DPOL_BPKVM
ID DPOL_BPKVM Reviewed; 850 AA.
AC Q6WI70;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=DNA-directed DNA polymerase {ECO:0000255|HAMAP-Rule:MF_04100};
DE EC=2.7.7.7 {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000255|RuleBase:RU000442};
DE EC=3.1.11.- {ECO:0000250|UniProtKB:P04415, ECO:0000255|HAMAP-Rule:MF_04100};
DE AltName: Full=Gene product 43;
DE Short=Gp43;
GN Name=43 {ECO:0000312|EMBL:AAQ64153.1};
GN ORFNames=KVP40.0082 {ECO:0000312|EMBL:AAQ64153.1};
OS Vibrio phage KVP40 (isolate Vibrio parahaemolyticus/Japan/Matsuzaki/1991)
OS (KVP40) (Bacteriophage KVP40).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Schizotequatrovirus.
OX NCBI_TaxID=1283340;
OH NCBI_TaxID=670; Vibrio parahaemolyticus.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Isolate Vibrio parahaemolyticus/Japan/Matsuzaki/1991
RC {ECO:0000312|Proteomes:UP000001785};
RX PubMed=12923095; DOI=10.1128/jb.185.17.5220-5233.2003;
RA Miller E.S., Heidelberg J.F., Eisen J.A., Nelson W.C., Durkin A.S.,
RA Ciecko A., Feldblyum T.V., White O., Paulsen I.T., Nierman W.C., Lee J.,
RA Szczypinski B., Fraser C.M.;
RT "Complete genome sequence of the broad-host-range vibriophage KVP40:
RT comparative genomics of a T4-related bacteriophage.";
RL J. Bacteriol. 185:5220-5233(2003).
CC -!- FUNCTION: Replicates the viral genomic DNA. This polymerase possesses
CC two enzymatic activities: DNA synthesis (polymerase) and an
CC exonucleolytic activity that degrades single-stranded DNA in the 3'- to
CC 5'-direction for proofreading purpose. {ECO:0000255|HAMAP-
CC Rule:MF_04100}.
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_04100};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04100};
CC -!- SUBUNIT: Part of the replicase complex that includes the DNA
CC polymerase, the polymerase clamp, the clamp loader complex, the single-
CC stranded DNA binding protein, and the primase/helicase. Interacts with
CC the polymerase clamp; this interaction constitutes the polymerase
CC holoenzyme. {ECO:0000255|HAMAP-Rule:MF_04100}.
CC -!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity. The C-
CC terminus contains the polymerase activity and is involved in binding to
CC the polymerase clamp protein. A beta hairpin structure is necessary for
CC the proofreading function of the polymerase. {ECO:0000255|HAMAP-
CC Rule:MF_04100}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family.
CC {ECO:0000255|HAMAP-Rule:MF_04100}.
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DR EMBL; AY283928; AAQ64153.1; -; Genomic_DNA.
DR RefSeq; NP_899330.1; NC_005083.2.
DR SMR; Q6WI70; -.
DR GeneID; 2545927; -.
DR KEGG; vg:2545927; -.
DR Proteomes; UP000001785; Genome.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:UniProtKB-UniRule.
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-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-UniRule.
DR GO; GO:0039686; P:bidirectional double-stranded viral DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 1.
DR HAMAP; MF_04100; DPOL_T4; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
DR InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR034749; DPOL_T4.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF00136; DNA_pol_B; 1.
DR Pfam; PF03104; DNA_pol_B_exo1; 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; Exonuclease;
KW Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotidyltransferase; Reference proteome; Transferase;
KW Viral DNA replication.
FT CHAIN 1..850
FT /note="DNA-directed DNA polymerase"
FT /id="PRO_0000431825"
FT REGION 98..322
FT /note="3'-5'exonuclease"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT REGION 228..245
FT /note="Beta hairpin"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT REGION 362..850
FT /note="Polymerase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT REGION 657..660
FT /note="Binding of DNA in B-conformation"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT REGION 845..850
FT /note="Interaction with the polymerase clamp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 109
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for 3'-5' exonuclease activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 111
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for 3'-5' exonuclease activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 202
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for 3'-5' exonuclease activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 309
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic; for 3'-5' exonuclease activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 309
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic; for 3'-5' exonuclease activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 393
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 393
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 394
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 396..398
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 469
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 521
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 584
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT BINDING 584
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT SITE 582
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT SITE 658
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
FT SITE 666
FT /note="Essential for viral replication"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100"
SQ SEQUENCE 850 AA; 98413 MW; 03A7599EF571E470 CRC64;
MTIYTSIERI GSNLCERYID DDGFEHMRKV KYEPTLFIHC NEETGYKDIY GRNCRPKMFD
TMGEASKYIK ETKQFNEVLG MDDFIVTYIS DVYKQREFDM SRIRIANIDI ETPSVEFPEA
AHAPVPITSI GHYDNIDDKF YVYGIPSNTE WKRESSIVKP ELLEKTVYIR CATEKELLVK
YLQFWREKTP AIVTGWNIES FDMPYIVNRY KNLFGEKVMN SLSPWGKVQV STTVNDYGQE
ICKVNILGVS ELDYLQLYKK FTYVTRPSYR LDYIGEVELD EKKVEFEQAN YLEFYEQDYQ
NFIDYQIQDV NLVKRLDEKL QLMLLTISLA YYAGINYQTV LGTIKPWDAI IFNSLKAEKK
VVPMMRSHEG GRFMGAFVKA PQVGYHRGIG SFDLTSLYPS IIRECNISPE TIVGQLDYEG
SLEDRIDKIV EGLITFPADE LSNSANGMQY RKDVRGVIPV EIEKVFFQRK ANKKKAFEYE
QQAIDIQKQM DEQGETPELR AAYEEAKHQA KIYDVQQMAR KILINSLYGA LGNEYFRFYD
LRNAEAVTAY GQLAIKWVAR DVNIWLNKVC KTTDKDYVIY GDTDSIYVNF DPLLELTGIN
KLEGDDYTDK FAKVCETVET KVINPSYEAL HKYMNTYERQ MFMDREVLAR TGFFIAKKRY
ALDVQDNEGI RKPKLKIMGI ETQRSSTPPL CQKGLKEAIR LILQEGEAKL QEFVKGYEKE
FKAAPYQEVS FVSSANNMNK YSDDKGNPGK GCPGHVKGAL YYNKLAEEHG FDKINEGDKI
AVVFLTRNKH GIDRIAYPSG GKLPEAISYL IDHVDYNRLY EDKFIKPLSA ISEAIKFDYK
KTITLESFFG
