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DNA-directed DNA polymerase (EC 2.7.7.7) (EC 3.1.11.-) (Gp43)

 DPOL_BPR69              Reviewed;         903 AA.
Q38087; Q76XX8;
15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
28-FEB-2018, entry version 130.
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:17098747, ECO:0000269|PubMed:18503083, ECO:0000269|PubMed:20795733, ECO:0000269|PubMed:22616982, ECO:0000269|PubMed:24116139};
EC=3.1.11.- {ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:17098747, ECO:0000269|PubMed:23214497, ECO:0000269|PubMed:24116139};
AltName: Full=Gp43;
Name=43;
Enterobacteria phage RB69 (Bacteriophage RB69).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Myoviridae;
Tevenvirinae; Rb69virus.
NCBI_TaxID=12353;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
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).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Petrov V., Nolan J., Chin D., Letarov A., Krisch H.M., Karam J.D.;
"Enterobacteria phage RB69 complete genome.";
Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases.
[3]
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).
[4]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS), AND DOMAIN.
PubMed=9215631; DOI=10.1016/S0092-8674(00)80296-2;
Wang J., Sattar A.K., Wang C.C., Karam J.D., Konigsberg W.H.,
Steitz T.A.;
"Crystal structure of a pol alpha family replication DNA polymerase
from bacteriophage RB69.";
Cell 89:1087-1099(1997).
[5]
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH THE POLYMERASE
CLAMP, AND INTERACTION WITH THE POLYMERASE CLAMP.
PubMed=10535734; DOI=10.1016/S0092-8674(00)81647-5;
Shamoo Y., Steitz T.A.;
"Building a replisome from interacting pieces: sliding clamp complexed
to a peptide from DNA polymerase and a polymerase editing complex.";
Cell 99:155-166(1999).
[6] {ECO:0000244|PDB:1IG9, ECO:0000244|PDB:1IH7}
X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS) IN COMPLEX WITH CALCIUM AND
TTP, AND COFACTOR.
PubMed=11389835; DOI=10.1016/S0092-8674(01)00367-1;
Franklin M.C., Wang J., Steitz T.A.;
"Structure of the replicating complex of a pol alpha family DNA
polymerase.";
Cell 105:657-667(2001).
[7] {ECO:0000244|PDB:1Q9X, ECO:0000244|PDB:1Q9Y}
X-RAY CRYSTALLOGRAPHY (2.69 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
COFACTOR.
PubMed=15057282; DOI=10.1038/sj.emboj.7600158;
Freisinger E., Grollman A.P., Miller H., Kisker C.;
"Lesion (in)tolerance reveals insights into DNA replication
fidelity.";
EMBO J. 23:1494-1505(2004).
[8] {ECO:0000244|PDB:2P5O}
X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS), AND COFACTOR.
PubMed=15057283; DOI=10.1038/sj.emboj.7600150;
Hogg M., Wallace S.S., Doublie S.;
"Crystallographic snapshots of a replicative DNA polymerase
encountering an abasic site.";
EMBO J. 23:1483-1493(2004).
[9] {ECO:0000244|PDB:2OYQ, ECO:0000244|PDB:2OZM, ECO:0000244|PDB:2OZS, ECO:0000244|PDB:2P5G}
X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
COFACTOR.
PubMed=17718515; DOI=10.1021/bi7008807;
Zahn K.E., Belrhali H., Wallace S.S., Doublie S.;
"Caught bending the A-rule: crystal structures of translesion DNA
synthesis with a non-natural nucleotide.";
Biochemistry 46:10551-10561(2007).
[10] {ECO:0000244|PDB:2DTU}
X-RAY CRYSTALLOGRAPHY (2.37 ANGSTROMS) OF 1-902, CATALYTIC ACTIVITY,
AND FUNCTION.
PubMed=17098747; DOI=10.1074/jbc.M605675200;
Hogg M., Aller P., Konigsberg W., Wallace S.S., Doublie S.;
"Structural and biochemical investigation of the role in proofreading
of a beta hairpin loop found in the exonuclease domain of a
replicative DNA polymerase of the B family.";
J. Biol. Chem. 282:1432-1444(2007).
[11] {ECO:0000244|PDB:2DY4}
X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
PubMed=17210917; DOI=10.1073/pnas.0606648104;
Aller P., Rould M.A., Hogg M., Wallace S.S., Doublie S.;
"A structural rationale for stalling of a replicative DNA polymerase
at the most common oxidative thymine lesion, thymine glycol.";
Proc. Natl. Acad. Sci. U.S.A. 104:814-818(2007).
