PF3D7_1304100 (LigI)

Genome location: Pf3D7_13_v3:221,623..225,748(-)

Genome classification: Core

Function and Localization

Product Description: DNA ligase I

SignalP Peptide: MNFLILVVLIKMVVC

# Transmembrane Domains: 0

EC Numbers: 6.5.1.1 (DNA ligase (ATP))

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0020011	apicoplast
Component	GO:0005737	cytoplasm
Component	GO:0005739	mitochondrion
Component	GO:0005634	nucleus
Function	GO:0003910	DNA ligase (ATP) activity
Function	GO:0005509	calcium ion binding
Function	GO:0000287	magnesium ion binding
Function	GO:0030145	manganese ion binding
Process	GO:0006266	DNA ligation
Process	GO:0051103	DNA ligation involved in DNA repair
Process	GO:0006273	lagging strand elongation

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

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	possibly expressed	N/A	N/A
Ring	expressed	0.09	0.96
Trophozoite	expressed	0.64	0.64
Schizont	expressed	0.56	0.65
Gametocyte	not expressed	0.41	0.77

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_1304100

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: 0.152 | MFS: -3.267 | #Insertions: 0

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1402600)

Relative Growth Rate: 0.10 ± nan
Confidence: 1.00

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: Q8IES4

"Best" AlphaFill ligand hit: AMP (adenosine monophosphate, Local RMSD=0.35) with 6P09 (Global RMSD=2.47)

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
6.5.1.1	DNA ligase (ATP)	ATPADPGTPCTPUTPKClNEMEDTANH4+dATPPCNAMgCl2...

Orthology to BindingDB Entries:

UniProt	Protein Name	Species	Homology Source	BindingDB Ligands
P18858	DNA ligase 1	Homo sapiens	OMA	alpha-ketooxazole, 5aalpha-ketooxazole, 5balpha-ketooxazole, 5calpha-ketooxazole, 5d...
P49916	DNA ligase 3		OrthoDB	CHEMBL4458668

Orthology Information

Ortholog Group (OrthoMCL): OG6_100906

Most Similar Human Ortholog: F5GZ28

TM-align score: 0.64 | RMSD: 5.37

Seq Identity: 0.37 | Length: 667 / 912

All Human Orthologs (OrthoMCL):

Gene ID	Description
ENSG00000105486	DNA ligase 1

Protein Information

Protein Length: 912 | Molecular Weight (kDa): 104.506

UniProt ID(s): Q8IES4, Q8WQK1

PDB ID(s): None

Isoelectric Point: 7.58

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR000977	DNA ligase, ATP-dependent
InterPro	IPR012308	DNA ligase, ATP-dependent, N-terminal
InterPro	IPR012309	DNA ligase, ATP-dependent, C-terminal
InterPro	IPR012310	DNA ligase, ATP-dependent, central
InterPro	IPR012340	Nucleic acid-binding, OB-fold
InterPro	IPR016059	DNA ligase, ATP-dependent, conserved site
InterPro	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily
PFam	PF01068	DNA ligase, ATP-dependent, central
PFam	PF04675	DNA ligase, ATP-dependent, N-terminal
PFam	PF04679	DNA ligase, ATP-dependent, C-terminal
Superfamily	SSF117018	DNA ligase, ATP-dependent, N-terminal domain superfamily
Superfamily	SSF50249	Nucleic acid-binding, OB-fold
Superfamily	SSF56091

Genetic Variation

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

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	16	52	28	62
disruptive	16	61	33	107
missense	10	58	30	90

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	27	101	33	64
disruptive	26	137	64	180
missense	16	117	57	133

PlasmoDB Total SNPs: 155

Non-coding: 105 | Synonymous: 33 | Nonsynonymous: 17 | Stop Codon: 0

PMID	Title	Authors	DOI/Link
17688957	Expression and biochemical characterization of Plasmodium falciparum DNA ligaseI.	Buguliskis JS, Casta LJ, ..., Taraschi TF	https://pubmed.ncbi.nlm.nih.gov/17688957/
30212465	Integrative proteomics and bioinformatic prediction enable a high-confidenceapicoplast proteome in malaria parasites.	Boucher MJ, Ghosh S, ..., Yeh E	10.1371/journal.pbio.2005895