DPOL_BPR69
ID DPOL_BPR69 Reviewed; 903 AA.
AC Q38087; Q76XX8;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 147.
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:0000269|PubMed:17098747, ECO:0000269|PubMed:18503083, ECO:0000269|PubMed:20795733, ECO:0000269|PubMed:22616982, ECO:0000269|PubMed:24116139};
DE EC=3.1.11.- {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:17098747, ECO:0000269|PubMed:23214497, ECO:0000269|PubMed:24116139};
DE AltName: Full=Gp43;
GN Name=43;
OS Escherichia phage RB69 (Bacteriophage RB69).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Myoviridae; Tevenvirinae; Mosigvirus.
OX NCBI_TaxID=12353;
OH NCBI_TaxID=562; Escherichia coli.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7592876; DOI=10.1074/jbc.270.44.26558;
RA Wang C.C., Yeh L.-S., Karam J.D.;
RT "Modular organization of T4 DNA polymerase. Evidence from phylogenetics.";
RL J. Biol. Chem. 270:26558-26564(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Petrov V., Nolan J., Chin D., Letarov A., Krisch H.M., Karam J.D.;
RT "Enterobacteria phage RB69 complete genome.";
RL Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP REVIEW.
RX PubMed=21129204; DOI=10.1186/1743-422x-7-359;
RA Mueser T.C., Hinerman J.M., Devos J.M., Boyer R.A., Williams K.J.;
RT "Structural analysis of bacteriophage T4 DNA replication: a review in the
RT Virology Journal series on bacteriophage T4 and its relatives.";
RL Virol. J. 7:359-359(2010).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND DOMAIN.
RX PubMed=9215631; DOI=10.1016/s0092-8674(00)80296-2;
RA Wang J., Sattar A.K., Wang C.C., Karam J.D., Konigsberg W.H., Steitz T.A.;
RT "Crystal structure of a pol alpha family replication DNA polymerase from
RT bacteriophage RB69.";
RL Cell 89:1087-1099(1997).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH THE POLYMERASE CLAMP,
RP AND INTERACTION WITH THE POLYMERASE CLAMP.
RX PubMed=10535734; DOI=10.1016/s0092-8674(00)81647-5;
RA Shamoo Y., Steitz T.A.;
RT "Building a replisome from interacting pieces: sliding clamp complexed to a
RT peptide from DNA polymerase and a polymerase editing complex.";
RL Cell 99:155-166(1999).
RN [6] {ECO:0007744|PDB:1IG9, ECO:0007744|PDB:1IH7}
RP X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP, AND
RP COFACTOR.
RX PubMed=11389835; DOI=10.1016/s0092-8674(01)00367-1;
RA Franklin M.C., Wang J., Steitz T.A.;
RT "Structure of the replicating complex of a pol alpha family DNA
RT polymerase.";
RL Cell 105:657-667(2001).
RN [7] {ECO:0007744|PDB:1Q9X, ECO:0007744|PDB:1Q9Y}
RP X-RAY CRYSTALLOGRAPHY (2.69 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
RP COFACTOR.
RX PubMed=15057282; DOI=10.1038/sj.emboj.7600158;
RA Freisinger E., Grollman A.P., Miller H., Kisker C.;
RT "Lesion (in)tolerance reveals insights into DNA replication fidelity.";
RL EMBO J. 23:1494-1505(2004).
RN [8] {ECO:0007744|PDB:2P5O}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), AND COFACTOR.
RX PubMed=15057283; DOI=10.1038/sj.emboj.7600150;
RA Hogg M., Wallace S.S., Doublie S.;
RT "Crystallographic snapshots of a replicative DNA polymerase encountering an
RT abasic site.";
RL EMBO J. 23:1483-1493(2004).
RN [9] {ECO:0007744|PDB:2OYQ, ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS, ECO:0007744|PDB:2P5G}
RP X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
RP COFACTOR.
RX PubMed=17718515; DOI=10.1021/bi7008807;
RA Zahn K.E., Belrhali H., Wallace S.S., Doublie S.;
RT "Caught bending the A-rule: crystal structures of translesion DNA synthesis
RT with a non-natural nucleotide.";
RL Biochemistry 46:10551-10561(2007).
RN [10] {ECO:0007744|PDB:2DTU}
RP X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 1-902, CATALYTIC ACTIVITY, AND
RP FUNCTION.
RX PubMed=17098747; DOI=10.1074/jbc.m605675200;
RA Hogg M., Aller P., Konigsberg W., Wallace S.S., Doublie S.;
RT "Structural and biochemical investigation of the role in proofreading of a
RT beta hairpin loop found in the exonuclease domain of a replicative DNA
RT polymerase of the B family.";
RL J. Biol. Chem. 282:1432-1444(2007).
RN [11] {ECO:0007744|PDB:2DY4}
RP X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
RX PubMed=17210917; DOI=10.1073/pnas.0606648104;
RA Aller P., Rould M.A., Hogg M., Wallace S.S., Doublie S.;
RT "A structural rationale for stalling of a replicative DNA polymerase at the
RT most common oxidative thymine lesion, thymine glycol.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:814-818(2007).
RN [12] {ECO:0007744|PDB:3CQ8}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH CALCIUM; DNA AND
RP TTP, FUNCTION, COFACTOR, CATALYTIC ACTIVITY, AND MUTAGENESIS OF LEU-415.
RX PubMed=18503083; DOI=10.1093/nar/gkn312;
RA Zhong X., Pedersen L.C., Kunkel T.A.;
RT "Characterization of a replicative DNA polymerase mutant with reduced
RT fidelity and increased translesion synthesis capacity.";
RL Nucleic Acids Res. 36:3892-3904(2008).
RN [13] {ECO:0007744|PDB:3LDS}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH MANGANESE,
RP MUTAGENESIS OF LEU-561, AND COFACTOR.
RX PubMed=20166748; DOI=10.1021/bi901488d;
RA Hogg M., Rudnicki J., Midkiff J., Reha-Krantz L., Doublie S., Wallace S.S.;
RT "Kinetics of mismatch formation opposite lesions by the replicative DNA
RT polymerase from bacteriophage RB69.";
RL Biochemistry 49:2317-2325(2010).
