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DNA-directed DNA polymerase (EC 2.7.7.7) (EC 3.1.11.-) (Gene product 43) (Gp43)

 DPOL_BPT4               Reviewed;         898 AA.
P04415;
13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
01-JAN-1988, sequence version 1.
28-FEB-2018, entry version 138.
RecName: Full=DNA-directed DNA polymerase {ECO:0000255|HAMAP-Rule:MF_04100};
EC=2.7.7.7 {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:1332748};
EC=3.1.11.- {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:10455197, ECO:0000269|PubMed:1332748, ECO:0000269|PubMed:15037066, ECO:0000269|PubMed:8262948};
AltName: Full=Gene product 43;
Short=Gp43;
Name=43;
Enterobacteria phage T4 (Bacteriophage T4).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;
Tevenvirinae; T4virus.
NCBI_TaxID=10665;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3286635;
Spicer E.K., Rush J., Fung C., Reha-Krantz L.J., Karam J.D.,
Konigsberg W.H.;
"Primary structure of T4 DNA polymerase. Evolutionary relatedness to
eucaryotic and other procaryotic DNA polymerases.";
J. Biol. Chem. 263:7478-7486(1988).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3054876; DOI=10.1073/pnas.85.21.7942;
Andrake M., Guild N., Hsu T., Gold L., Tuerk C., Karam J.;
"DNA polymerase of bacteriophage T4 is an autogenous translational
repressor.";
Proc. Natl. Acad. Sci. U.S.A. 85:7942-7946(1988).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=12626685; DOI=10.1128/MMBR.67.1.86-156.2003;
Miller E.S., Kutter E., Mosig G., Arisaka F., Kunisawa T., Ruger W.;
"Bacteriophage T4 genome.";
Microbiol. Mol. Biol. Rev. 67:86-156(2003).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 338-898.
PubMed=3350013; DOI=10.1111/j.1432-1033.1988.tb13925.x;
Lamm N., Wang Y., Mathews C.K., Rueger W.;
"Deoxycytidylate hydroxymethylase gene of bacteriophage T4. Nucleotide
sequence determination and over-expression of the gene.";
Eur. J. Biochem. 172:553-563(1988).
[5]
CATALYTIC ACTIVITY, AND FUNCTION.
PubMed=1332748; DOI=10.1021/bi00160a007;
Capson T.L., Peliska J.A., Kaboord B.F., Frey M.W., Lively C.,
Dahlberg M., Benkovic S.J.;
"Kinetic characterization of the polymerase and exonuclease activities
of the gene 43 protein of bacteriophage T4.";
Biochemistry 31:10984-10994(1992).
[6]
INTERACTION WITH THE POLYMERASE CLAMP.
PubMed=8475061; DOI=10.1073/pnas.90.8.3211;
Reddy M.K., Weitzel S.E., von Hippel P.H.;
"Assembly of a functional replication complex without ATP hydrolysis:
a direct interaction of bacteriophage T4 gp45 with T4 DNA
polymerase.";
Proc. Natl. Acad. Sci. U.S.A. 90:3211-3215(1993).
[7]
MUTAGENESIS OF ASP-112; GLU-114; ASP-219 AND ASP-324, AND CATALYTIC
ACTIVITY.
PubMed=8262948;
Reha-Krantz L.J., Nonay R.L.;
"Genetic and biochemical studies of bacteriophage T4 DNA polymerase
3'-->5'-exonuclease activity.";
J. Biol. Chem. 268:27100-27108(1993).
[8]
DOMAIN.
PubMed=7592876; DOI=10.1074/jbc.270.44.26558;
Wang C.C., Yeh L.-S., Karam J.D.;
"Modular organization of T4 DNA polymerase. Evidence from
phylogenetics.";
J. Biol. Chem. 270:26558-26564(1995).
[9]
INTERACTION WITH THE POLYMERASE CLAMP.
PubMed=8917503; DOI=10.1073/pnas.93.23.12822;
Berdis A.J., Soumillion P., Benkovic S.J.;
"The carboxyl terminus of the bacteriophage T4 DNA polymerase is
required for holoenzyme complex formation.";
Proc. Natl. Acad. Sci. U.S.A. 93:12822-12827(1996).
[10]
COFACTOR.
PubMed=9665720; DOI=10.1021/bi980074b;
Beechem J.M., Otto M.R., Bloom L.B., Eritja R., Reha-Krantz L.J.,
Goodman M.F.;
"Exonuclease-polymerase active site partitioning of primer-template
DNA strands and equilibrium Mg2+ binding properties of bacteriophage
T4 DNA polymerase.";
Biochemistry 37:10144-10155(1998).
