About Gene List

PF3D7_0625300 (MtDNAP)

Genome location: Pf3D7_06_v3:1,026,468..1,031,411(-)

Genome classification: Core

Function and Localization

Product Description: mitochondrial DNA polymerase

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 2.7.7.7 (DNA-directed DNA polymerase)

Curated GO (PlasmoDB):

Type GO Term Name
Component GO:0005737 cytoplasm
Component GO:0005739 mitochondrion
Function GO:0008409 5'-3' exonuclease activity
Function GO:0003677 DNA binding
Function GO:0003887 DNA-directed DNA polymerase activity
Process GO:0006260 DNA replication
Process GO:0006261 DNA-dependent DNA replication

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 0.16 0.92
Trophozoite expressed 1.19 0.44
Schizont expressed 0.81 0.61
Gametocyte expressed 0.44 0.76

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_0625300

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: 0.144 | MFS: -2.934 | #Insertions: 0

PlasmoGEM Phenotype: Essential (Pb ortholog: PBANKA_1124200)

  • Relative Growth Rate: 0.10 ± 0.08
  • Confidence: 6.35

RMgmDB ABS Phenotype: N/A

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: C6KT89

"Best" AlphaFill ligand hit: DCP (2'-deoxycytidine-5'-triphosphate, Local RMSD=0.27) with 3PX0 (Global RMSD=9.83)

BRENDA EC Inhibitors:

EC # Name EC Inhibitors
2.7.7.7 DNA-directed DNA polymerase KClEDTANH4+dATPNH4ClddTTPMK886UracilalliinsucroseethanolAllicin...

Orthology to BindingDB Entries:

UniProt Protein Name Species Homology Source BindingDB Ligands
O75417 DNA polymerase theta OrthoDB CHEMBL5185248CHEMBL5190448CHEMBL5175626CHEMBL5188740...

Orthology Information

Ortholog Group (OrthoMCL): OG6_101669

Most Similar Human Ortholog: Q7Z5Q5

TM-align score: 0.50 | RMSD: 4.38

Seq Identity: 0.21 | Length: 501 / 1444

All Human Orthologs (OrthoMCL):

Gene ID Description
ENSG00000130997 DNA polymerase nu

Protein Information

Protein Length: 1444 | Molecular Weight (kDa): 171.13

UniProt ID(s): C6KT89

PDB ID(s): None

Isoelectric Point: 8.47

Protein Domain Annotations:

Source Family ID Description
InterPro IPR001098 DNA-directed DNA polymerase, family A, palm domain
InterPro IPR002298 DNA polymerase A
InterPro IPR043502 DNA/RNA polymerase superfamily
PFam PF00476 DNA-directed DNA polymerase, family A, palm domain
Superfamily SSF56672 DNA/RNA polymerase superfamily

Genetic Variation

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

Homozygous genotype calls only

variant type common rare doubleton singleton
synonymous 11 53 35 82
disruptive 68 178 100 218
missense 37 125 74 156

Any inclusion in genotype call

variant type common rare doubleton singleton
synonymous 23 118 60 73
disruptive 129 401 166 403
missense 64 262 120 247

PlasmoDB Total SNPs: 271

Non-coding: 70 | Synonymous: 112 | Nonsynonymous: 89 | Stop Codon: 0

Associated Publications

PMID Title Authors DOI/Link
12368867 Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13. Hall N, Pain A, ..., Barrell BG 10.1038/nature01095
34730376 Bloom Helicase Along with Recombinase Rad51 Repairs the Mitochondrial Genome ofthe Malaria Parasite. Jha P, Gahlawat A, ..., Bhattacharyya MK 10.1128/mSphere.00718-21