RN [14] {ECO:0007744|PDB:3L8B}
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), AND COFACTOR.
RX PubMed=20166752; DOI=10.1021/bi902195p;
RA Aller P., Ye Y., Wallace S.S., Burrows C.J., Doublie S.;
RT "Crystal structure of a replicative DNA polymerase bound to the oxidized
RT guanine lesion guanidinohydantoin.";
RL Biochemistry 49:2502-2509(2010).
RN [15] {ECO:0007744|PDB:3LZI, ECO:0007744|PDB:3LZJ}
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CTP AND CALCIUM, AND
RP MUTAGENESIS OF TYR-567.
RX PubMed=20411947; DOI=10.1021/bi100102s;
RA Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.;
RT "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be
RT inserted opposite 7,8-dihydro-8-oxoguanine.";
RL Biochemistry 49:4116-4125(2010).
RN [16] {ECO:0007744|PDB:3NAE}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH CALCIUM, MUTAGENESIS
RP OF TYR-567, AND CATALYTIC ACTIVITY.
RX PubMed=20795733; DOI=10.1021/bi100913v;
RA Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.;
RT "Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and dGMP
RT to be inserted opposite Guanidinohydantoin.";
RL Biochemistry 49:8554-8563(2010).
RN [17] {ECO:0007744|PDB:3SQ2, ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN, ECO:0007744|PDB:3SUO, ECO:0007744|PDB:3SUP, ECO:0007744|PDB:3SUQ}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 1-902 IN COMPLEX WITH DNA AND
RP TTP, AND MUTAGENESIS OF TYR-567.
RX PubMed=22023103; DOI=10.1021/bi2014618;
RA Reha-Krantz L.J., Hariharan C., Subuddhi U., Xia S., Zhao C., Beckman J.,
RA Christian T., Konigsberg W.;
RT "Structure of the 2-aminopurine-cytosine base pair formed in the polymerase
RT active site of the RB69 Y567A-DNA polymerase.";
RL Biochemistry 50:10136-10149(2011).
RN [18] {ECO:0007744|PDB:3TAB, ECO:0007744|PDB:3TAE, ECO:0007744|PDB:3TAF, ECO:0007744|PDB:3TAG}
RP X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS), AND COFACTOR.
RX PubMed=22026756; DOI=10.1021/bi201219s;
RA Zahn K.E., Averill A., Wallace S.S., Doublie S.;
RT "The miscoding potential of 5-hydroxycytosine arises due to template
RT instability in the replicative polymerase active site.";
RL Biochemistry 50:10350-10358(2011).
RN [19] {ECO:0007744|PDB:3NCI}
RP X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
RP COFACTOR.
RX PubMed=21158418; DOI=10.1021/bi101192f;
RA Wang M., Xia S., Blaha G., Steitz T.A., Konigsberg W.H., Wang J.;
RT "Insights into base selectivity from the 1.8 A resolution structure of an
RT RB69 DNA polymerase ternary complex.";
RL Biochemistry 50:581-590(2011).
RN [20] {ECO:0007744|PDB:3S9H, ECO:0007744|PDB:3SCX, ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SJJ, ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY, ECO:0007744|PDB:3SPZ, ECO:0007744|PDB:3SQ0, ECO:0007744|PDB:3SQ1}
RP X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) OF 1-901 IN COMPLEXES WITH MAGNESIUM
RP AND MANGANESE, AND COFACTOR.
RX PubMed=21923197; DOI=10.1021/bi201260h;
RA Xia S., Wang M., Blaha G., Konigsberg W.H., Wang J.;
RT "Structural insights into complete metal ion coordination from ternary
RT complexes of B family RB69 DNA polymerase.";
RL Biochemistry 50:9114-9124(2011).
RN [21] {ECO:0007744|PDB:3QEP, ECO:0007744|PDB:3RWU}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ATP; CALCIUM AND
RP TTP.
RX PubMed=21667997; DOI=10.1021/ja2021735;
RA Xia S., Konigsberg W.H., Wang J.;
RT "Hydrogen-bonding capability of a templating difluorotoluene nucleotide
RT residue in an RB69 DNA polymerase ternary complex.";
RL J. Am. Chem. Soc. 133:10003-10005(2011).
RN [22] {ECO:0007744|PDB:3KD1, ECO:0007744|PDB:3KD5}
RP X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
RP COFACTOR.
RX PubMed=21566148; DOI=10.1074/jbc.m111.248864;
RA Zahn K.E., Tchesnokov E.P., Gotte M., Doublie S.;
RT "Phosphonoformic acid inhibits viral replication by trapping the closed
RT form of the DNA polymerase.";
RL J. Biol. Chem. 286:25246-25255(2011).
RN [23] {ECO:0007744|PDB:3NDK, ECO:0007744|PDB:3NE6, ECO:0007744|PDB:3NGI, ECO:0007744|PDB:3NHG}
RP X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP, AND
RP MUTAGENESIS OF SER-565 AND TYR-567.
RX PubMed=21216248; DOI=10.1016/j.jmb.2010.12.033;
RA Xia S., Wang M., Lee H.R., Sinha A., Blaha G., Christian T., Wang J.,
RA Konigsberg W.;
RT "Variation in mutation rates caused by RB69pol fidelity mutants can be
RT rationalized on the basis of their kinetic behavior and crystal
RT structures.";
RL J. Mol. Biol. 406:558-570(2011).
RN [24] {ECO:0007744|PDB:3RMA, ECO:0007744|PDB:3RMB, ECO:0007744|PDB:3RMC, ECO:0007744|PDB:3RMD}
RP X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
RX PubMed=21781974; DOI=10.1016/j.jmb.2011.07.007;
RA Aller P., Duclos S., Wallace S.S., Doublie S.;
RT "A crystallographic study of the role of sequence context in thymine glycol
RT bypass by a replicative DNA polymerase serendipitously sheds light on the
RT exonuclease complex.";
RL J. Mol. Biol. 412:22-34(2011).
RN [25] {ECO:0007744|PDB:3QEI, ECO:0007744|PDB:3QER, ECO:0007744|PDB:3QES}
RP X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH CALCIUM.
