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HAMAP rule MF_04073

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General rule information [?]

Accession MF_04073
Dates 9-MAY-2017 (Created)
19-NOV-2022 (Last updated, Version 8)
Viruses; Orthohepadnavirus
Template Q69028 (DPOL_HBVCJ)

Propagated annotation [?]

Identifier, protein and gene names [?]

Protein name
RecName: Full=Protein P;
RecName: Full=DNA-directed DNA polymerase;
RecName: Full=RNA-directed DNA polymerase;
RecName: Full=Ribonuclease H;
Gene name

Comments [?]

Function Multifunctional enzyme that converts the viral RNA genome into dsDNA in viral cytoplasmic capsids. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3'- to 5'-endonucleasic mode. Neo-synthesized pregenomic RNA (pgRNA) are encapsidated together with the P protein, and reverse-transcribed inside the nucleocapsid. Initiation of reverse-transcription occurs first by binding the epsilon loop on the pgRNA genome, and is initiated by protein priming, thereby the 5'-end of (-)DNA is covalently linked to P protein. Partial (+)DNA is synthesized from the (-)DNA template and generates the relaxed circular DNA (RC-DNA) genome. After budding and infection, the RC-DNA migrates in the nucleus, and is converted into a plasmid-like covalently closed circular DNA (cccDNA). The activity of P protein does not seem to be necessary for cccDNA generation, and is presumably released from (+)DNA by host nuclear DNA repair machinery.
Catalytic activity RHEA:22508: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
RHEA:22508: a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1)
Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=;
Activity regulation Activated by host HSP70 and HSP40 in vitro to be able to bind the epsilon loop of the pgRNA. Because deletion of the RNase H region renders the protein partly chaperone-independent, the chaperones may be needed indirectly to relieve occlusion of the RNA-binding site by this domain. Inhibited by several reverse-transcriptase inhibitors: Lamivudine, Adefovir and Entecavir.
Domain Terminal protein domain (TP) is hepadnavirus-specific. Spacer domain is highly variable and separates the TP and RT domains. Polymerase/reverse-transcriptase domain (RT) and ribonuclease H domain (RH) are similar to retrovirus reverse transcriptase/RNase H.
The polymerase/reverse transcriptase (RT) and ribonuclease H (RH) domains are structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the 'primer grip' region is thought to be involved in the positioning of the primer terminus for accommodating the incoming nucleotide. The RH domain stabilizes the association of RT with primer-template.
Miscellaneous Hepadnaviral virions contain probably just one P protein molecule per particle.
Similarity Belongs to the hepadnaviridae P protein family.

Keywords [?]

Gene Ontology [?]

GO:0003677; Molecular function: DNA binding.
GO:0003887; Molecular function: DNA-directed DNA polymerase activity.
GO:0046872; Molecular function: metal ion binding.
GO:0003964; Molecular function: RNA-directed DNA polymerase activity.
GO:0004523; Molecular function: RNA-DNA hybrid ribonuclease activity.
GO:0006260; Biological process: DNA replication.
GO:0039503; Biological process: suppression by virus of host innate immune response.

Cross-references [?]

Pfam PF00336; DNA_pol_viral_C; 1;
PF00242; DNA_pol_viral_N; 1;
PF00078; RVT_1; 1;

Features [?]

From: DPOL_HBVCJ (Q69028)
Key     From     To       Description   Tag   Condition   FTGroup
DOMAIN     357     600       Reverse transcriptase        
REGION     1     177       Terminal protein domain (TP)        
REGION     178     346       Spacer        
REGION     347     690       Polymerase/reverse transcriptase domain (RT)        
BINDING     429     429       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic     D  
BINDING     551     551       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic     D  
BINDING     552     552       /ligand="Mg(2+)" /ligand_id="ChEBI:CHEBI:18420" /ligand_note="catalytic     D  
SITE     63     63       Priming of reverse-transcription by covalently linking the first nucleotide of the (-)DNA     Y  

Additional information [?]

Size range 832-884 amino acids
Related rules None
Fusion None