ID M4T0C3_9CAUD Unreviewed; 832 AA.
AC M4T0C3;
DT 29-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 29-MAY-2013, sequence version 1.
DT 24-JAN-2024, entry version 45.
DE RecName: Full=DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00012417, ECO:0000256|HAMAP-Rule:MF_04100};
DE EC=2.7.7.7 {ECO:0000256|ARBA:ARBA00012417, ECO:0000256|HAMAP-Rule:MF_04100};
DE EC=3.1.11.- {ECO:0000256|HAMAP-Rule:MF_04100};
GN ORFNames=CPRG_00130 {ECO:0000313|EMBL:AGH56214.1};
OS Synechococcus phage Syn30.
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Kyanoviridae; Leucotheavirus; Leucotheavirus syn30.
OX NCBI_TaxID=536474 {ECO:0000313|EMBL:AGH56214.1, ECO:0000313|Proteomes:UP000203676};
RN [1] {ECO:0000313|EMBL:AGH56214.1, ECO:0000313|Proteomes:UP000203676}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Syn30 {ECO:0000313|EMBL:AGH56214.1,
RC ECO:0000313|Proteomes:UP000203676};
RG The Broad Institute Genome Sequencing Platform;
RA Henn M.R., Sullivan M.S., Osburne M.S., Levin J., Malboeuf C., Casali M.,
RA Russ C., Lennon N., Chapman S.B., Erlich R., Young S.K., Yandava C.,
RA Zeng Q., Alvarado L., Anderson S., Berlin A., Chen Z., Freedman E.,
RA Gellesch M., Goldberg J., Green L., Griggs A., Gujja S., Heilman E.R.,
RA Heiman D., Hollinger A., Howarth C., Larson L., Mehta T., Pearson M.,
RA Roberts A., Ryan E., Saif S., Shea T., Shenoy N., Sisk P., Stolte C.,
RA Sykes S., White J., Yu Q., Coleman M.L., Huang K.H., Weigele P.R.,
RA DeFrancesco A.S., Kern S.E., Thompson L.R., Fu R., Hombeck B.,
RA Chisholm S.W., Haas B., Nusbaum C., Birren B.;
RT "The Genome Sequence of Cyanophage Syn30.";
RL Submitted (NOV-2010) to the EMBL/GenBank/DDBJ databases.
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00024632, ECO:0000256|HAMAP-
CC Rule:MF_04100};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|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:0000256|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:0000256|HAMAP-
CC Rule:MF_04100}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family.
CC {ECO:0000256|ARBA:ARBA00005755, ECO:0000256|HAMAP-Rule:MF_04100}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_04100}.
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DR EMBL; HQ634189; AGH56214.1; -; Genomic_DNA.
DR RefSeq; YP_007877894.1; NC_021072.1.
DR GeneID; 15312320; -.
DR KEGG; vg:15312320; -.
DR OrthoDB; 165at10239; -.
DR Proteomes; UP000203676; 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; 1.20.1280.300; -; 1.
DR Gene3D; 3.30.342.10; DNA Polymerase, chain B, domain 1; 1.
DR Gene3D; 3.40.1820.10; DnaQ-like 3'-5' exonuclease; 1.
DR Gene3D; 3.90.1600.10; Palm domain of DNA polymerase; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR HAMAP; MF_04100; DPOL_T4; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
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 PANTHER; PTHR10322; DNA POLYMERASE CATALYTIC SUBUNIT; 1.
DR PANTHER; PTHR10322:SF23; DNA POLYMERASE DELTA CATALYTIC SUBUNIT; 1.
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; SSF56672; DNA/RNA polymerases; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
PE 3: Inferred from homology;
KW DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW Rule:MF_04100};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_04100};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932,
KW ECO:0000256|HAMAP-Rule:MF_04100};
KW Exonuclease {ECO:0000256|HAMAP-Rule:MF_04100};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_04100};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_04100};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_04100};
KW Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_04100};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|HAMAP-Rule:MF_04100};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695, ECO:0000256|HAMAP-
KW Rule:MF_04100}; Reference proteome {ECO:0000313|Proteomes:UP000203676};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_04100};
KW Viral DNA replication {ECO:0000256|ARBA:ARBA00023109, ECO:0000256|HAMAP-
KW Rule:MF_04100}.
FT DOMAIN 104..265
FT /note="DNA-directed DNA polymerase family B exonuclease"
FT /evidence="ECO:0000259|Pfam:PF03104"
FT DOMAIN 342..568
FT /note="DNA-directed DNA polymerase family B
FT multifunctional"
FT /evidence="ECO:0000259|Pfam:PF00136"
FT REGION 220..236
FT /note="Beta hairpin"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT REGION 354..832
FT /note="Polymerase"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT REGION 635..638
FT /note="Binding of DNA in B-conformation"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT REGION 827..832
FT /note="Interaction with the polymerase clamp"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 112
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:0000256|HAMAP-Rule:MF_04100"
FT BINDING 114
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:0000256|HAMAP-Rule:MF_04100"
FT BINDING 194
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:0000256|HAMAP-Rule:MF_04100"
FT BINDING 301
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:0000256|HAMAP-Rule:MF_04100"
FT BINDING 301
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:0000256|HAMAP-Rule:MF_04100"
FT BINDING 386
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 386
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 387
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 389..391
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 457
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 498
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 561
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="3"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT BINDING 561
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="4"
FT /ligand_note="catalytic; for polymerase activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT SITE 559
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT SITE 636
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
FT SITE 644
FT /note="Essential for viral replication"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_04100"
SQ SEQUENCE 832 AA; 97494 MW; 0EB6CC25FD6A602A CRC64;
MSSFYTNIQL AGDTILYRGY EDGQPVQFRA HFSPTLYVLS KNTEEYKTLD GRNVSPIDFT
NTRSAREFIK QYDGVEGFEI HGYDRFVYQY IRREFPGEVD YDISQMKIYA MDIEVQCENG
FPNVEEAAEE MLSITIKDMV TKQYYCWCTR EFEAPKGVKA EFFWTEHEML SNFLKWWGEN
TPDILTGWNV NLYDVPYIAR RVCRVLGEKW MKGLSPWNRA NEREVYVKGR KNIAYDISGV
NILDYLDLYR KFTYSNQESY RLDHIAFVEL GQRKVDHSEY ENFKDFYTRD WQKFMEYNIQ
DVELIDRLED KMKLLELAIT MSYDAKVNFE DVYSQVRMWD TMIYNYLTDR HIVVPPKKGA
KKDEKYAGAY VKEPIPGKYD WVVSFDLNSL YPHLIMQYNI SPETLVDARH PTATVDKILG
QQINVDKEYC VCANGAQYRK DVHGFLPEMM QEIYNERTIY KKRMLESKQA LEHATTPAET
LALQKDISKF NNIQMARKIQ LNSAYGAIGN QYFRYYNLAN AEAITLSGQV SIRWIEGKVN
QYLNKLLKTE DHDYVIASDT DSIYICLDLL VRSVFDGKDV SKERIVNFLD TACKERIEPY
IDKSYKELAD YVGAYEQKMF MKRENIANKG IWTAKKRYIL NVWDSEGVRY EKPKLKIMGL
EAVKSSTPAA CRTAIRECMK VIMNESEEQA QKFIADFREQ FSSLPIEDIS FPRGCNGINK
WSHPVTIYGK GTPIHVRGAL LYNFHNKKNK LTHKYPLIQD GEKIKFVYLK TPNKIGENVI
SYLNTFPKEF GLDKQVDYDL QFSKSFLEPI KVIMDTIGWQ PEKVASLEFL FG
//
