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DNA-directed DNA polymerase (EC 2.7.7.7) (EC 3.1.11.-)

 A0A1D7RA97_9CAUD        Unreviewed;       832 AA.
A0A1D7RA97;
18-JAN-2017, integrated into UniProtKB/TrEMBL.
18-JAN-2017, sequence version 1.
27-SEP-2017, entry version 7.
RecName: Full=DNA-directed DNA polymerase {ECO:0000256|HAMAP-Rule:MF_04100};
EC=2.7.7.7 {ECO:0000256|HAMAP-Rule:MF_04100};
EC=3.1.11.- {ECO:0000256|HAMAP-Rule:MF_04100};
ORFNames=Fa020709_165 {ECO:0000313|EMBL:AON97678.1},
Fa100709_165 {ECO:0000313|EMBL:AON97892.1},
Fa240709_165 {ECO:0000313|EMBL:AON98106.1},
LIS011010_166 {ECO:0000313|EMBL:AON98321.1},
LIS061010_167 {ECO:0000313|EMBL:AON98752.1},
LIS121010_166 {ECO:0000313|EMBL:AON99395.1},
LIS141013_165 {ECO:0000313|EMBL:AON99609.1},
NJ_05_1013_164 {ECO:0000313|EMBL:AON99822.1},
Np011112_165 {ECO:0000313|EMBL:AOO00251.1},
Np111112_166 {ECO:0000313|EMBL:AOO01320.1},
Np140912_165 {ECO:0000313|EMBL:AOO01748.1},
Np150709_165 {ECO:0000313|EMBL:AOO01962.1},
Np361112_165 {ECO:0000313|EMBL:AOO03673.1},
RW020113_165 {ECO:0000313|EMBL:AOO04101.1},
RW030709_165 {ECO:0000313|EMBL:AOO04529.1},
RW081112_164 {ECO:0000313|EMBL:AOO04742.1},
RW110905_165 {ECO:0000313|EMBL:AOO04956.1},
RW120113_165 {ECO:0000313|EMBL:AOO05170.1},
RW120709_165 {ECO:0000313|EMBL:AOO05384.1},
RW160905_165 {ECO:0000313|EMBL:AOO05812.1},
RW300905_165 {ECO:0000313|EMBL:AOO06667.1},
RW340905_165 {ECO:0000313|EMBL:AOO06881.1},
RW401112_165 {ECO:0000313|EMBL:AOO07095.1},
W1010709_165 {ECO:0000313|EMBL:AOO07523.1},
W1010910_166 {ECO:0000313|EMBL:AOO07738.1},
W1030709_167 {ECO:0000313|EMBL:AOO07954.1},
W1080709_166 {ECO:0000313|EMBL:AOO08169.1},
W1090709_165 {ECO:0000313|EMBL:AOO08383.1},
W1120909_166 {ECO:0000313|EMBL:AOO08598.1},
W1130709_166 {ECO:0000313|EMBL:AOO08813.1},
W1160709_165 {ECO:0000313|EMBL:AOO09027.1},
W2020709_166 {ECO:0000313|EMBL:AOO09242.1},
W2130910_165 {ECO:0000313|EMBL:AOO09456.1},
W2140910_165 {ECO:0000313|EMBL:AOO09670.1},
W2320910_166 {ECO:0000313|EMBL:AOO09885.1},
W2390910_166 {ECO:0000313|EMBL:AOO10100.1};
Synechococcus phage S-RIM2.
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae.
NCBI_TaxID=687800 {ECO:0000313|EMBL:AON98321.1};
[1] {ECO:0000313|EMBL:AON98321.1}
NUCLEOTIDE SEQUENCE.
