C3V235 · C3V235_BPR51
- ProteinDNA-directed DNA polymerase
- Gene43
- StatusUniProtKB unreviewed (TrEMBL)
- Amino acids898 (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
- a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
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 | ||||
Sequence: D | ||||||
Binding site | 114 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | ||||
Sequence: E | ||||||
Binding site | 219 | Mg2+ 2 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | ||||
Sequence: D | ||||||
Binding site | 324 | Mg2+ 1 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | ||||
Sequence: D | ||||||
Binding site | 324 | Mg2+ 2 (UniProtKB | ChEBI); catalytic; for 3'-5' exonuclease activity | ||||
Sequence: D | ||||||
Binding site | 408 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for polymerase activity | ||||
Sequence: D | ||||||
Binding site | 408 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | ||||
Sequence: D | ||||||
Binding site | 409 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | ||||
Sequence: L | ||||||
Binding site | 411-413 | substrate | ||||
Sequence: SLY | ||||||
Binding site | 479 | substrate | ||||
Sequence: R | ||||||
Binding site | 557 | substrate | ||||
Sequence: K | ||||||
Site | 618 | Optimization of metal coordination by the polymerase active site | ||||
Sequence: D | ||||||
Binding site | 620 | Mg2+ 3 (UniProtKB | ChEBI); catalytic; for polymerase activity | ||||
Sequence: D | ||||||
Binding site | 620 | Mg2+ 4 (UniProtKB | ChEBI); catalytic; for polymerase activity | ||||
Sequence: D | ||||||
Site | 703 | Optimization of metal coordination by the polymerase active site | ||||
Sequence: K | ||||||
Site | 711 | Essential for viral replication | ||||
Sequence: D |
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 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
- Taxonomic lineageViruses > Duplodnaviria > Heunggongvirae > Uroviricota > Caudoviricetes > Straboviridae > Tevenvirinae > Tequatrovirus > Tequatrovirus RB51
- Virus hosts
Accessions
- Primary accessionC3V235
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 region, domain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Region | 101-337 | 3'-5'exonuclease | ||||
Sequence: YDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMVLGERSMKRFSPIGRVKSKLIQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGF | ||||||
Domain | 106-290 | DNA-directed DNA polymerase family B exonuclease | ||||
Sequence: VRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMVLGERSMKRFSPIGRVKSKLIQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESV | ||||||
Region | 245-261 | Beta hairpin | ||||
Sequence: VKSKLIQNMYGSKEIYS | ||||||
Domain | 365-492 | DNA-directed DNA polymerase family B multifunctional | ||||
Sequence: IIFNSLKGEHKVIPQQGSHVKQSFPGAFVFEPKPIARRYIMSFDLTSLYPSIIRQVNISPETIRGQFKVHPIHEYIAGTAPKPSDEYSCSPNGWMYDKHQEGIIPKEIAKVFFQRKDWKKKMFAEEMN | ||||||
Region | 377-898 | Polymerase | ||||
Sequence: IPQQGSHVKQSFPGAFVFEPKPIARRYIMSFDLTSLYPSIIRQVNISPETIRGQFKVHPIHEYIAGTAPKPSDEYSCSPNGWMYDKHQEGIIPKEIAKVFFQRKDWKKKMFAEEMNAEAIKKIIMKGAGSCSTKPEVERYVKFSDDFLNELSNYTESVLNSLIEECEKAATLANTNQLNRKILINSLYGALGNIHFRYYDLRNATAITIFGQVGIQWIARKINEYLNKVCGTNGEDFIAAGDTDSVYVCVDKVIEKVGLDRFKEQNDLVEFMNQFGKKKMEPMIDVAYRELCDYMNNREHLMHMDREAISCPPLGSKGVGGFWKAKKRYALNVYDMEDKRFAEPHLKIMGMETQQSSTPKAVQEALEESIRRILQEGEESVQEYYKNFEKEYRQLDYKVIAEVKTANDIAKYDDKGWPGFKCPFHIRGVLTYRRAVSGLGVAPILDGNKVMVLPLREGNPFGDKCIAWPSGTELPKEIRSDVLSWIDYSTLFQKSFVKPLAGMCESAGMDYEEKASLDFLFG | ||||||
Domain | 542-627 | DNA-directed DNA polymerase family B multifunctional | ||||
Sequence: CEKAATLANTNQLNRKILINSLYGALGNIHFRYYDLRNATAITIFGQVGIQWIARKINEYLNKVCGTNGEDFIAAGDTDSVYVCVD | ||||||
Region | 702-705 | Binding of DNA in B-conformation | ||||
Sequence: KKRY | ||||||
Region | 893-898 | Interaction with the polymerase clamp | ||||
Sequence: LDFLFG |
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.
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length898
- Mass (Da)103,564
- Last updated2009-06-16 v1
- Checksum1F48C327E1BCB226
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
FJ839693 EMBL· GenBank· DDBJ | ACP30967.1 EMBL· GenBank· DDBJ | Genomic DNA |