[12] {ECO:0000244|PDB:3CQ8}
X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH CALCIUM; DNA
AND TTP, FUNCTION, COFACTOR, CATALYTIC ACTIVITY, AND MUTAGENESIS OF
LEU-415.
PubMed=18503083; DOI=10.1093/nar/gkn312;
Zhong X., Pedersen L.C., Kunkel T.A.;
"Characterization of a replicative DNA polymerase mutant with reduced
fidelity and increased translesion synthesis capacity.";
Nucleic Acids Res. 36:3892-3904(2008).
[13] {ECO:0000244|PDB:3LDS}
X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH MANGANESE,
MUTAGENESIS OF LEU-561, AND COFACTOR.
PubMed=20166748; DOI=10.1021/bi901488d;
Hogg M., Rudnicki J., Midkiff J., Reha-Krantz L., Doublie S.,
Wallace S.S.;
"Kinetics of mismatch formation opposite lesions by the replicative
DNA polymerase from bacteriophage RB69.";
Biochemistry 49:2317-2325(2010).
[14] {ECO:0000244|PDB:3L8B}
X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), AND COFACTOR.
PubMed=20166752; DOI=10.1021/bi902195p;
Aller P., Ye Y., Wallace S.S., Burrows C.J., Doublie S.;
"Crystal structure of a replicative DNA polymerase bound to the
oxidized guanine lesion guanidinohydantoin.";
Biochemistry 49:2502-2509(2010).
[15] {ECO:0000244|PDB:3LZI, ECO:0000244|PDB:3LZJ}
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CTP AND
CALCIUM, AND MUTAGENESIS OF TYR-567.
PubMed=20411947; DOI=10.1021/bi100102s;
Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.;
"Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to
be inserted opposite 7,8-dihydro-8-oxoguanine.";
Biochemistry 49:4116-4125(2010).
[16] {ECO:0000244|PDB:3NAE}
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH CALCIUM,
MUTAGENESIS OF TYR-567, AND CATALYTIC ACTIVITY.
PubMed=20795733; DOI=10.1021/bi100913v;
Beckman J., Wang M., Blaha G., Wang J., Konigsberg W.H.;
"Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP and
dGMP to be inserted opposite Guanidinohydantoin.";
Biochemistry 49:8554-8563(2010).
[17] {ECO:0000244|PDB:3SQ2, ECO:0000244|PDB:3SQ4, ECO:0000244|PDB:3SUN, ECO:0000244|PDB:3SUO, ECO:0000244|PDB:3SUP, ECO:0000244|PDB:3SUQ}
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 1-902 IN COMPLEX WITH DNA
AND TTP, AND MUTAGENESIS OF TYR-567.
PubMed=22023103; DOI=10.1021/bi2014618;
Reha-Krantz L.J., Hariharan C., Subuddhi U., Xia S., Zhao C.,
Beckman J., Christian T., Konigsberg W.;
"Structure of the 2-aminopurine-cytosine base pair formed in the
polymerase active site of the RB69 Y567A-DNA polymerase.";
Biochemistry 50:10136-10149(2011).
[18] {ECO:0000244|PDB:3TAB, ECO:0000244|PDB:3TAE, ECO:0000244|PDB:3TAF, ECO:0000244|PDB:3TAG}
X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS), AND COFACTOR.
PubMed=22026756; DOI=10.1021/bi201219s;
Zahn K.E., Averill A., Wallace S.S., Doublie S.;
"The miscoding potential of 5-hydroxycytosine arises due to template
instability in the replicative polymerase active site.";
Biochemistry 50:10350-10358(2011).
[19] {ECO:0000244|PDB:3NCI}
X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
COFACTOR.
PubMed=21158418; DOI=10.1021/bi101192f;
Wang M., Xia S., Blaha G., Steitz T.A., Konigsberg W.H., Wang J.;
"Insights into base selectivity from the 1.8 A resolution structure of
an RB69 DNA polymerase ternary complex.";
Biochemistry 50:581-590(2011).
[20] {ECO:0000244|PDB:3S9H, ECO:0000244|PDB:3SCX, ECO:0000244|PDB:3SI6, ECO:0000244|PDB:3SJJ, ECO:0000244|PDB:3SNN, ECO:0000244|PDB:3SPY, ECO:0000244|PDB:3SPZ, ECO:0000244|PDB:3SQ0, ECO:0000244|PDB:3SQ1}
X-RAY CRYSTALLOGRAPHY (1.82 ANGSTROMS) OF 1-901 IN COMPLEXES WITH
MAGNESIUM AND MANGANESE, AND COFACTOR.