STRAIN=Fa_02_0709 {ECO:0000313|EMBL:AON97678.1},
Fa_10_0709 {ECO:0000313|EMBL:AON97892.1},
Fa_24_0709 {ECO:0000313|EMBL:AON98106.1},
LIS_01_1010 {ECO:0000313|EMBL:AON98321.1},
LIS_06_1010 {ECO:0000313|EMBL:AON98752.1},
LIS_12_1010 {ECO:0000313|EMBL:AON99395.1},
LIS_14_1013 {ECO:0000313|EMBL:AON99609.1},
NJ_05_1013 {ECO:0000313|EMBL:AON99822.1},
Np_01_1112 {ECO:0000313|EMBL:AOO00251.1},
Np_11_1112 {ECO:0000313|EMBL:AOO01320.1},
Np_14_0912 {ECO:0000313|EMBL:AOO01748.1},
Np_15_0709 {ECO:0000313|EMBL:AOO01962.1},
Np_36_1112 {ECO:0000313|EMBL:AOO03673.1},
RW_02_0113 {ECO:0000313|EMBL:AOO04101.1},
RW_03_0709 {ECO:0000313|EMBL:AOO04529.1},
RW_08_1112 {ECO:0000313|EMBL:AOO04742.1},
RW_11_0905 {ECO:0000313|EMBL:AOO04956.1},
RW_12_0113 {ECO:0000313|EMBL:AOO05170.1},
RW_12_0709 {ECO:0000313|EMBL:AOO05384.1},
RW_16_0905 {ECO:0000313|EMBL:AOO05812.1},
RW_30_0905 {ECO:0000313|EMBL:AOO06667.1},
RW_34_0905 {ECO:0000313|EMBL:AOO06881.1},
RW_40_1112 {ECO:0000313|EMBL:AOO07095.1},
W1_01_0709 {ECO:0000313|EMBL:AOO07523.1},
W1_01_0910 {ECO:0000313|EMBL:AOO07738.1},
W1_03_0709 {ECO:0000313|EMBL:AOO07954.1},
W1_08_0709 {ECO:0000313|EMBL:AOO08169.1},
W1_09_0709 {ECO:0000313|EMBL:AOO08383.1},
W1_12_0909 {ECO:0000313|EMBL:AOO08598.1},
W1_13_0709 {ECO:0000313|EMBL:AOO08813.1},
W1_16_0709 {ECO:0000313|EMBL:AOO09027.1},
W2_02_0709 {ECO:0000313|EMBL:AOO09242.1},
W2_13_0910 {ECO:0000313|EMBL:AOO09456.1},
W2_14_0910 {ECO:0000313|EMBL:AOO09670.1},
W2_32_0910 {ECO:0000313|EMBL:AOO09885.1}, and
W2_39_0910 {ECO:0000313|EMBL:AOO10100.1};
PubMed=27696643;
Marston M.F., Martiny J.B.;
"Genomic diversification of marine cyanophages into stable ecotypes.";
Environ. Microbiol. 0:0-0(2016).
-!- FUNCTION: Replicates the viral genomic DNA. This polymerase
possesses two enzymatic activities: DNA synthesis (polymerase) and
an exonucleolytic activity that degrades single-stranded DNA in
the 3'- to 5'-direction for proofreading purpose.
{ECO:0000256|HAMAP-Rule:MF_04100}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000256|HAMAP-Rule:MF_04100}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|HAMAP-Rule:MF_04100};
-!- SUBUNIT: Part of the replicase complex that includes the DNA
polymerase, the polymerase clamp, the clamp loader complex, the
single-stranded DNA binding protein, and the primase/helicase.
Interacts with the polymerase clamp; this interaction constitutes
the polymerase holoenzyme. {ECO:0000256|HAMAP-Rule:MF_04100}.
-!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity.
The C-terminus contains the polymerase activity and is involved in
binding to the polymerase clamp protein. A beta hairpin structure
is necessary for the proofreading function of the polymerase.
{ECO:0000256|HAMAP-Rule:MF_04100}.
-!- SIMILARITY: Belongs to the DNA polymerase type-B family.
{ECO:0000256|HAMAP-Rule:MF_04100}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_04100}.
-----------------------------------------------------------------------
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EMBL; KX349226; AON97678.1; -; Genomic_DNA.
EMBL; KX349227; AON97892.1; -; Genomic_DNA.
EMBL; KX349228; AON98106.1; -; Genomic_DNA.
EMBL; KX349229; AON98321.1; -; Genomic_DNA.