RX PubMed=22304682; DOI=10.1021/bi2016487;
RA Xia S., Eom S.H., Konigsberg W.H., Wang J.;
RT "Structural basis for differential insertion kinetics of dNMPs opposite a
RT difluorotoluene nucleotide residue.";
RL Biochemistry 51:1476-1485(2012).
RN [26] {ECO:0007744|PDB:4DU1, ECO:0007744|PDB:4DU3, ECO:0007744|PDB:4DU4, ECO:0007744|PDB:4E3S}
RP X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) IN COMPLEX WITH CALCIUM, FUNCTION,
RP CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-621 AND LYS-706, AND COFACTOR.
RX PubMed=22571765; DOI=10.1021/bi300416z;
RA Xia S., Christian T.D., Wang J., Konigsberg W.H.;
RT "Probing minor groove hydrogen bonding interactions between RB69 DNA
RT polymerase and DNA.";
RL Biochemistry 51:4343-4353(2012).
RN [27] {ECO:0007744|PDB:3QNN, ECO:0007744|PDB:3QNO}
RP X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP AND
RP CALCIUM, AND MUTAGENESIS OF TYR-567.
RX PubMed=22616982; DOI=10.1021/bi300241m;
RA Xia S., Beckman J., Wang J., Konigsberg W.H.;
RT "Using a fluorescent cytosine analogue tC(o) to probe the effect of the
RT Y567 to Ala substitution on the preinsertion steps of dNMP incorporation by
RT RB69 DNA polymerase.";
RL Biochemistry 51:4609-4617(2012).
RN [28] {ECO:0007744|PDB:4DTJ, ECO:0007744|PDB:4DTM, ECO:0007744|PDB:4DTN, ECO:0007744|PDB:4DTO, ECO:0007744|PDB:4DTP, ECO:0007744|PDB:4DTR, ECO:0007744|PDB:4DTS, ECO:0007744|PDB:4DTU, ECO:0007744|PDB:4DTX}
RP X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEXES WITH CALCIUM; DNA; ATP;
RP CTP; GTP AND TTP, CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=22630605; DOI=10.1021/bi300296q;
RA Xia S., Vashishtha A., Bulkley D., Eom S.H., Wang J., Konigsberg W.H.;
RT "Contribution of partial charge interactions and base stacking to the
RT efficiency of primer extension at and beyond abasic sites in DNA.";
RL Biochemistry 51:4922-4931(2012).
RN [29] {ECO:0007744|PDB:3UIQ}
RP X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
RP COFACTOR.
RX PubMed=22238207; DOI=10.1002/pro.2026;
RA Xia S., Eom S.H., Konigsberg W.H., Wang J.;
RT "Bidentate and tridentate metal-ion coordination states within ternary
RT complexes of RB69 DNA polymerase.";
RL Protein Sci. 21:447-451(2012).
RN [30]
RP X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP,
RP COFACTOR, MUTAGENESIS OF ASP-222 AND ASP-327, AND CATALYTIC ACTIVITY.
RX PubMed=23214497; DOI=10.1021/ja3079048;
RA Xia S., Wang J., Konigsberg W.H.;
RT "DNA mismatch synthesis complexes provide insights into base selectivity of
RT a B family DNA polymerase.";
RL J. Am. Chem. Soc. 135:193-202(2013).
RN [31] {ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2E}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP;
RP CALCIUM AND TTP, MUTAGENESIS OF LEU-415, AND COFACTOR.
RX PubMed=23921641; DOI=10.1093/nar/gkt674;
RA Xia S., Wood M., Bradley M.J., De La Cruz E.M., Konigsberg W.H.;
RT "Alteration in the cavity size adjacent to the active site of RB69 DNA
RT polymerase changes its conformational dynamics.";
RL Nucleic Acids Res. 41:9077-9089(2013).
RN [32] {ECO:0007744|PDB:4I9L, ECO:0007744|PDB:4I9Q, ECO:0007744|PDB:4KHN}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), MUTAGENESIS OF ASP-714, CATALYTIC
RP ACTIVITY, AND COFACTOR.
RX PubMed=24116139; DOI=10.1371/journal.pone.0076700;
RA Jacewicz A., Trzemecka A., Guja K.E., Plochocka D., Yakubovskaya E.,
RA Bebenek A., Garcia-Diaz M.;
RT "A remote palm domain residue of RB69 DNA polymerase is critical for enzyme
RT activity and influences the conformation of the active site.";
RL PLoS ONE 8:76700-76700(2013).
RN [33] {ECO:0007744|PDB:4KHQ, ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6}
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CALCIUM AND TTP.
RX PubMed=24082122; DOI=10.1073/pnas.1309119110;
RA Clausen A.R., Murray M.S., Passer A.R., Pedersen L.C., Kunkel T.A.;
RT "Structure-function analysis of ribonucleotide bypass by B family DNA
RT replicases.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:16802-16807(2013).
RN [34] {ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45}
RP X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEX WITH ATP AND CALCIUM.
RX PubMed=24458997; DOI=10.1002/pro.2434;
RA Xia S., Konigsberg W.H.;
RT "Mispairs with Watson-Crick base-pair geometry observed in ternary
RT complexes of an RB69 DNA polymerase variant.";
RL Protein Sci. 23:508-513(2014).
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, ECO:0000269|PubMed:17098747,
CC ECO:0000269|PubMed:18503083, ECO:0000269|PubMed:22571765,
CC ECO:0000269|PubMed:22616982}.
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, ECO:0000269|PubMed:17098747,
CC ECO:0000269|PubMed:18503083, ECO:0000269|PubMed:20795733,
CC ECO:0000269|PubMed:22616982, ECO:0000269|PubMed:24116139};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04100,
CC ECO:0000269|PubMed:20166752, ECO:0000269|PubMed:22026756,
CC ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282,
CC ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:17718515,
CC ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:20166748,
CC ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:21566148,
CC ECO:0000305|PubMed:21923197, ECO:0000305|PubMed:22571765,
CC ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641,
CC ECO:0000305|PubMed:24116139};
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 (By similarity).
