PF3D7_1368800 (ERCC4)

Genome location: Pf3D7_13_v3:2,730,239..2,736,221(-)

Genome classification: Core

Function and Localization

Product Description: DNA repair endonuclease XPF, putative

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 3.1.21.1 (Deoxyribonuclease I)

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0000110	nucleotide-excision repair factor 1 complex
Function	GO:0003677	DNA binding
Function	GO:0003684	damaged DNA binding
Function	GO:0004520	endodeoxyribonuclease activity
Function	GO:0003697	single-stranded DNA binding
Function	GO:0000014	single-stranded DNA endodeoxyribonuclease activity
Process	GO:0006281	DNA repair
Process	GO:0000724	double-strand break repair via homologous recombination
Process	GO:1901255	nucleotide-excision repair involved in interstrand cross-link repair
Process	GO:0006296	nucleotide-excision repair, DNA incision, 5'-to lesion
Process	GO:0000712	resolution of meiotic recombination intermediates

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	not expressed	0.10	0.95
Trophozoite	expressed	0.80	0.57
Schizont	expressed	0.34	0.80
Gametocyte	possibly expressed	0.83	0.57

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1368800

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: 0.119 | MFS: -3.061 | #Insertions: 0

PlasmoGEM Phenotype: Slow (Pb ortholog: PBANKA_1144700)

Relative Growth Rate: 0.79 ± 0.16
Confidence: 5.01

RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_1144700)

Modification: Disrupted | RMgm-3159

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8ID22

"Best" AlphaFill ligand hit: PH2 (2-amino-6-hydroxymethyl-7,8-dihydro-3h-pteridin-4-one, Local RMSD=0.07) with 6JWR (Global RMSD=8.72)

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
3.1.21.1	deoxyribonuclease I	KClSDSDTTRNAEDTAEGTAactin3'-AMP5'-GMPHPO42-P2O74-5'-GTP...

Orthology to BindingDB Entries:

UniProt	Protein Name	Species	Homology Source	BindingDB Ligands
Q92889	DNA repair endonuclease XPF		OrthoDB	MLS002701988CHEMBL4470176MLS002701988CHEMBL4759590

Orthology Information

Ortholog Group (OrthoMCL): OG6_101959

Most Similar Human Ortholog: A0A804HIY2

TM-align score: 0.86 | RMSD: 2.14

Seq Identity: 0.28 | Length: 259 / 1700

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000175595	ERCC excision repair 4, endonuclease catalytic subunit

Protein Information

Protein Length: 1700 | Molecular Weight (kDa): 204.533

UniProt ID(s): Q8ID22

PDB ID(s): None

Isoelectric Point: 7.77

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR006166	ERCC4 domain
InterPro	IPR010994	RuvA domain 2-like
InterPro	IPR011335	Restriction endonuclease type II-like
PFam	N/A	N/A
Superfamily	SSF47781	RuvA domain 2-like
Superfamily	SSF52980	Restriction endonuclease type II-like

Genetic Variation

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

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	26	94	55	122
disruptive	73	260	160	347
missense	52	224	141	295

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	34	191	92	120
disruptive	125	570	214	383
missense	88	475	173	283

PlasmoDB Total SNPs: 298

Non-coding: 61 | Synonymous: 144 | Nonsynonymous: 93 | Stop Codon: 0