PF3D7_0821500 (NEP1)

Genome location: Pf3D7_08_v3:967,747..969,151(-)

Genome classification: Core

Function and Localization

Product Description: ribosomal RNA small subunit methyltransferase NEP1, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 2.1.1.260 (rRNA small subunit pseudouridine methyltransferase Nep1)

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0005730	nucleolus
Component	GO:0032040	small-subunit processome
Function	GO:0070037	rRNA (pseudouridine) methyltransferase activity
Function	GO:0019843	rRNA binding
Process	GO:0070475	rRNA base methylation
Process	GO:0042274	ribosomal small subunit biogenesis
Process	GO:0042254	ribosome biogenesis

Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	no data	N/A	N/A
Ring	no data	0.65	0.69
Trophozoite	no data	0.42	0.75
Schizont	no data	0.07	0.96
Gametocyte	no data	0.32	0.82

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_0821500

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: 0.126 | MFS: -2.864 | #Insertions: 0

PlasmoGEM Phenotype: N/A

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IB49

"Best" AlphaFill ligand hit: SAM (s-adenosylmethionine, Local RMSD=0.84) with 2V3K (Global RMSD=1.49)

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
2.1.1.260	rRNA small subunit pseudouridine methyltransferase Nep1	sinefungin

Orthology to BindingDB Entries:

UniProt	Protein Name	Species	Homology Source	BindingDB Ligands
Q92979	Angiotensin-converting enzyme/Ribosomal RNA small subunit methyltransferase NEP1	Homo sapiens	HOGENOM, OrthoDB	US11174219, Example 1GUS11174219, Example 1IUS11174219, Example 1LUS11174219, Example 1M...

Orthology Information

Ortholog Group (OrthoMCL): OG6_101493

Most Similar Human Ortholog: Q92979

TM-align score: 0.83 | RMSD: 2.21

Seq Identity: 0.35 | Length: 218 / 279

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000126749	EMG1 N1-specific pseudouridine methyltransferase

Protein Information

Protein Length: 279 | Molecular Weight (kDa): 32.757

UniProt ID(s): Q8IB49

PDB ID(s): None

Isoelectric Point: 6.74

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR005304	Ribosomal biogenesis, methyltransferase, EMG1/NEP1
InterPro	IPR029028	Alpha/beta knot methyltransferases
PFam	PF03587	Ribosomal biogenesis, methyltransferase, EMG1/NEP1
Superfamily	SSF75217	Alpha/beta knot methyltransferases

Genetic Variation

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

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	8	20	11	20
disruptive	19	55	20	49
missense	10	30	14	33

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	15	33	13	18
disruptive	34	98	40	88
missense	16	55	29	45

PlasmoDB Total SNPs: 78

Non-coding: 36 | Synonymous: 22 | Nonsynonymous: 20 | Stop Codon: 0