DPOL_BPNF
ID DPOL_BPNF Reviewed; 572 AA.
AC B7SSM2;
DT 11-MAY-2016, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 51.
DE RecName: Full=DNA polymerase;
DE EC=2.7.7.7 {ECO:0000269|PubMed:23110220};
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 {ECO:0000312|EMBL:ACH57069.1};
OS Bacillus phage Nf (Bacteriophage Nf).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Salasmaviridae; Picovirinae; Beecentumtrevirus.
OX NCBI_TaxID=10753;
OH NCBI_TaxID=1423; Bacillus subtilis.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=19207565; DOI=10.1111/j.1462-2920.2008.01845.x;
RA Castilla-Llorente V., Salas M., Meijer W.J.;
RT "Different responses to Spo0A-mediated suppression of the related Bacillus
RT subtilis phages Nf and phi29.";
RL Environ. Microbiol. 11:1137-1149(2009).
RN [2]
RP FUNCTION.
RX PubMed=19011105; DOI=10.1073/pnas.0809882105;
RA Longas E., Villar L., Lazaro J.M., de Vega M., Salas M.;
RT "Phage phi29 and Nf terminal protein-priming domain specifies the internal
RT template nucleotide to initiate DNA replication.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18290-18295(2008).
RN [3]
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=23110220; DOI=10.1371/journal.pone.0048257;
RA Rodriguez I., Longas E., de Vega M., Salas M.;
RT "The essential role of the 3' terminal template base in the first steps of
RT protein-primed DNA replication.";
RL PLoS ONE 7:E48257-E48257(2012).
CC -!- FUNCTION: Polymerase responsible for protein-primed viral DNA
CC replication by strand displacement with high processivity and fidelity
CC (By similarity). To start replication, the DNA polymerase forms a
CC heterodimer with a free primer terminal protein (TP), recognizes the
CC replication origins at both 5' ends of the linear chromosome, and
CC initiates replication using as primer the OH-group of Ser-232 of the TP
CC (PubMed:23110220). This polymerase possesses three enzymatic
CC activities: DNA synthesis (polymerase), primer terminal protein (TP)
CC deoxynucleotidylation, which is the formation of a covalent linkage
CC (phosphoester) between the hydroxyl group of a specific serine residue
CC in TP and 5'-dAMP, a reaction directed by the third T at the 3' end,
CC and 3' to 5' exonuclease activity (PubMed:23110220, PubMed:19011105).
CC Exonuclease activity has a proofreading purpose (By similarity). Since
CC the polymerase initiates the replication on the third thymine, the TP-
CC dAMP initiation product translocates backwards to recover the template
CC information of the 2 terminal nucleotide (sliding back-mechanism)
CC (PubMed:23110220, PubMed:19011105). {ECO:0000250|UniProtKB:P03680,
CC ECO:0000269|PubMed:19011105, ECO:0000269|PubMed:23110220}.
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:0000269|PubMed:23110220};
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; EU622808; ACH57069.1; -; Genomic_DNA.
DR SMR; B7SSM2; -.
DR PRIDE; B7SSM2; -.
DR Proteomes; UP000000744; 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 1: Evidence at protein level;
KW DNA replication; DNA-binding; DNA-directed DNA polymerase; Early protein;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW Transferase; Viral DNA replication.
FT CHAIN 1..572
FT /note="DNA polymerase"
FT /id="PRO_0000436072"
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="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; 66451 MW; 8E260DFCFC981F76 CRC64;
MSRKMFSCDF ETTTKLDDCR VWAYGYMEIG NLDNYKIGNS LDEFMQWVME IQADLYFHNL
KFDGAFIVNW LEQHGFKWSN EGLPNTYNTI ISKMGQWYMI DICFGYRGKR KLHTVIYDSL
KKLPFPVKKI AKDFQLPLLK GDIDYHTERP VGHEITPEEY EYIKNDIEII ARALDIQFKQ
GLDRMTAGSD SLKGFKDILS TKKFNKVFPK LSLPMDKEIR KAYRGGFTWL NDKYKEKEIG
EGMVFDVNSL YPSQMYSRPL PYGAPIVFQG KYEKDEQYPL YIQRIRFEFE LKEGYIPTIQ
IKKNPFFKGN EYLKNSGVEP VELYLTNVDL ELIQEHYELY NVEYIDGFKF REKTGLFKDF
IDKWTYVKTH EEGAKKQLAK LMLNSLYGKF ASNPDVTGKV PYLKDDGSLG FRVGDEEYKD
PVYTPMGVFI TAWARFTTIT AAQACYDRII YCDTDSIHLT GTEVPEIIKD IVDPKKLGYW
AHESTFKRAK YLRQKTYIQD IYVKEVDGKL KECSPDEATT TKFSVKCAGM TDTIKKKVTF
DNFAVGFSSM GKPKPVQVNG GVVLVDSVFT IK