CC Interacts with the polymerase clamp; this interaction constitutes the
CC polymerase holoenzyme (PubMed:10535734). {ECO:0000255|HAMAP-
CC Rule:MF_04100, ECO:0000269|PubMed:10535734}.
CC -!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity
CC (PubMed:9215631). The C-terminus contains the polymerase activity and
CC is involved in binding to the polymerase clamp protein
CC (PubMed:9215631). A beta hairpin structure is necessary for the
CC proofreading function of the polymerase (By similarity).
CC {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:9215631}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family.
CC {ECO:0000255|HAMAP-Rule:MF_04100}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; U34036; AAA93077.1; -; Genomic_DNA.
DR EMBL; AY303349; AAP75958.1; -; Genomic_DNA.
DR RefSeq; NP_861746.1; NC_004928.1.
DR PDB; 1B8H; X-ray; 3.00 A; D=893-903.
DR PDB; 1CLQ; X-ray; 2.70 A; A=1-903.
DR PDB; 1IG9; X-ray; 2.60 A; A=1-903.
DR PDB; 1IH7; X-ray; 2.21 A; A=1-903.
DR PDB; 1Q9X; X-ray; 2.69 A; A/B/C/D=1-903.
DR PDB; 1Q9Y; X-ray; 2.80 A; A=1-903.
DR PDB; 1WAF; X-ray; 3.20 A; A/B=1-903.
DR PDB; 1WAJ; X-ray; 2.80 A; A=1-903.
DR PDB; 2ATQ; X-ray; 3.20 A; A=1-903.
DR PDB; 2DTU; X-ray; 2.37 A; A/B/C/D=1-902.
DR PDB; 2DY4; X-ray; 2.65 A; A/B/C/D=1-903.
DR PDB; 2OYQ; X-ray; 2.86 A; A/B/C/D=1-903.
DR PDB; 2OZM; X-ray; 2.86 A; A=1-903.
DR PDB; 2OZS; X-ray; 2.75 A; A=1-903.
DR PDB; 2P5G; X-ray; 2.80 A; A/B/C/D=1-903.
DR PDB; 2P5O; X-ray; 2.80 A; A/B/C/D=1-903.
DR PDB; 3CFO; X-ray; 2.60 A; A=1-903.
DR PDB; 3CFP; X-ray; 2.50 A; A=1-903.
DR PDB; 3CFR; X-ray; 2.40 A; A=1-903.
DR PDB; 3CQ8; X-ray; 2.50 A; A=1-903.
DR PDB; 3KD1; X-ray; 2.66 A; E=1-903.
DR PDB; 3KD5; X-ray; 2.69 A; E=1-903.
DR PDB; 3L8B; X-ray; 2.15 A; A/B=1-903.
DR PDB; 3LDS; X-ray; 3.00 A; A=1-903.
DR PDB; 3LZI; X-ray; 2.30 A; A=1-903.
DR PDB; 3LZJ; X-ray; 2.05 A; A=1-903.
DR PDB; 3NAE; X-ray; 2.00 A; A=1-903.
DR PDB; 3NCI; X-ray; 1.79 A; A=1-903.
DR PDB; 3NDK; X-ray; 2.00 A; A=1-903.
DR PDB; 3NE6; X-ray; 2.00 A; A=1-903.
DR PDB; 3NGI; X-ray; 1.89 A; A=1-903.
DR PDB; 3NHG; X-ray; 2.50 A; A=1-903.
DR PDB; 3QEI; X-ray; 2.18 A; A=1-903.
DR PDB; 3QEP; X-ray; 1.80 A; A=1-903.
DR PDB; 3QER; X-ray; 1.96 A; A=1-903.
DR PDB; 3QES; X-ray; 1.98 A; A=1-903.
DR PDB; 3QET; X-ray; 2.08 A; A=1-903.
DR PDB; 3QEV; X-ray; 1.77 A; A=1-903.
DR PDB; 3QEW; X-ray; 1.84 A; A=1-903.
DR PDB; 3QEX; X-ray; 1.73 A; A=1-903.
DR PDB; 3QNN; X-ray; 1.92 A; A=1-901.
DR PDB; 3QNO; X-ray; 1.88 A; A=1-901.
DR PDB; 3RMA; X-ray; 2.84 A; A/B/C/D=1-903.
DR PDB; 3RMB; X-ray; 2.65 A; A/B/C/D=1-903.
DR PDB; 3RMC; X-ray; 3.00 A; A/B/C/D=1-903.
DR PDB; 3RMD; X-ray; 2.98 A; A/B/C/D=1-903.
DR PDB; 3RWU; X-ray; 2.33 A; A=1-901.
DR PDB; 3S9H; X-ray; 1.95 A; A=1-903.
DR PDB; 3SCX; X-ray; 2.35 A; A=1-901.
DR PDB; 3SI6; X-ray; 1.85 A; A=1-901.
DR PDB; 3SJJ; X-ray; 2.38 A; A=1-901.
DR PDB; 3SNN; X-ray; 2.00 A; A=1-901.
DR PDB; 3SPY; X-ray; 2.14 A; A=1-901.
DR PDB; 3SPZ; X-ray; 2.43 A; A=1-903.
DR PDB; 3SQ0; X-ray; 2.00 A; A=1-903.
DR PDB; 3SQ1; X-ray; 1.82 A; A=1-901.
DR PDB; 3SQ2; X-ray; 2.10 A; A=1-902.
DR PDB; 3SQ4; X-ray; 2.23 A; A=1-902.
DR PDB; 3SUN; X-ray; 2.42 A; A=1-895.
DR PDB; 3SUO; X-ray; 2.23 A; A=1-900.
DR PDB; 3SUP; X-ray; 2.32 A; A=1-903.
DR PDB; 3SUQ; X-ray; 3.15 A; A=1-897.
DR PDB; 3TAB; X-ray; 2.80 A; A/B/C/D=1-903.
DR PDB; 3TAE; X-ray; 2.71 A; A/B/C/D=1-903.
DR PDB; 3TAF; X-ray; 3.00 A; A/B/C/D=1-903.
DR PDB; 3TAG; X-ray; 2.95 A; A/B/C/D=1-903.
DR PDB; 3UIQ; X-ray; 1.88 A; A=1-903.