EMBL; KX349231; AON98752.1; -; Genomic_DNA.
EMBL; KX349234; AON99395.1; -; Genomic_DNA.
EMBL; KX349235; AON99609.1; -; Genomic_DNA.
EMBL; KX349236; AON99822.1; -; Genomic_DNA.
EMBL; KX349238; AOO00251.1; -; Genomic_DNA.
EMBL; KX349243; AOO01320.1; -; Genomic_DNA.
EMBL; KX349245; AOO01748.1; -; Genomic_DNA.
EMBL; KX349246; AOO01962.1; -; Genomic_DNA.
EMBL; KX349254; AOO03673.1; -; Genomic_DNA.
EMBL; KX349256; AOO04101.1; -; Genomic_DNA.
EMBL; KX349258; AOO04529.1; -; Genomic_DNA.
EMBL; KX349259; AOO04742.1; -; Genomic_DNA.
EMBL; KX349260; AOO04956.1; -; Genomic_DNA.
EMBL; KX349261; AOO05170.1; -; Genomic_DNA.
EMBL; KX349262; AOO05384.1; -; Genomic_DNA.
EMBL; KX349264; AOO05812.1; -; Genomic_DNA.
EMBL; KX349268; AOO06667.1; -; Genomic_DNA.
EMBL; KX349269; AOO06881.1; -; Genomic_DNA.
EMBL; KX349270; AOO07095.1; -; Genomic_DNA.
EMBL; KX349272; AOO07523.1; -; Genomic_DNA.
EMBL; KX349273; AOO07738.1; -; Genomic_DNA.
EMBL; KX349274; AOO07954.1; -; Genomic_DNA.
EMBL; KX349275; AOO08169.1; -; Genomic_DNA.
EMBL; KX349276; AOO08383.1; -; Genomic_DNA.
EMBL; KX349277; AOO08598.1; -; Genomic_DNA.
EMBL; KX349278; AOO08813.1; -; Genomic_DNA.
EMBL; KX349279; AOO09027.1; -; Genomic_DNA.
EMBL; KX349280; AOO09242.1; -; Genomic_DNA.
EMBL; KX349281; AOO09456.1; -; Genomic_DNA.
EMBL; KX349282; AOO09670.1; -; Genomic_DNA.
EMBL; KX349283; AOO09885.1; -; Genomic_DNA.
EMBL; KX349284; AOO10100.1; -; Genomic_DNA.
GO; GO:0008408; F:3'-5' exonuclease activity; IEA:UniProtKB-UniRule.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-UniRule.
GO; GO:0039686; P:bidirectional double-stranded viral DNA replication; IEA:UniProtKB-UniRule.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
Gene3D; 3.90.1600.10; -; 1.
HAMAP; MF_04100; DPOL_T4; 1.
InterPro; IPR006172; DNA-dir_DNA_pol_B.
InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
InterPro; IPR023211; DNA_pol_palm_dom.
InterPro; IPR034749; DPOL_T4.
InterPro; IPR012337; RNaseH-like_dom.
Pfam; PF00136; DNA_pol_B; 1.
Pfam; PF03104; DNA_pol_B_exo1; 1.
PRINTS; PR00106; DNAPOLB.
SMART; SM00486; POLBc; 1.
SUPFAM; SSF53098; SSF53098; 1.
3: Inferred from homology;
DNA replication {ECO:0000256|HAMAP-Rule:MF_04100};
DNA-binding {ECO:0000256|HAMAP-Rule:MF_04100};
DNA-directed DNA polymerase {ECO:0000256|HAMAP-Rule:MF_04100};
Exonuclease {ECO:0000256|HAMAP-Rule:MF_04100};
Hydrolase {ECO:0000256|HAMAP-Rule:MF_04100};
Magnesium {ECO:0000256|HAMAP-Rule:MF_04100};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_04100};
Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_04100};
Nuclease {ECO:0000256|HAMAP-Rule:MF_04100};
Nucleotidyltransferase {ECO:0000256|HAMAP-Rule:MF_04100};
Transferase {ECO:0000256|HAMAP-Rule:MF_04100};
Viral DNA replication {ECO:0000256|HAMAP-Rule:MF_04100}.
