate
Process GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation

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 0.28 0.86
Trophozoite expressed 0.23 0.85
Schizont expressed 0.06 0.96
Gametocyte expressed 0.22 0.87

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1105700

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: Non - Mutable in CDS

MIS: 0.164 | MFS: -2.833 | #Insertions: 0

PlasmoGEM Phenotype: N/A

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IIU6

"Best" AlphaFill ligand hit: 5GP (guanosine-5'-monophosphate, Local RMSD=0.53) with 7P3B (Global RMSD=0.81)

BRENDA EC Inhibitors:

EC # Name EC Inhibitors
6.5.1.8 3'-phosphate/5'-hydroxy nucleic acid ligase No BRENDA inhibitors

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_101445

Most Similar Human Ortholog: Q9Y3I0

TM-align score: 0.99 | RMSD: 1.07

Seq Identity: 0.64 | Length: 504 / 506

All Human Orthologs (OrthoMCL):

Gene ID Description
ENSG00000100220 RNA 2,3-cyclic phosphate and 5-OH ligase

Genetic Variation

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

Homozygous genotype calls only

variant type common rare doubleton singleton
synonymous 3 31 13 37
disruptive 6 35 16 50
missense 6 35 16 47

Any inclusion in genotype call

variant type common rare doubleton singleton
synonymous 10 63 23 30
disruptive 12 66 41 126
missense 10 63 37 69

PlasmoDB Total SNPs: 134

Non-coding: 104 | Synonymous: 20 | Nonsynonymous: 10 | Stop Codon: 0

Protein Information

Protein Length: 506 | Molecular Weight (kDa): 56.321

UniProt ID(s): A0A143ZZZ9, Q8IIU6

PDB ID(s): None

Isoelectric Point: 8.29

Protein Domain Annotations:

Source Family ID Description
InterPro IPR001233 RNA-splicing ligase, RtcB
InterPro IPR027513 RNA-splicing ligase RtcB homologue, eukaryotic
InterPro IPR036025 tRNA-splicing ligase RtcB-like superfamily
PFam PF01139 RNA-splicing ligase, RtcB
Superfamily SSF103365 tRNA-splicing ligase RtcB-like superfamily

Associated Publications

PMID Title Authors DOI/Link
12368864 Genome sequence of the human malaria parasite Plasmodium falciparum. Gardner MJ, Hall N, ..., Barrell B 10.1038/nature01097
23181666 Organellar proteomics reveals hundreds of novel nuclear proteins in the malariaparasite Plasmodium falciparum. Oehring SC, Woodcroft BJ, ..., Voss TS 10.1186/gb-2012-13-11-r108
30379851 Identification of Plasmodium falciparum nuclear proteins by mass spectrometry andproposed protein annotation. Briquet S, Ourimi A, ..., Vaquero C 10.1371/journal.pone.0205596
37935993 Insights into the structure and function of the RNA ligase RtcB Moncan M, Rakhsh-Khorshid H, ..., Gorman AM 10.1007/s00018-023-05001-5
37648453 Thioredoxin regulates the redox state and the activity of the human tRNA ligase complex Jaksch D, Irnstorfer J, Kalman PF, Martinez J 10.1261/rna.079732.123
35742896 RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin Maviza TP, Zarechenskaia AS, ..., Osterman IA 10.3390/ijms23126453
38238085 Characterization of tRNA splicing enzymes RNA ligase and tRNA2'-phosphotransferase from the pathogenic fungi Mucorales Ghosh S, Dantuluri S, ..., Shuman S 10.1261/rna.079911.123
37556111 The RNA-Splicing Ligase RTCB Promotes Influenza A Virus Replication bySuppressing Innate Immunity via Interaction with RNA Helicase DDX1 Cao L, Hui X, ..., Jin M 10.4049/jimmunol.2200799
35858322 Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfHand RtcB Tian Y, Zeng F, ..., Huang RH 10.1073/pnas.2202464119