DR PDB; 4DTJ; X-ray; 1.90 A; A=1-901.
DR PDB; 4DTM; X-ray; 1.95 A; A=1-901.
DR PDB; 4DTN; X-ray; 1.96 A; A=1-903.
DR PDB; 4DTO; X-ray; 2.05 A; A=1-903.
DR PDB; 4DTP; X-ray; 2.05 A; A=1-903.
DR PDB; 4DTR; X-ray; 2.04 A; A=1-903.
DR PDB; 4DTS; X-ray; 1.96 A; A=1-903.
DR PDB; 4DTU; X-ray; 1.86 A; A=1-903.
DR PDB; 4DTX; X-ray; 1.84 A; A=1-903.
DR PDB; 4DU1; X-ray; 2.15 A; A=1-903.
DR PDB; 4DU3; X-ray; 2.02 A; A=1-903.
DR PDB; 4DU4; X-ray; 2.28 A; A=1-903.
DR PDB; 4E3S; X-ray; 2.04 A; A=1-903.
DR PDB; 4FJ5; X-ray; 2.05 A; A=1-903.
DR PDB; 4FJ7; X-ray; 1.90 A; A=1-903.
DR PDB; 4FJ8; X-ray; 2.19 A; A=1-903.
DR PDB; 4FJ9; X-ray; 1.97 A; A=1-903.
DR PDB; 4FJG; X-ray; 2.02 A; A=1-903.
DR PDB; 4FJH; X-ray; 2.11 A; A=1-903.
DR PDB; 4FJI; X-ray; 2.20 A; A=1-903.
DR PDB; 4FJJ; X-ray; 1.99 A; A=1-903.
DR PDB; 4FJK; X-ray; 2.00 A; A=1-903.
DR PDB; 4FJL; X-ray; 1.87 A; A=1-903.
DR PDB; 4FJM; X-ray; 2.02 A; A=1-903.
DR PDB; 4FJN; X-ray; 1.98 A; A=1-903.
DR PDB; 4FJX; X-ray; 2.11 A; A=1-903.
DR PDB; 4FK0; X-ray; 2.18 A; A=1-903.
DR PDB; 4FK2; X-ray; 1.98 A; A=1-903.
DR PDB; 4FK4; X-ray; 1.90 A; A=1-903.
DR PDB; 4I9L; X-ray; 2.60 A; A=1-903.
DR PDB; 4I9Q; X-ray; 2.30 A; A/B=1-903.
DR PDB; 4J2A; X-ray; 1.80 A; A=1-901.
DR PDB; 4J2B; X-ray; 2.04 A; A=1-901.
DR PDB; 4J2D; X-ray; 1.76 A; A=1-901.
DR PDB; 4J2E; X-ray; 2.02 A; A=1-901.
DR PDB; 4KHN; X-ray; 2.55 A; A/B=1-903.
DR PDB; 4KHQ; X-ray; 2.19 A; A=1-903.
DR PDB; 4KHS; X-ray; 2.12 A; A=1-903.
DR PDB; 4KHU; X-ray; 2.05 A; A=1-903.
DR PDB; 4KHW; X-ray; 2.37 A; A=1-903.
DR PDB; 4KHY; X-ray; 2.25 A; A=1-903.
DR PDB; 4KI4; X-ray; 2.45 A; A=1-903.
DR PDB; 4KI6; X-ray; 2.55 A; A=1-903.
DR PDB; 4M3R; X-ray; 2.07 A; A=1-903.
DR PDB; 4M3T; X-ray; 1.90 A; A=1-903.
DR PDB; 4M3U; X-ray; 2.07 A; A=1-903.
DR PDB; 4M3W; X-ray; 2.10 A; A=1-903.
DR PDB; 4M3X; X-ray; 2.20 A; A=1-903.
DR PDB; 4M3Y; X-ray; 1.86 A; A=1-903.
DR PDB; 4M3Z; X-ray; 1.84 A; A=1-903.
DR PDB; 4M41; X-ray; 2.15 A; A=1-903.
DR PDB; 4M42; X-ray; 2.04 A; A=1-903.
DR PDB; 4M45; X-ray; 1.89 A; A=1-903.
DR PDB; 7F4Y; X-ray; 2.20 A; A/B=1-903.
DR PDBsum; 1B8H; -.
DR PDBsum; 1CLQ; -.
DR PDBsum; 1IG9; -.
DR PDBsum; 1IH7; -.
DR PDBsum; 1Q9X; -.
DR PDBsum; 1Q9Y; -.
DR PDBsum; 1WAF; -.
DR PDBsum; 1WAJ; -.
DR PDBsum; 2ATQ; -.
DR PDBsum; 2DTU; -.
DR PDBsum; 2DY4; -.
DR PDBsum; 2OYQ; -.
DR PDBsum; 2OZM; -.
DR PDBsum; 2OZS; -.
DR PDBsum; 2P5G; -.
DR PDBsum; 2P5O; -.
DR PDBsum; 3CFO; -.
DR PDBsum; 3CFP; -.
DR PDBsum; 3CFR; -.
DR PDBsum; 3CQ8; -.
DR PDBsum; 3KD1; -.
DR PDBsum; 3KD5; -.
DR PDBsum; 3L8B; -.
DR PDBsum; 3LDS; -.
DR PDBsum; 3LZI; -.
DR PDBsum; 3LZJ; -.
DR PDBsum; 3NAE; -.
DR PDBsum; 3NCI; -.
DR PDBsum; 3NDK; -.
DR PDBsum; 3NE6; -.
DR PDBsum; 3NGI; -.
DR PDBsum; 3NHG; -.
DR PDBsum; 3QEI; -.
DR PDBsum; 3QEP; -.
DR PDBsum; 3QER; -.
DR PDBsum; 3QES; -.
DR PDBsum; 3QET; -.
DR PDBsum; 3QEV; -.
DR PDBsum; 3QEW; -.
DR PDBsum; 3QEX; -.
DR PDBsum; 3QNN; -.
DR PDBsum; 3QNO; -.
DR PDBsum; 3RMA; -.
DR PDBsum; 3RMB; -.
DR PDBsum; 3RMC; -.
