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DPOL_HBVB3
ID   DPOL_HBVB3              Reviewed;         843 AA.
AC   Q9QAB8;
DT   18-MAR-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   03-AUG-2022, entry version 83.
DE   RecName: Full=Protein P {ECO:0000255|HAMAP-Rule:MF_04073};
DE   Includes:
DE     RecName: Full=DNA-directed DNA polymerase {ECO:0000255|HAMAP-Rule:MF_04073};
DE              EC=2.7.7.7 {ECO:0000255|HAMAP-Rule:MF_04073};
DE   Includes:
DE     RecName: Full=RNA-directed DNA polymerase {ECO:0000255|HAMAP-Rule:MF_04073};
DE              EC=2.7.7.49 {ECO:0000255|HAMAP-Rule:MF_04073};
DE   Includes:
DE     RecName: Full=Ribonuclease H {ECO:0000255|HAMAP-Rule:MF_04073};
DE              EC=3.1.26.4 {ECO:0000255|HAMAP-Rule:MF_04073};
GN   Name=P {ECO:0000255|HAMAP-Rule:MF_04073};
OS   Hepatitis B virus genotype B2 (isolate Vietnam/9873/1997) (HBV-B).
OC   Viruses; Riboviria; Pararnavirae; Artverviricota; Revtraviricetes;
OC   Blubervirales; Hepadnaviridae; Orthohepadnavirus.
OX   NCBI_TaxID=489461;
OH   NCBI_TaxID=9606; Homo sapiens (Human).
OH   NCBI_TaxID=9598; Pan troglodytes (Chimpanzee).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=10640544; DOI=10.1099/0022-1317-81-1-75;
RA   Hannoun C., Horal P., Lindh M.;
RT   "Long-term mutation rates in the hepatitis B virus genome.";
RL   J. Gen. Virol. 81:75-83(2000).
RN   [2]
RP   REVIEW.
RX   PubMed=17206754; DOI=10.3748/wjg.v13.i1.48;
RA   Beck J., Nassal M.;
RT   "Hepatitis B virus replication.";
RL   World J. Gastroenterol. 13:48-64(2007).
CC   -!- FUNCTION: Multifunctional enzyme that converts the viral RNA genome
CC       into dsDNA in viral cytoplasmic capsids. This enzyme displays a DNA
CC       polymerase activity that can copy either DNA or RNA templates, and a
CC       ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-
CC       DNA heteroduplexes in a partially processive 3'- to 5'-endonucleasic
CC       mode. Neo-synthesized pregenomic RNA (pgRNA) are encapsidated together
CC       with the P protein, and reverse-transcribed inside the nucleocapsid.
CC       Initiation of reverse-transcription occurs first by binding the epsilon
CC       loop on the pgRNA genome, and is initiated by protein priming, thereby
CC       the 5'-end of (-)DNA is covalently linked to P protein. Partial (+)DNA
CC       is synthesized from the (-)DNA template and generates the relaxed
CC       circular DNA (RC-DNA) genome. After budding and infection, the RC-DNA
CC       migrates in the nucleus, and is converted into a plasmid-like
CC       covalently closed circular DNA (cccDNA). The activity of P protein does
CC       not seem to be necessary for cccDNA generation, and is presumably
CC       released from (+)DNA by host nuclear DNA repair machinery.
CC       {ECO:0000255|HAMAP-Rule:MF_04073}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.7; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_04073};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC         diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC         Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC         ChEBI:CHEBI:173112; EC=2.7.7.49; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_04073};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.4;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_04073};
CC   -!- ACTIVITY REGULATION: Activated by host HSP70 and HSP40 in vitro to be
CC       able to bind the epsilon loop of the pgRNA. Because deletion of the
CC       RNase H region renders the protein partly chaperone-independent, the
CC       chaperones may be needed indirectly to relieve occlusion of the RNA-
CC       binding site by this domain. Inhibited by several reverse-transcriptase
CC       inhibitors: Lamivudine, Adefovir and Entecavir. {ECO:0000255|HAMAP-
CC       Rule:MF_04073}.
CC   -!- DOMAIN: Terminal protein domain (TP) is hepadnavirus-specific. Spacer
CC       domain is highly variable and separates the TP and RT domains.
CC       Polymerase/reverse-transcriptase domain (RT) and ribonuclease H domain
CC       (RH) are similar to retrovirus reverse transcriptase/RNase H.
CC       {ECO:0000255|HAMAP-Rule:MF_04073}.
CC   -!- DOMAIN: The polymerase/reverse transcriptase (RT) and ribonuclease H
CC       (RH) domains are structured in five subdomains: finger, palm, thumb,
CC       connection and RNase H. Within the palm subdomain, the 'primer grip'
CC       region is thought to be involved in the positioning of the primer
CC       terminus for accommodating the incoming nucleotide. The RH domain
CC       stabilizes the association of RT with primer-template.