DOMAIN 104 265 DNA_pol_B_exo1.
{ECO:0000259|Pfam:PF03104}.
DOMAIN 340 815 DNA_pol_B. {ECO:0000259|Pfam:PF00136}.
REGION 220 236 Beta hairpin. {ECO:0000256|HAMAP-
Rule:MF_04100}.
REGION 354 832 Polymerase. {ECO:0000256|HAMAP-
Rule:MF_04100}.
REGION 389 391 Substrate binding. {ECO:0000256|HAMAP-
Rule:MF_04100}.
REGION 635 638 Binding of DNA in B-conformation.
{ECO:0000256|HAMAP-Rule:MF_04100}.
REGION 827 832 Interaction with the polymerase clamp.
{ECO:0000256|HAMAP-Rule:MF_04100}.
METAL 112 112 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 114 114 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 194 194 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 301 301 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 301 301 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 386 386 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 386 386 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 387 387 Magnesium 4; catalytic; via carbonyl
oxygen; for polymerase activity.
{ECO:0000256|HAMAP-Rule:MF_04100}.
METAL 561 561 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
METAL 561 561 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000256|HAMAP-
Rule:MF_04100}.
BINDING 457 457 Substrate. {ECO:0000256|HAMAP-
Rule:MF_04100}.
BINDING 498 498 Substrate. {ECO:0000256|HAMAP-
Rule:MF_04100}.
SITE 559 559 Optimization of metal coordination by the
polymerase active site.
{ECO:0000256|HAMAP-Rule:MF_04100}.
SITE 636 636 Optimization of metal coordination by the
polymerase active site.
{ECO:0000256|HAMAP-Rule:MF_04100}.
SITE 644 644 Essential for viral replication.
{ECO:0000256|HAMAP-Rule:MF_04100}.
SEQUENCE 832 AA; 97283 MW; 8C06CFCEB857B87A CRC64;
MSSFYTNIQL AGDTILYRGY EDGKPISYRA NFAPTLYVLS RKQEDFRTLG GKYVSPIKFQ
TAREARDFIK QYDGVEGFEV HGYERFVYQY IRQEFPGEVD YNINQMKIYA MDIEVQCENG
FPNVEEAAEE MLSITIKDMV TKQYYCWATR EFEAPKGVET HIFWTEHEML NHFLEWWVQN
TPDILTGWNV NLYDVPYIAR RVCRVLGEKW MKSLSPWNRA NEREVYVQGR KNYAYDISGV
NILDYLDLYR KFTYSNQESY RLDHIAFVEL GQRKVDHSEY ENFKDFYTSD WQKFMEYNIQ
DVELIDRLED KMKLLELAIT MSYDAKVNFE DVYSQVRMWD TMIYNYLTDR NVVVPPRKGA
KKDEKYAGAY VKEPIPGKYD WVVSFDLNSL YPHLIMQYNI SPETLIDARH PTATVDRILE
ETLNVDGEYC VCANGAQYRK DIHGFLPEMM QKIYDERTIY KKRMLAAKQS LEHAKTPAET
SSLQKDISKF NNIQMARKIQ LNSAYGAIGN QYFRYYNLAN AEAITLSGQV SIRWIEGKVN
SYLNKLLKTE DHDYVIASDT DSIYICLDLL VRSVFNAQDV PAERIVNFLD AACKDRIEPF
IDRSYKELAD YVGAYEQKMS MKRENIANKG IWTAKKRYIL NVWDSEGVRY EKPKLKIMGL
EAVKSSTPAA CRTAIKECMT VIMNKEEEDA QAFIAKFKDE FSSLPVEDIS FPRGCNGINK
WSNPATIYSK GTPIHVRGAL LYNFYNKKNK LTHKYPLIQD GEKIKFVYLK TPNKINENVI
SYLNTFPKEF GLDKQVDYDL QFSKSFLDPI KVIMDTIGWQ AEKVASLEFL FG


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