DR PDBsum; 3RMD; -.
DR PDBsum; 3RWU; -.
DR PDBsum; 3S9H; -.
DR PDBsum; 3SCX; -.
DR PDBsum; 3SI6; -.
DR PDBsum; 3SJJ; -.
DR PDBsum; 3SNN; -.
DR PDBsum; 3SPY; -.
DR PDBsum; 3SPZ; -.
DR PDBsum; 3SQ0; -.
DR PDBsum; 3SQ1; -.
DR PDBsum; 3SQ2; -.
DR PDBsum; 3SQ4; -.
DR PDBsum; 3SUN; -.
DR PDBsum; 3SUO; -.
DR PDBsum; 3SUP; -.
DR PDBsum; 3SUQ; -.
DR PDBsum; 3TAB; -.
DR PDBsum; 3TAE; -.
DR PDBsum; 3TAF; -.
DR PDBsum; 3TAG; -.
DR PDBsum; 3UIQ; -.
DR PDBsum; 4DTJ; -.
DR PDBsum; 4DTM; -.
DR PDBsum; 4DTN; -.
DR PDBsum; 4DTO; -.
DR PDBsum; 4DTP; -.
DR PDBsum; 4DTR; -.
DR PDBsum; 4DTS; -.
DR PDBsum; 4DTU; -.
DR PDBsum; 4DTX; -.
DR PDBsum; 4DU1; -.
DR PDBsum; 4DU3; -.
DR PDBsum; 4DU4; -.
DR PDBsum; 4E3S; -.
DR PDBsum; 4FJ5; -.
DR PDBsum; 4FJ7; -.
DR PDBsum; 4FJ8; -.
DR PDBsum; 4FJ9; -.
DR PDBsum; 4FJG; -.
DR PDBsum; 4FJH; -.
DR PDBsum; 4FJI; -.
DR PDBsum; 4FJJ; -.
DR PDBsum; 4FJK; -.
DR PDBsum; 4FJL; -.
DR PDBsum; 4FJM; -.
DR PDBsum; 4FJN; -.
DR PDBsum; 4FJX; -.
DR PDBsum; 4FK0; -.
DR PDBsum; 4FK2; -.
DR PDBsum; 4FK4; -.
DR PDBsum; 4I9L; -.
DR PDBsum; 4I9Q; -.
DR PDBsum; 4J2A; -.
DR PDBsum; 4J2B; -.
DR PDBsum; 4J2D; -.
DR PDBsum; 4J2E; -.
DR PDBsum; 4KHN; -.
DR PDBsum; 4KHQ; -.
DR PDBsum; 4KHS; -.
DR PDBsum; 4KHU; -.
DR PDBsum; 4KHW; -.
DR PDBsum; 4KHY; -.
DR PDBsum; 4KI4; -.
DR PDBsum; 4KI6; -.
DR PDBsum; 4M3R; -.
DR PDBsum; 4M3T; -.
DR PDBsum; 4M3U; -.
DR PDBsum; 4M3W; -.
DR PDBsum; 4M3X; -.
DR PDBsum; 4M3Y; -.
DR PDBsum; 4M3Z; -.
DR PDBsum; 4M41; -.
DR PDBsum; 4M42; -.
DR PDBsum; 4M45; -.
DR PDBsum; 7F4Y; -.
DR SMR; Q38087; -.
DR DrugBank; DB08245; 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-NITRO-1H-INDOLE.
DR DrugBank; DB02857; Guanosine.
DR DrugBank; DB01972; Guanosine-5'-Monophosphate.
DR PRIDE; Q38087; -.
DR GeneID; 1494172; -.
DR KEGG; vg:1494172; -.
DR BRENDA; 2.7.7.7; 9245.
DR SABIO-RK; Q38087; -.
DR EvolutionaryTrace; Q38087; -.
DR Proteomes; UP000000876; Genome.
DR GO; GO:0008408; F:3'-5' exonuclease activity; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:UniProtKB.
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 1: Evidence at protein level;
KW 3D-structure; DNA replication; DNA-binding; DNA-directed DNA polymerase;
KW Exonuclease; Hydrolase; Magnesium; Metal-binding; Multifunctional enzyme;
KW Nuclease; Nucleotidyltransferase; Reference proteome; Transferase;
KW Viral DNA replication.
FT CHAIN 1..903
FT /note="DNA-directed DNA polymerase"
FT /id="PRO_0000046547"
FT REGION 103..340
FT /note="3'-5'exonuclease"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:9215631"
FT REGION 248..264
FT /note="Beta hairpin"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:17098747"
FT REGION 380..903
FT /note="Polymerase"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:9215631"
FT REGION 705..708
FT /note="Binding of DNA in B-conformation"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:11389835, ECO:0000269|PubMed:24116139"
FT REGION 897..903
FT /note="Interaction with the polymerase clamp"
FT /evidence="ECO:0000255|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:0000255|HAMAP-Rule:MF_04100"
FT BINDING 116
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 222
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 ECO:0000305|PubMed:23214497"
FT BINDING 327
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 ECO:0000305|PubMed:23214497"
FT BINDING 327
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 ECO:0000305|PubMed:23214497"
FT BINDING 411
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 ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515,
FT ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197,
FT ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835,
FT ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083,
FT ECO:0000305|PubMed:20166748, ECO:0000305|PubMed:21158418,
FT ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497,
FT ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139,
FT ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS,
FT ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6,
FT ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY"
FT BINDING 411
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 ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515,
FT ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197,
FT ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835,
FT ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083,
FT ECO:0000305|PubMed:20166748, ECO:0000305|PubMed:21158418,
FT ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:23214497,
FT ECO:0000305|PubMed:23921641, ECO:0000305|PubMed:24116139,
FT ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS,
FT ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6,
FT ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY"
FT BINDING 412
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 ECO:0000269|PubMed:17718515, ECO:0000269|PubMed:21566148,
FT ECO:0000269|PubMed:21923197, ECO:0000305|PubMed:18503083,
FT ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641,
FT ECO:0007744|PDB:2OZM, ECO:0007744|PDB:2OZS,
FT ECO:0007744|PDB:3KD5, ECO:0007744|PDB:3SI6,
FT ECO:0007744|PDB:3SNN, ECO:0007744|PDB:3SPY"
FT BINDING 414..416
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP,
FT ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8,
FT ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI,
FT ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP,
FT ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO,
FT ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2,