CC       {ECO:0000255|HAMAP-Rule:MF_04073}.
CC   -!- MISCELLANEOUS: Hepadnaviral virions contain probably just one P protein
CC       molecule per particle. {ECO:0000255|HAMAP-Rule:MF_04073}.
CC   -!- SIMILARITY: Belongs to the hepadnaviridae P protein family.
CC       {ECO:0000255|HAMAP-Rule:MF_04073}.
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DR   EMBL; AF121251; AAF24740.1; -; Genomic_DNA.
DR   Proteomes; UP000007915; Genome.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0004523; F:RNA-DNA hybrid ribonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
DR   GO; GO:0039503; P:suppression by virus of host innate immune response; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.30.70.270; -; 1.
DR   HAMAP; MF_04073; HBV_DPOL; 1.
DR   InterPro; IPR043502; DNA/RNA_pol_sf.
DR   InterPro; IPR001462; DNApol_viral_C.
DR   InterPro; IPR000201; DNApol_viral_N.
DR   InterPro; IPR037531; HBV_DPOL.
DR   InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR   InterPro; IPR000477; RT_dom.
DR   Pfam; PF00336; DNA_pol_viral_C; 1.
DR   Pfam; PF00242; DNA_pol_viral_N; 1.
DR   Pfam; PF00078; RVT_1; 1.
DR   SUPFAM; SSF56672; SSF56672; 1.
DR   PROSITE; PS50878; RT_POL; 1.
PE   3: Inferred from homology;
KW   DNA replication; DNA-binding; DNA-directed DNA polymerase; Endonuclease;
KW   Host-virus interaction; Hydrolase;
KW   Inhibition of host innate immune response by virus;
KW   Inhibition of host RLR pathway by virus; Magnesium; Metal-binding;
KW   Multifunctional enzyme; Nuclease; Nucleotidyltransferase;
KW   RNA-directed DNA polymerase; Transferase; Viral immunoevasion.
FT   CHAIN           1..843
FT                   /note="Protein P"
FT                   /id="PRO_0000323255"
FT   DOMAIN          357..600
FT                   /note="Reverse transcriptase"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   REGION          1..177
FT                   /note="Terminal protein domain (TP)"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   REGION          178..346
FT                   /note="Spacer"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   REGION          220..265
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          347..690
FT                   /note="Polymerase/reverse transcriptase domain (RT)"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   COMPBIAS        220..238
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         429
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   BINDING         551
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   BINDING         552
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
FT   SITE            63
FT                   /note="Priming of reverse-transcription by covalently
FT                   linking the first nucleotide of the (-)DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_04073"
SQ   SEQUENCE   843 AA;  94363 MW;  2AC03C8E57972851 CRC64;
     MPLSYQHFRK LLLLDEEAGP LEEELPRLAD EGLNRRVAED LNLGNLNVSI PWTHKVGNFT
     GLYSSTVPCF NPNWQTPSFP DIHLQEDIVD RCQQFVGPLT VNENRRLKLI MPARFYPNVT
     KYLPLDKGIK PYYPEHVVNH YFQTRHYLHT LWKAGILYKR ESTRSASFCG SPYSWEQDLQ
     HGRLVFQTSK RHGDKSCCPQ SPGILSRSSV GPCIQSQLRQ SRLGPQPAQG QLAGRQQGGS
     GSIRARVHPS PWGTVGVEPS GSGPTHNCAS SSSSCLHQSA VRKAAYSLVS TSKGYSSSGH
     AVELHHFPPN SSRSQSQGPV LSCWWLQFRN SEPCSEYCLC HIVNLIEDWG PCTEHGEHLI
     RTPRTPARVT GGVFLVDKNP HNTTESRLVV DFSQFSRANT RVSWPKFAVP NLQSLTNLLS
     SNLSWLSLDV SAAFYHLPLH PAAMPHLLVG SSGLSRYVAR LSSNSRIINN QHRTMQNLHN
     SCSRNLYVSL MLLYKTYGRK LHLYSHPIIL GFRKIPMGVG LSPFLLAQFT SAICSVVRRA
     FPHCLAFSYM DDVVLGAKSV QHLESLYAAV THFLLSLGIH LNPHKTKRWG YSLNFMGYVI
     GSWGTLPQEH IVQKIKMCFR KLPVNRPIDW KVCQRIVGLL GFAAPFTQCG YPALMPLYAC
     IQAKQAFTFS PTYKAFLRNQ YLNLYPVARQ RPGLCQVFAD ATPTGWGLAI GHQRMRGTFV
     SPLPIHTAEL LAACFARSRS GAKLIGTDNS VVLSRKYTSF PWLLGCAANW ILRGTSFVYV
     PSALNPADDP SRGRLGLYRP LLRLLYRPTT GRTSLYADSP SVPSHLPDRV HFASPLHVAW
     RPP
 
 
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