DNA polymerase - P03680 (DPOL_BPPH2)

 

Protein Feature View of PDB entries mapped to a UniProtKB sequence  

  • Number of PDB entries for P03680: 8
 
Function
Polymerase responsible for protein-primed viral DNA replication by strand displacement with high processivity and fidelity (PubMed:3863101) (PubMed:2498321). To start replication, the DNA polymerase forms a heterodimer with a free primer terminal protein (TP), recognizes the replication origins at both 5' ends of the linear chromosome, and initiates replication using as primer the OH-group of Ser-232 of the TP (PubMed:22210885). This polymerase possesses three enzymatic activities: DNA synthesis (polymerase), primer terminal protein (TP) deoxynucleotidylation, which is the formation of a covalent linkage (phosphoester) between the hydroxyl group of a specific serine residue in TP and 5'-dAMP, a reaction directed by the second T at the 3' end, and 3' to 5' exonuclease activity (PubMed:2790959). Exonuclease activity has a proofreading purpose (PubMed:2790959). DNA polymerase edits the polymerization errors using an intramolecular pathway as the primer terminus travels from one active site to the other without dissociation from the DNA (PubMed:10493855). DNA polymerization catalyzed by the DNA polymerase is a highly accurate process, but the protein-primed initiation is a quite inaccurate reaction (PubMed:8428945). Since the polymerase initiates the replication on the second thymine, the TP-dAMP initiation product translocates backwards to recover the template information of the first nucleotide (sliding back-mechanism) (PubMed:19011105). UniProt
Catalytic Activity
Deoxynucleoside triphosphate + DNAn = diphosphate + DNAn+1. UniProt
Pathway Maps
Maps:       
Reactions:
      ESCHER  BiGG
Subunit Structure
Interacts with the primer terminal protein; this interaction allows the initiation of TP-primed DNA replication at both viral DNA ends. Interacts with DNA. UniProt
Domain
The N-terminus contains the 3'-5' exonuclease activity and strand displacement ability (PubMed:8621470). The conserved motif YxGG/A located between the 3'-5' exonuclease and polymerization domains is important for DNA-binding, coordination between DNA synthesis and degradation and for the formation of a stable complex between TP and the DNA polymerase (PubMed:8670845, PubMed:9931249, PubMed:15777661). The C-terminus is involved in the protein-primed initiation, DNA polymerization and pyrophosphorolytic activities (PubMed:8621470, PubMed:1850426). The YCDTD motif is essential for the pyrophosphorolytic activity (PubMed:1850426). The TPR2 region is necessary for the strand displacement coupled to DNA synthesis and probably also for allowing the TP priming domain to move out from the polymerase during transition from initiation to elongation (PubMed:15845765, PubMed:19033368). UniProt
Legend
The Protein Feature View requires a browser that supports SVG (Scalable Vector Graphics). Mouse over tracks and labels for more information.
Data origin/color codes
The vertical color bar on the left side indicates data provenance.
Data in green originates from UniProtKB  
Variation data (sourced from UniProt) shows non-genetic variation from the ExPASy   and dbSNP   websites.
Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
Data in purple originates from Phosphosite  .
Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
  • Red: potentially disorderd region
  • Blue: probably ordered region.
Hydropathy has been calculated using a sliding window of 15 residues and summing up scores from standard hydrophobicity tables.
  • Red: hydrophobic
  • Blue: hydrophilic.
Data in lilac represent the genomic exon structure projected onto the UniProt sequence.
Data in blue originates from PDB
  • Secstruc: Secondary structure projected from representative PDB entries onto the UniProt sequence.
Sequence Mismatches It is now possible to see information about expression tags, cloning artifacts, and many other details related to sequence mismatches.
Icons represent a number of different sequence modifications that can be observed in PDB files. For example the 'T' icon T represents expression tags that have been added to the sequence. The 'E' icon E represents an engineered mutation. However, besides these two, there are many other icons. For more information about the meaning and exact position of a sequence modification, move the cursor over the icon.
Validation Track

For more details on the Validation Track (Structure Summary Page only) see the dedicated help page.

Data in red indicates combined ranges of Homology Models from SBKB   and the Protein Model Portal  
The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
Organism icons generated by flaticon.com under CC BY. The authors are: Freepik, Icons8, OCHA, Scott de Jonge.

For more details on the Protein Feature view see the dedicated help page.