FT ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN,
FT ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ,
FT ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJ9,
FT ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN,
FT ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A,
FT ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D,
FT ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS,
FT ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW,
FT ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4,
FT ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R,
FT ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U,
FT ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X,
FT ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z,
FT ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42,
FT ECO:0007744|PDB:4M45"
FT BINDING 482
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP,
FT ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8,
FT ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI,
FT ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP,
FT ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO,
FT ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2,
FT ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN,
FT ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ,
FT ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJ9,
FT ECO:0007744|PDB:4FJJ, ECO:0007744|PDB:4FJN,
FT ECO:0007744|PDB:4FK2, ECO:0007744|PDB:4J2A,
FT ECO:0007744|PDB:4J2B, ECO:0007744|PDB:4J2D,
FT ECO:0007744|PDB:4J2E, ECO:0007744|PDB:4KHS,
FT ECO:0007744|PDB:4KHU, ECO:0007744|PDB:4KHW,
FT ECO:0007744|PDB:4KHY, ECO:0007744|PDB:4KI4,
FT ECO:0007744|PDB:4KI6, ECO:0007744|PDB:4M3R,
FT ECO:0007744|PDB:4M3T, ECO:0007744|PDB:4M3U,
FT ECO:0007744|PDB:4M3W, ECO:0007744|PDB:4M3X,
FT ECO:0007744|PDB:4M3Y, ECO:0007744|PDB:4M3Z,
FT ECO:0007744|PDB:4M41, ECO:0007744|PDB:4M42,
FT ECO:0007744|PDB:4M45"
FT BINDING 560
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0007744|PDB:1IG9, ECO:0007744|PDB:3CFP,
FT ECO:0007744|PDB:3CFR, ECO:0007744|PDB:3CQ8,
FT ECO:0007744|PDB:3LZJ, ECO:0007744|PDB:3NGI,
FT ECO:0007744|PDB:3NHG, ECO:0007744|PDB:3QEP,
FT ECO:0007744|PDB:3QET, ECO:0007744|PDB:3QNO,
FT ECO:0007744|PDB:3RWU, ECO:0007744|PDB:3SQ2,
FT ECO:0007744|PDB:3SQ4, ECO:0007744|PDB:3SUN,
FT ECO:0007744|PDB:3SUO, ECO:0007744|PDB:4DTJ,
FT ECO:0007744|PDB:4DTX, ECO:0007744|PDB:4FJJ,
FT ECO:0007744|PDB:4FJN, ECO:0007744|PDB:4FK2,
FT ECO:0007744|PDB:4J2A, ECO:0007744|PDB:4J2B,
FT ECO:0007744|PDB:4J2D, ECO:0007744|PDB:4J2E,
FT ECO:0007744|PDB:4KHS, ECO:0007744|PDB:4KHU,
FT ECO:0007744|PDB:4KHW, ECO:0007744|PDB:4KHY,
FT ECO:0007744|PDB:4KI4, ECO:0007744|PDB:4KI6,
FT ECO:0007744|PDB:4M3R, ECO:0007744|PDB:4M3T,
FT ECO:0007744|PDB:4M3U, ECO:0007744|PDB:4M3W,
FT ECO:0007744|PDB:4M3X, ECO:0007744|PDB:4M3Y,
FT ECO:0007744|PDB:4M3Z, ECO:0007744|PDB:4M41,
FT ECO:0007744|PDB:4M42, ECO:0007744|PDB:4M45"
FT BINDING 623
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 ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515,
FT ECO:0000269|PubMed:20166748, ECO:0000269|PubMed:20166752,
FT ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197,
FT ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835,
FT ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083,
FT ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765,
FT ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641,
FT ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM,
FT ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5,
FT ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN,
FT ECO:0007744|PDB:3SPY"
FT BINDING 623
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 ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:17718515,
FT ECO:0000269|PubMed:20166748, ECO:0000269|PubMed:20166752,
FT ECO:0000269|PubMed:21566148, ECO:0000269|PubMed:21923197,
FT ECO:0000269|PubMed:22026756, ECO:0000305|PubMed:11389835,
FT ECO:0000305|PubMed:15057282, ECO:0000305|PubMed:18503083,
FT ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:22571765,
FT ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641,
FT ECO:0000305|PubMed:24116139, ECO:0007744|PDB:2OZM,
FT ECO:0007744|PDB:2OZS, ECO:0007744|PDB:3KD5,
FT ECO:0007744|PDB:3SI6, ECO:0007744|PDB:3SNN,
FT ECO:0007744|PDB:3SPY"
FT SITE 621
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:20166752,
FT ECO:0000305|PubMed:22571765, ECO:0000305|PubMed:24116139"
FT SITE 706
FT /note="Optimization of metal coordination by the polymerase
FT active site"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:15057283, ECO:0000269|PubMed:22571765"
FT SITE 714
FT /note="Essential for viral replication"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04100,
FT ECO:0000269|PubMed:24116139"
FT MUTAGEN 222
FT /note="D->A: Complete loss of 3'-5' exonuclease activity."
FT /evidence="ECO:0000269|PubMed:23214497"
FT MUTAGEN 327
FT /note="D->A: Complete loss of 3'-5' exonuclease activity."
FT /evidence="ECO:0000269|PubMed:23214497"
FT MUTAGEN 415
FT /note="L->A,G: Decreases base selectivity by several
FT hundred fold."
FT /evidence="ECO:0000269|PubMed:23921641"
FT MUTAGEN 415
FT /note="L->G,F: Increased misinsertion, increased mismatch
FT extension and inefficient proofreading."
FT /evidence="ECO:0000269|PubMed:18503083"
FT MUTAGEN 415
FT /note="L->M: No effect on base selectivity."
FT /evidence="ECO:0000269|PubMed:23921641"
FT MUTAGEN 561
FT /note="L->A: No effect on the ability to recognize damaged
FT DNA. Increase in probability of nucleotide incorporation."