[11]
SUBUNIT.
PubMed=16800624; DOI=10.1021/bi0603322;
Smiley R.D., Zhuang Z., Benkovic S.J., Hammes G.G.;
"Single-molecule investigation of the T4 bacteriophage DNA polymerase
holoenzyme: multiple pathways of holoenzyme formation.";
Biochemistry 45:7990-7997(2006).
[12]
CATALYTIC ACTIVITY.
PubMed=10455197; DOI=10.1074/jbc.274.35.25151;
Elisseeva E., Mandal S.S., Reha-Krantz L.J.;
"Mutational and pH studies of the 3' --> 5' exonuclease activity of
bacteriophage T4 DNA polymerase.";
J. Biol. Chem. 274:25151-25158(1999).
[13]
FUNCTION, MUTAGENESIS OF ASP-219, AND CATALYTIC ACTIVITY.
PubMed=15037066; DOI=10.1016/j.jmb.2004.01.005;
Tanguy Le Gac N., Delagoutte E., Germain M., Villani G.;
"Inactivation of the 3'-5' exonuclease of the replicative T4 DNA
polymerase allows translesion DNA synthesis at an abasic site.";
J. Mol. Biol. 336:1023-1034(2004).
[14]
REVIEW.
PubMed=21129204; DOI=10.1186/1743-422X-7-359;
Mueser T.C., Hinerman J.M., Devos J.M., Boyer R.A., Williams K.J.;
"Structural analysis of bacteriophage T4 DNA replication: a review in
the Virology Journal series on bacteriophage T4 and its relatives.";
Virol. J. 7:359-359(2010).
[15]
DOMAIN.
PubMed=25753811; DOI=10.1016/j.dnarep.2015.02.014;
Darmawan H., Harrison M., Reha-Krantz L.J.;
"DNA polymerase 3'->5' exonuclease activity: Different roles of the
beta hairpin structure in family-B DNA polymerases.";
DNA Repair 29:36-46(2015).
[16]
REVIEW, AND SUBUNIT.
PubMed=26102578; DOI=10.3390/v7062766;
Noble E., Spiering M.M., Benkovic S.J.;
"Coordinated DNA replication by the bacteriophage T4 replisome.";
Viruses 7:3186-3200(2015).
[17]
X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-388.
PubMed=8679562; DOI=10.1021/bi960178r;
Wang J., Yu P., Lin T.C., Konigsberg W.H., Steitz T.A.;
"Crystal structures of an NH2-terminal fragment of T4 DNA polymerase
and its complexes with single-stranded DNA and with divalent metal
ions.";
Biochemistry 35:8110-8119(1996).
-!- 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:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:1332748,
ECO:0000269|PubMed:15037066}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:1332748}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:9665720};
-!- SUBUNIT: Part of the replicase complex that includes the DNA
polymerase, the polymerase clamp, the clamp loader complex, the
single-stranded DNA binding protein, the primase, the helicase and
the helicase assembly factor (PubMed:16800624). Interacts with the
polymerase clamp; this interaction constitutes the polymerase
holoenzyme (PubMed:8475061, PubMed:8917503).
{ECO:0000269|PubMed:16800624, ECO:0000269|PubMed:8475061,
ECO:0000269|PubMed:8917503}.
-!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity
(PubMed:7592876). The C-terminus contains the polymerase activity
and is involved in binding to the polymerase clamp protein
(PubMed:7592876). A beta hairpin structure is necessary for the
proofreading function of the polymerase (PubMed:25753811).
{ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:25753811,
ECO:0000269|PubMed:7592876}.
-!- SIMILARITY: Belongs to the DNA polymerase type-B family.
{ECO:0000255|HAMAP-Rule:MF_04100}.
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EMBL; M10160; AAC05397.1; -; Genomic_DNA.
EMBL; X00769; CAA25344.1; -; Genomic_DNA.
EMBL; AF158101; AAD42468.1; -; Genomic_DNA.
EMBL; M37159; AAA21706.1; -; Genomic_DNA.
PIR; JS0791; DJBPT4.
RefSeq; NP_049662.1; NC_000866.4.
PDB; 1NOY; X-ray; 2.20 A; A/B=1-388.
PDB; 1NOZ; X-ray; 2.20 A; A/B=1-388.
PDBsum; 1NOY; -.
