DPOL_BPPZA
ID DPOL_BPPZA Reviewed; 572 AA.
AC P06950;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1988, sequence version 1.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=DNA polymerase;
DE EC=2.7.7.7 {ECO:0000250|UniProtKB:P03680};
DE EC=3.1.11.- {ECO:0000250|UniProtKB:P03680};
DE AltName: Full=Gene product 2 {ECO:0000305};
DE Short=gp2 {ECO:0000305};
DE AltName: Full=Protein p2;
GN Name=2;
OS Bacillus phage PZA (Bacteriophage PZA).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Salasmaviridae; Picovirinae; Salasvirus; Bacillus virus PZA.
OX NCBI_TaxID=10757;
OH NCBI_TaxID=1423; Bacillus subtilis.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3934048; DOI=10.1016/0378-1119(85)90202-1;
RA Paces V., Vlcek C., Urbanek P., Hostomsky Z.;
RT "Nucleotide sequence of the major early region of Bacillus subtilis phage
RT PZA, a close relative of phi 29.";
RL Gene 38:45-56(1985).
CC -!- FUNCTION: Polymerase responsible for protein-primed viral DNA
CC replication by strand displacement with high processivity and fidelity.
CC To start replication, the DNA polymerase forms a heterodimer with a
CC free primer terminal protein (TP), recognizes the replication origins
CC at both 5' ends of the linear chromosome, and initiates replication
CC using as primer the OH-group of Ser-232 of the TP. This polymerase
CC possesses three enzymatic activities: DNA synthesis (polymerase),
CC primer terminal protein (TP) deoxynucleotidylation, which is the
CC formation of a covalent linkage (phosphoester) between the hydroxyl
CC group of a specific serine residue in TP and 5'-dAMP, a reaction
CC directed by the second T at the 3' end, and 3' to 5' exonuclease
CC activity. Exonuclease activity has a proofreading purpose.
CC {ECO:0000250|UniProtKB:P03680}.
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;
CC Evidence={ECO:0000250|UniProtKB:P03680};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P03680};
CC -!- SUBUNIT: Interacts with the primer terminal protein; this interaction
CC allows the initiation of TP-primed DNA replication at both viral DNA
CC ends. Interacts with DNA. {ECO:0000250|UniProtKB:P03680}.
CC -!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity and
CC strand displacement ability. The C-terminus contains the protein-primed
CC initiation, DNA polymerization and pyrophosphorolytic activities.
CC {ECO:0000250|UniProtKB:P03680}.
CC -!- MISCELLANEOUS: This DNA polymerase requires a protein as a primer.
CC {ECO:0000250|UniProtKB:P03680}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
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DR EMBL; M11813; AAA88478.1; -; Genomic_DNA.
DR PIR; D24528; ERBP2Z.
DR SMR; P06950; -.
DR Proteomes; UP000000855; Genome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0001882; F:nucleoside binding; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0039693; P:viral DNA genome replication; IEA:UniProtKB-KW.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR004868; DNA-dir_DNA_pol_B_mt/vir.
DR InterPro; IPR014416; DNA-dir_DNA_polB_phi29_vir.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF03175; DNA_pol_B_2; 1.
DR PIRSF; PIRSF004178; Dpol_Bac_phage; 1.
DR PRINTS; PR00106; DNAPOLB.
DR SMART; SM00486; POLBc; 1.
DR SUPFAM; SSF53098; SSF53098; 1.
DR SUPFAM; SSF56672; SSF56672; 1.
DR PROSITE; PS00116; DNA_POLYMERASE_B; 1.
PE 3: Inferred from homology;
KW DNA replication; DNA-binding; DNA-directed DNA polymerase; Early protein;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Transferase;
KW Viral DNA replication.
FT CHAIN 1..572
FT /note="DNA polymerase"
FT /id="PRO_0000046543"
FT REGION 1..222
FT /note="3'-5' exonuclease and strand displacement
FT activities"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT REGION 56..66
FT /note="Interaction with the primer terminal protein"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT REGION 223..226
FT /note="DNA-binding; Involved in the formation of a stable
FT complex between TP and phi29 DNA polymerase"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT REGION 227..572
FT /note="Initiation, polymerization and pyrophosphorolytic
FT activities"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 142
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 246
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 251
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 368
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 380
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 453
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 455
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT BINDING 455
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 9
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 11
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 62
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 90
FT /note="Involved in binding template-primer structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 119
FT /note="Critical for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 119
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 120
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 249
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 251
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 380
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 384
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 387
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 388
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 431
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 435
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 495
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 497
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000250|UniProtKB:P03680"
FT SITE 526
FT /note="Stabilizes the primer-terminus at the polymerization
FT active site and contributes to the coordination between the
FT exonuclease and polymerazation activities"
FT /evidence="ECO:0000250|UniProtKB:P03680"
SQ SEQUENCE 572 AA; 66262 MW; 17F6D99EB4E1AA67 CRC64;
MPRKMYSCDF ETTTKVEDCR VWAYGYMNIE DHSEYKIGNS LDEFMAWVLK VQADLYFHNL
KFDGAFIINW LERNGFKWSA DGLPNTYNTI ISRMGQWYMI DICLGYKGKR KIHTVIYDSL
KKLPFPVKKI AKDFKLTVLK GDIDYHKERP VGYEITPDEY AYIKNDIQII AEALLIQFKQ
GLDRMTAGSD DLKGFKDIIT TKKFKKVFPT LSLGLDKEVR YAYRGGFTWL NDRFKEKEIG
EGMVFDVNSL YPAQMYSRLL PYGEPIVFEG KYVWDEDYPL HIQHIRCEFE LKEGYIPTIQ
IKRSRFYKGN EYLKSSGGEI ADLWVSNVDL ELMKEHYDLY NVEYISGLKF KATTGLFKDF
IDKWTHIKTT SEGAIKQLAK LMLNSLYGKF ASNPDVTGKV PYLKENGALG FRLGEEETKD
PVYTPMGVFI TAWARYTTIT AAQACFDRII YCDTDSIHLT GTEIPDVIKD IVDPKKLGYW
AHESTFKRAK YLRQKTYIQD IYMKEVDGKL VEGSPDDYTT IKFSVKCAGM TDKIKKEVTF
ENFKVGFSRK MKPKPVQVPG GVVLVDDTFT IK