FT /evidence="ECO:0000269|PubMed:20166748"
FT MUTAGEN 565
FT /note="S->G: Increased incorporation efficiency of correct
FT dNMPs; when associated with A-567."
FT /evidence="ECO:0000269|PubMed:21216248"
FT MUTAGEN 567
FT /note="Y->A: Inserts both dCMP and dAMP opposite 8-oxoG
FT rapidly and with equal efficiency. 100-fold increase of
FT dAMP and dGMP when situated opposite guanidinohydantoin.
FT Increased incorporation efficiency of correct dNMPs; when
FT associated with G-565."
FT /evidence="ECO:0000269|PubMed:20411947,
FT ECO:0000269|PubMed:21216248, ECO:0000269|PubMed:22616982"
FT MUTAGEN 621
FT /note="D->A: Drastic decrease in the efficiency of
FT incorporation of dGMP."
FT /evidence="ECO:0000269|PubMed:22571765"
FT MUTAGEN 706
FT /note="K->A: Almost complete loss of polymerase activity."
FT /evidence="ECO:0000269|PubMed:22571765"
FT MUTAGEN 714
FT /note="D->A: Complete loss of viral replication."
FT /evidence="ECO:0000269|PubMed:24116139"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 14..20
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:1WAJ"
FT STRAND 26..31
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:4DTU"
FT STRAND 48..51
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 56..61
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 65..78
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:1WAJ"
FT HELIX 88..96
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 110..116
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:3SQ1"
FT TURN 126..128
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:3QEX"
FT TURN 141..144
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:2ATQ"
FT HELIX 164..168
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:3QEX"
FT TURN 176..179
FT /evidence="ECO:0007829|PDB:2ATQ"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 186..193
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 194..207
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 211..214
FT /evidence="ECO:0007829|PDB:3QEX"
FT TURN 218..221
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 222..234
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 236..239
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 248..255
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 258..265
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 269..272
FT /evidence="ECO:0007829|PDB:1IH7"
FT HELIX 273..280
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 290..298
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 312..338
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 340..351
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 355..359
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 361..374
FT /evidence="ECO:0007829|PDB:3QEX"
FT TURN 375..377
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 402..404
FT /evidence="ECO:0007829|PDB:3RWU"
FT STRAND 405..412
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 415..423
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 427..429
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 430..433
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 439..443
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 452..456
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 460..463
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 465..467
FT /evidence="ECO:0007829|PDB:3QEV"
FT HELIX 470..502
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 503..505
FT /evidence="ECO:0007829|PDB:4I9L"
FT STRAND 507..509
FT /evidence="ECO:0007829|PDB:3QEV"
FT STRAND 518..520
FT /evidence="ECO:0007829|PDB:2DY4"
FT HELIX 524..530
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 531..533
FT /evidence="ECO:0007829|PDB:3RMB"
FT HELIX 535..569
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 580..609
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 617..621
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 624..628
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 630..636
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 638..640
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 644..657
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 659..673
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 683..689
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 693..695
FT /evidence="ECO:0007829|PDB:1WAJ"
FT STRAND 700..704
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 707..715
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 718..730
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 731..733
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 739..754
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 757..770
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 771..773
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 776..779
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 781..784
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 789..791
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 792..797
FT /evidence="ECO:0007829|PDB:3LZJ"
FT HELIX 803..814
FT /evidence="ECO:0007829|PDB:3QEX"
FT TURN 815..817
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 819..821
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 828..835
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 837..839
FT /evidence="ECO:0007829|PDB:3RMC"
FT STRAND 842..849
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 856..865
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 868..875
FT /evidence="ECO:0007829|PDB:3QEX"
FT HELIX 877..887
FT /evidence="ECO:0007829|PDB:3QEX"
FT STRAND 891..894
FT /evidence="ECO:0007829|PDB:2DTU"
FT HELIX 897..900
FT /evidence="ECO:0007829|PDB:3QEX"
SQ SEQUENCE 903 AA; 104613 MW; A3983FC16D4C0509 CRC64;
MKEFYLTVEQ IGDSIFERYI DSNGRERTRE VEYKPSLFAH CPESQATKYF DIYGKPCTRK
LFANMRDASQ WIKRMEDIGL EALGMDDFKL AYLSDTYNYE IKYDHTKIRV ANFDIEVTSP
DGFPEPSQAK HPIDAITHYD SIDDRFYVFD LLNSPYGNVE EWSIEIAAKL QEQGGDEVPS
EIIDKIIYMP FDNEKELLME YLNFWQQKTP VILTGWNVES FDIPYVYNRI KNIFGESTAK
RLSPHRKTRV KVIENMYGSR EIITLFGISV LDYIDLYKKF SFTNQPSYSL DYISEFELNV
GKLKYDGPIS KLRESNHQRY ISYNIIDVYR VLQIDAKRQF INLSLDMGYY AKIQIQSVFS
PIKTWDAIIF NSLKEQNKVI PQGRSHPVQP YPGAFVKEPI PNRYKYVMSF DLTSLYPSII
RQVNISPETI AGTFKVAPLH DYINAVAERP SDVYSCSPNG MMYYKDRDGV VPTEITKVFN
QRKEHKGYML AAQRNGEIIK EALHNPNLSV DEPLDVDYRF DFSDEIKEKI KKLSAKSLNE
MLFRAQRTEV AGMTAQINRK LLINSLYGAL GNVWFRYYDL RNATAITTFG QMALQWIERK
VNEYLNEVCG TEGEAFVLYG DTDSIYVSAD KIIDKVGESK FRDTNHWVDF LDKFARERME
PAIDRGFREM CEYMNNKQHL MFMDREAIAG PPLGSKGIGG FWTGKKRYAL NVWDMEGTRY
AEPKLKIMGL ETQKSSTPKA VQKALKECIR RMLQEGEESL QEYFKEFEKE FRQLNYISIA
SVSSANNIAK YDVGGFPGPK CPFHIRGILT YNRAIKGNID APQVVEGEKV YVLPLREGNP
FGDKCIAWPS GTEITDLIKD DVLHWMDYTV LLEKTFIKPL EGFTSAAKLD YEKKASLFDM
FDF