PDBsum; 1NOZ; -.
ProteinModelPortal; P04415; -.
SMR; P04415; -.
BindingDB; P04415; -.
ChEMBL; CHEMBL5946; -.
GeneID; 1258685; -.
KEGG; vg:1258685; -.
KO; K18942; -.
OrthoDB; VOG0900001M; -.
BRENDA; 2.7.7.7; 9245.
SABIO-RK; P04415; -.
EvolutionaryTrace; P04415; -.
PRO; PR:P04415; -.
Proteomes; UP000009087; Genome.
GO; GO:0008408; F:3'-5' exonuclease activity; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
GO; GO:0039686; P:bidirectional double-stranded viral DNA replication; IDA:UniProtKB.
GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
Gene3D; 3.30.420.10; -; 1.
HAMAP; MF_04100; DPOL_T4; 1.
InterPro; IPR006172; DNA-dir_DNA_pol_B.
InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
InterPro; IPR034749; DPOL_T4.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR036397; RNaseH_sf.
Pfam; PF00136; DNA_pol_B; 1.
Pfam; PF03104; DNA_pol_B_exo1; 1.
PRINTS; PR00106; DNAPOLB.
SMART; SM00486; POLBc; 1.
SUPFAM; SSF53098; SSF53098; 1.
PROSITE; PS00116; DNA_POLYMERASE_B; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; DNA replication; DNA-binding;
DNA-directed DNA polymerase; Exonuclease; Hydrolase; Magnesium;
Metal-binding; Multifunctional enzyme; Nuclease;
Nucleotidyltransferase; Reference proteome; Transferase;
Viral DNA replication.
CHAIN 1 898 DNA-directed DNA polymerase.
/FTId=PRO_0000046546.
REGION 101 337 3'-5'exonuclease. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:7592876}.
REGION 245 261 Beta hairpin. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:25753811}.
REGION 377 898 Polymerase. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:7592876}.
REGION 411 413 Substrate binding. {ECO:0000255|HAMAP-
Rule:MF_04100}.
REGION 702 705 Binding of DNA in B-conformation.
{ECO:0000255|HAMAP-Rule:MF_04100}.
REGION 893 898 Interaction with the polymerase clamp.
{ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:8917503}.
METAL 112 112 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:8679562}.
METAL 114 114 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:8679562}.
METAL 219 219 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:8679562}.
METAL 324 324 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:8679562}.
METAL 324 324 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:8679562}.
METAL 408 408 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
METAL 408 408 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
METAL 409 409 Magnesium 4; catalytic; via carbonyl
oxygen; for polymerase activity.
{ECO:0000255|HAMAP-Rule:MF_04100}.
METAL 620 620 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
METAL 620 620 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
BINDING 479 479 Substrate. {ECO:0000255|HAMAP-
Rule:MF_04100}.
BINDING 557 557 Substrate. {ECO:0000255|HAMAP-
Rule:MF_04100}.
SITE 618 618 Optimization of metal coordination by the
polymerase active site.
{ECO:0000255|HAMAP-Rule:MF_04100}.
SITE 703 703 Optimization of metal coordination by the
polymerase active site.
{ECO:0000255|HAMAP-Rule:MF_04100}.
SITE 711 711 Essential for viral replication.
{ECO:0000255|HAMAP-Rule:MF_04100}.
MUTAGEN 112 112 D->A: Almost complete loss of exonuclease
activity. Decreased replication fidelity.
{ECO:0000269|PubMed:8262948}.
MUTAGEN 114 114 E->A: Almost complete loss of exonuclease
activity. Decreased replication fidelity.
{ECO:0000269|PubMed:8262948}.
MUTAGEN 219 219 D->A: Almost complete loss of exonuclease
activity. Decreased replication fidelity.
{ECO:0000269|PubMed:15037066,
ECO:0000269|PubMed:8262948}.
MUTAGEN 324 324 D->A: Almost complete loss of exonuclease
activity. Decreased replication fidelity.
{ECO:0000269|PubMed:8262948}.
CONFLICT 89 89 A -> V (in Ref. 2; CAA25344).
{ECO:0000305}.
STRAND 4 11 {ECO:0000244|PDB:1NOY}.
STRAND 14 20 {ECO:0000244|PDB:1NOY}.
STRAND 26 32 {ECO:0000244|PDB:1NOY}.
STRAND 36 38 {ECO:0000244|PDB:1NOY}.
HELIX 40 43 {ECO:0000244|PDB:1NOY}.
