PF3D7_1005500 (UPF1)

Genome location: Pf3D7_10_v3:236,121..242,888(-)

Genome classification: Core

Function and Localization

Product Description: regulator of nonsense transcripts 1, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: None

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0005737	cytoplasm
Function	GO:0003723	RNA binding
Function	GO:0003724	RNA helicase activity
Process	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

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	0.27	0.88
Trophozoite	expressed	1.26	0.39
Schizont	expressed	0.78	0.59
Gametocyte	expressed	1.67	0.25

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1005500

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: 1 | MFS: 0.093 | #Insertions: 8

PlasmoGEM Phenotype: Dispensable (Pb ortholog: PBANKA_1203700)

Relative Growth Rate: 0.85 ± 0.37
Confidence: 3.35

RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_1203700)

Modification: Disrupted | RMgm-4260

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: A0A143ZY29

"Best" AlphaFill ligand hit: ANP (phosphoaminophosphonic acid-adenylate ester, Local RMSD=0.07) with 4PJ3 (Global RMSD=2.37)

No associated EC numbers

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_101981

Most Similar Human Ortholog: Q92900

TM-align score: 0.73 | RMSD: 3.94

Seq Identity: 0.51 | Length: 885 / 1579

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000005007	UPF1 RNA helicase and ATPase

Genetic Variation

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

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	22	101	46	110
disruptive	47	145	79	214
missense	34	132	69	183

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	36	200	82	112
disruptive	87	313	153	347
missense	59	266	125	257

PlasmoDB Total SNPs: 249

Non-coding: 150 | Synonymous: 51 | Nonsynonymous: 48 | Stop Codon: 0

Protein Information

Protein Length: 1579 | Molecular Weight (kDa): 183.964

UniProt ID(s): A0A143ZY29

PDB ID(s): None

Isoelectric Point: 7.63

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR018999	RNA helicase UPF1, UPF2-interacting domain
InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
InterPro	IPR040812	Domain of unknown function DUF5599
InterPro	IPR041677	DNA2/NAM7 helicase, helicase domain
InterPro	IPR041679	DNA2/NAM7 helicase-like, C-terminal
PFam	PF09416	RNA helicase UPF1, UPF2-interacting domain
PFam	PF13086	DNA2/NAM7 helicase, helicase domain
PFam	PF13087	DNA2/NAM7 helicase-like, C-terminal
PFam	PF18141	Domain of unknown function DUF5599
Superfamily	SSF52540	P-loop containing nucleoside triphosphate hydrolase

PMID	Title	Authors	DOI/Link
12368864	Genome sequence of the human malaria parasite Plasmodium falciparum.	Gardner MJ, Hall N, ..., Barrell B	10.1038/nature01097
38081826	An allele-selective inter-chromosomal protein bridge supports monogenic antigenexpression in the African trypanosome	Faria JRC, Tinti M, ..., Horn D	10.1038/s41467-023-44043-y
38198768	Genetic screens in Saccharomyces cerevisiae identify a role for 40S ribosomerecycling factors Tma20/22 in nonsense mediated decay	Pacheco M, D'Orazio KN, ..., Green R	10.1093/g3journal/jkad295