A0A5B9NJF4 · A0A5B9NJF4_9CAUD
- ProteinDNA-directed DNA polymerase
- StatusUniProtKB unreviewed (TrEMBL)
- Organism
- Amino acids901 (go to sequence)
- Protein existenceInferred from homology
- Annotation score3/5
Function
function
Replicates the viral genomic DNA. This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction for proofreading purpose.
Catalytic activity
- DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
Cofactor
Features
Showing features for binding site, site.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Binding site | 112 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | |||
Binding site | 114 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | |||
Binding site | 219 | Mg2+ 2 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | |||
Binding site | 325 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | |||
Binding site | 325 | Mg2+ 2 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | |||
Binding site | 409 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | |||
Binding site | 409 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for polymerase activity | |||
Binding site | 410 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | |||
Binding site | 412-414 | substrate | |||
Binding site | 480 | substrate | |||
Binding site | 558 | substrate | |||
Site | 619 | Optimization of metal coordination by the polymerase active site | |||
Binding site | 621 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for polymerase activity | |||
Binding site | 621 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | |||
Site | 704 | Optimization of metal coordination by the polymerase active site | |||
Site | 712 | Essential for viral replication | |||
GO annotations
Aspect | Term | |
---|---|---|
Molecular Function | 3'-5' exonuclease activity | |
Molecular Function | DNA binding | |
Molecular Function | DNA-directed DNA polymerase activity | |
Molecular Function | metal ion binding | |
Molecular Function | nucleotide binding | |
Biological Process | bidirectional double-stranded viral DNA replication | |
Biological Process | DNA-templated DNA replication |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA-directed DNA polymerase
- EC number
Gene names
Organism names
- Organism
- Taxonomic lineageViruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Marfavirus > Marfavirus F48
Accessions
- Primary accessionA0A5B9NJF4
Proteomes
Interaction
Subunit
Part of the replicase complex that includes the DNA polymerase, the polymerase clamp, the clamp loader complex, the single-stranded DNA binding protein, and the primase/helicase. Interacts with the polymerase clamp; this interaction constitutes the polymerase holoenzyme.
Structure
Family & Domains
Features
Showing features for domain, region.
Type | ID | Position(s) | Description | ||
---|---|---|---|---|---|
Domain | 184-291 | DNA-directed DNA polymerase family B exonuclease | |||
Domain | 366-493 | DNA-directed DNA polymerase family B multifunctional | |||
Region | 378-901 | Polymerase | |||
Domain | 553-627 | DNA-directed DNA polymerase family B multifunctional | |||
Region | 703-706 | Binding of DNA in B-conformation | |||
Region | 895-901 | Interaction with the polymerase clamp | |||
Domain
The N-terminus contains the 3'-5' exonuclease activity. The C-terminus contains the polymerase activity and is involved in binding to the polymerase clamp protein. A beta hairpin structure is necessary for the proofreading function of the polymerase.
Sequence similarities
Belongs to the DNA polymerase type-B family.
Family and domain databases
Sequence
- Sequence statusComplete
- Length901
- Mass (Da)104,231
- Last updated2019-11-13 v1
- MD5 Checksum454125071E1EF597447744200FD81084
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
MN013081 EMBL· GenBank· DDBJ | QEG12702.1 EMBL· GenBank· DDBJ | Genomic DNA |