DPOL_BPB03
ID DPOL_BPB03 Reviewed; 572 AA.
AC Q37882;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 105.
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 B103 (Bacteriophage B103).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Salasmaviridae; Picovirinae; Beecentumtrevirus.
OX NCBI_TaxID=10778;
OH NCBI_TaxID=1423; Bacillus subtilis.
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=9358052; DOI=10.1016/s0378-1119(97)00363-6;
RA Pecenkova T., Benes V., Paces J., Vlcek C., Paces V.;
RT "Bacteriophage B103: complete DNA sequence of its genome and relationship
RT to other Bacillus phages.";
RL Gene 199:157-163(1997).
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; X99260; CAA67649.1; -; Genomic_DNA.
DR RefSeq; NP_690635.1; NC_004165.1.
DR SMR; Q37882; -.
DR GeneID; 955357; -.
DR KEGG; vg:955357; -.
DR Proteomes; UP000000971; 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_0000046540"
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 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; 66504 MW; 8828E62AB67E309F CRC64;
MPRKMFSCDF ETTTKLDDCR VWAYGYMEIG NLDNYKIGNS LDEFMQWVME IQADLYFHNL
KFDGAFIVNW LEHHGFKWSN EGLPNTYNTI ISKMGQWYMI DICFGYKGKR KLHTVIYDSL
KKLPFPVKKI AKDFQLPLLK GDIDYHAERP VGHEITPEEY EYIKNDIEII ARALDIQFKQ
GLDRMTAGSD SLKGFKDILS TKKFNKVFPK LSLPMDKEIR RAYRGGFTWL NDKYKEKEIG
EGMVFDVNSL YPSQMYSRPL PYGAPIVFQG KYEKDEQYPL YIQRIRFEFE LKEGYIPTIQ
IKKNPFFKGN EYLKNSGAEP VELYLTNVDL ELIQEHYEMY NVEYIDGFKF REKTGLFKEF
IDKWTYVKTH EKGAKKQLAK LMFDSLYGKF ASNPDVTGKV PYLKEDGSLG FRVGDEEYKD
PVYTPMGVFI TAWARFTTIT AAQACYDRII YCDTDSIHLT GTEVPEIIKD IVDPKKLGYW
AHESTFKRAK YLRQKTYIQD IYAKEVDGKL IECSPDEATT TKFSVKCAGM TDTIKKKVTF
DNFRVGFSST GKPKPVQVNG GVVLVDSVFT IK
