PF3D7_1366500 (NDK)

Genome location: Pf3D7_13_v3:2,660,521..2,662,797(+)

Genome classification: Core

Function and Localization

Product Description: nucleoside diphosphate kinase

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 2.7.4.6 (Nucleoside-diphosphate kinase)

Curated GO (PlasmoDB):

Type	GO Term	Name
Function	GO:0005524	ATP binding
Function	GO:0000287	magnesium ion binding
Function	GO:0004550	nucleoside diphosphate kinase activity
Process	GO:0006241	CTP biosynthetic process
Process	GO:0006183	GTP biosynthetic process
Process	GO:0006228	UTP biosynthetic process

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	possibly expressed	0.04	0.98
Trophozoite	expressed	0.40	0.76
Schizont	expressed	0.05	0.96
Gametocyte	expressed	0.19	0.89

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1366500

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 *tentative

MIS: 0.119 | MFS: -2.705 | #Insertions: 0

PlasmoGEM Phenotype: Slow (Pb ortholog: PBANKA_1142400)

Relative Growth Rate: 0.57 ± 0.08
Confidence: 6.46

RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_1142400)

Modification: Disrupted | RMgm-3145

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8ID43

"Best" AlphaFill ligand hit: TAM (tris(hydroxyethyl)aminomethane, Local RMSD=0.02) with 6QA2 (Global RMSD=0.58)

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
2.7.4.6	nucleoside-diphosphate kinase	ATPUDPAMPGDPGMPEDTAcAMPcGMPdTDPDTNBdCDPMgADP-...

Orthology to BindingDB Entries:

UniProt	Protein Name	Species	Homology Source	BindingDB Ligands
O00746	Nucleoside diphosphate kinase, mitochondrial		HOGENOM, OrthoDB	CHEMBL5204662

Orthology Information

Ortholog Group (OrthoMCL): OG6_100304

Most Similar Human Ortholog: P15531

TM-align score: 0.99 | RMSD: 0.36

Seq Identity: 0.59 | Length: 149 / 149

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000011052	NME1-NME2 readthrough
ENSG00000103024	NME/NM23 nucleoside diphosphate kinase 3
ENSG00000103202	NME/NM23 nucleoside diphosphate kinase 4
ENSG00000239672	NME/NM23 nucleoside diphosphate kinase 1
ENSG00000243678	NME/NM23 nucleoside diphosphate kinase 2

Protein Information

Protein Length: 149 | Molecular Weight (kDa): 17.012

UniProt ID(s): Q8ID43

PDB ID(s): 1XIQ

Isoelectric Point: 9.42

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR001564	Nucleoside diphosphate kinase
InterPro	IPR023005	Nucleoside diphosphate kinase, active site
InterPro	IPR034907	Nucleoside diphosphate kinase-like domain
InterPro	IPR036850	Nucleoside diphosphate kinase-like domain superfamily
PFam	PF00334	Nucleoside diphosphate kinase-like domain
Superfamily	SSF54919	Nucleoside diphosphate kinase-like domain superfamily

Genetic Variation

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

No passing variants found

PlasmoDB Total SNPs: 143

Non-coding: 133 | Synonymous: 7 | Nonsynonymous: 3 | Stop Codon: 0