TURN 49 52 {ECO:0000244|PDB:1NOY}.
HELIX 63 76 {ECO:0000244|PDB:1NOY}.
HELIX 82 94 {ECO:0000244|PDB:1NOY}.
HELIX 103 105 {ECO:0000244|PDB:1NOY}.
STRAND 108 115 {ECO:0000244|PDB:1NOY}.
TURN 123 125 {ECO:0000244|PDB:1NOY}.
STRAND 130 137 {ECO:0000244|PDB:1NOY}.
TURN 138 141 {ECO:0000244|PDB:1NOY}.
STRAND 142 148 {ECO:0000244|PDB:1NOY}.
STRAND 150 153 {ECO:0000244|PDB:1NOZ}.
HELIX 161 165 {ECO:0000244|PDB:1NOY}.
HELIX 168 170 {ECO:0000244|PDB:1NOY}.
HELIX 177 180 {ECO:0000244|PDB:1NOY}.
STRAND 183 189 {ECO:0000244|PDB:1NOY}.
HELIX 191 204 {ECO:0000244|PDB:1NOY}.
STRAND 208 211 {ECO:0000244|PDB:1NOY}.
TURN 215 218 {ECO:0000244|PDB:1NOY}.
HELIX 219 236 {ECO:0000244|PDB:1NOY}.
HELIX 237 239 {ECO:0000244|PDB:1NOY}.
STRAND 245 249 {ECO:0000244|PDB:1NOY}.
HELIX 252 254 {ECO:0000244|PDB:1NOY}.
STRAND 258 262 {ECO:0000244|PDB:1NOY}.
STRAND 265 267 {ECO:0000244|PDB:1NOY}.
HELIX 270 277 {ECO:0000244|PDB:1NOY}.
HELIX 287 295 {ECO:0000244|PDB:1NOY}.
HELIX 306 308 {ECO:0000244|PDB:1NOY}.
HELIX 309 335 {ECO:0000244|PDB:1NOY}.
HELIX 337 348 {ECO:0000244|PDB:1NOY}.
HELIX 352 356 {ECO:0000244|PDB:1NOY}.
HELIX 358 369 {ECO:0000244|PDB:1NOY}.
SEQUENCE 898 AA; 103610 MW; 925300C4CA5C7A24 CRC64;
MKEFYISIET VGNNIVERYI DENGKERTRE VEYLPTMFRH CKEESKYKDI YGKNCAPQKF
PSMKDARDWM KRMEDIGLEA LGMNDFKLAY ISDTYGSEIV YDRKFVRVAN CDIEVTGDKF
PDPMKAEYEI DAITHYDSID DRFYVFDLLN SMYGSVSKWD AKLAAKLDCE GGDEVPQEIL
DRVIYMPFDN ERDMLMEYIN LWEQKRPAIF TGWNIEGFDV PYIMNRVKMI LGERSMKRFS
PIGRVKSKLI QNMYGSKEIY SIDGVSILDY LDLYKKFAFT NLPSFSLESV AQHETKKGKL
PYDGPINKLR ETNHQRYISY NIIDVESVQA IDKIRGFIDL VLSMSYYAKM PFSGVMSPIK
TWDAIIFNSL KGEHKVIPQQ GSHVKQSFPG AFVFEPKPIA RRYIMSFDLT SLYPSIIRQV
NISPETIRGQ FKVHPIHEYI AGTAPKPSDE YSCSPNGWMY DKHQEGIIPK EIAKVFFQRK
DWKKKMFAEE MNAEAIKKII MKGAGSCSTK PEVERYVKFS DDFLNELSNY TESVLNSLIE
ECEKAATLAN TNQLNRKILI NSLYGALGNI HFRYYDLRNA TAITIFGQVG IQWIARKINE
YLNKVCGTND EDFIAAGDTD SVYVCVDKVI EKVGLDRFKE QNDLVEFMNQ FGKKKMEPMI
DVAYRELCDY MNNREHLMHM DREAISCPPL GSKGVGGFWK AKKRYALNVY DMEDKRFAEP
HLKIMGMETQ QSSTPKAVQE ALEESIRRIL QEGEESVQEY YKNFEKEYRQ LDYKVIAEVK
TANDIAKYDD KGWPGFKCPF HIRGVLTYRR AVSGLGVAPI LDGNKVMVLP LREGNPFGDK
CIAWPSGTEL PKEIRSDVLS WIDHSTLFQK SFVKPLAGMC ESAGMDYEEK ASLDFLFG


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