PubMed=21923197; DOI=10.1021/bi201260h;
Xia S., Wang M., Blaha G., Konigsberg W.H., Wang J.;
"Structural insights into complete metal ion coordination from ternary
complexes of B family RB69 DNA polymerase.";
Biochemistry 50:9114-9124(2011).
[21] {ECO:0000244|PDB:3QEP, ECO:0000244|PDB:3RWU}
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH ATP; CALCIUM
AND TTP.
PubMed=21667997; DOI=10.1021/ja2021735;
Xia S., Konigsberg W.H., Wang J.;
"Hydrogen-bonding capability of a templating difluorotoluene
nucleotide residue in an RB69 DNA polymerase ternary complex.";
J. Am. Chem. Soc. 133:10003-10005(2011).
[22] {ECO:0000244|PDB:3KD1, ECO:0000244|PDB:3KD5}
X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
COFACTOR.
PubMed=21566148; DOI=10.1074/jbc.M111.248864;
Zahn K.E., Tchesnokov E.P., Gotte M., Doublie S.;
"Phosphonoformic acid inhibits viral replication by trapping the
closed form of the DNA polymerase.";
J. Biol. Chem. 286:25246-25255(2011).
[23] {ECO:0000244|PDB:3NDK, ECO:0000244|PDB:3NE6, ECO:0000244|PDB:3NGI, ECO:0000244|PDB:3NHG}
X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEX WITH CALCIUM AND
TTP, AND MUTAGENESIS OF SER-565 AND TYR-567.
PubMed=21216248; DOI=10.1016/j.jmb.2010.12.033;
Xia S., Wang M., Lee H.R., Sinha A., Blaha G., Christian T., Wang J.,
Konigsberg W.;
"Variation in mutation rates caused by RB69pol fidelity mutants can be
rationalized on the basis of their kinetic behavior and crystal
structures.";
J. Mol. Biol. 406:558-570(2011).
[24] {ECO:0000244|PDB:3RMA, ECO:0000244|PDB:3RMB, ECO:0000244|PDB:3RMC, ECO:0000244|PDB:3RMD}
X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS).
PubMed=21781974; DOI=10.1016/j.jmb.2011.07.007;
Aller P., Duclos S., Wallace S.S., Doublie S.;
"A crystallographic study of the role of sequence context in thymine
glycol bypass by a replicative DNA polymerase serendipitously sheds
light on the exonuclease complex.";
J. Mol. Biol. 412:22-34(2011).
[25] {ECO:0000244|PDB:3QEI, ECO:0000244|PDB:3QER, ECO:0000244|PDB:3QES}
X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH CALCIUM.
PubMed=22304682; DOI=10.1021/bi2016487;
Xia S., Eom S.H., Konigsberg W.H., Wang J.;
"Structural basis for differential insertion kinetics of dNMPs
opposite a difluorotoluene nucleotide residue.";
Biochemistry 51:1476-1485(2012).
[26] {ECO:0000244|PDB:4DU1, ECO:0000244|PDB:4DU3, ECO:0000244|PDB:4DU4, ECO:0000244|PDB:4E3S}
X-RAY CRYSTALLOGRAPHY (2.02 ANGSTROMS) IN COMPLEX WITH CALCIUM,
FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-621 AND LYS-706, AND
COFACTOR.
PubMed=22571765; DOI=10.1021/bi300416z;
Xia S., Christian T.D., Wang J., Konigsberg W.H.;
"Probing minor groove hydrogen bonding interactions between RB69 DNA
polymerase and DNA.";
Biochemistry 51:4343-4353(2012).
[27] {ECO:0000244|PDB:3QNN, ECO:0000244|PDB:3QNO}
X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP
AND CALCIUM, AND MUTAGENESIS OF TYR-567.
PubMed=22616982; DOI=10.1021/bi300241m;
Xia S., Beckman J., Wang J., Konigsberg W.H.;
"Using a fluorescent cytosine analogue tC(o) to probe the effect of
the Y567 to Ala substitution on the preinsertion steps of dNMP
incorporation by RB69 DNA polymerase.";
Biochemistry 51:4609-4617(2012).
[28] {ECO:0000244|PDB:4DTJ, ECO:0000244|PDB:4DTM, ECO:0000244|PDB:4DTN, ECO:0000244|PDB:4DTO, ECO:0000244|PDB:4DTP, ECO:0000244|PDB:4DTR, ECO:0000244|PDB:4DTS, ECO:0000244|PDB:4DTU, ECO:0000244|PDB:4DTX}
X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEXES WITH CALCIUM; DNA;
ATP; CTP; GTP AND TTP, CATALYTIC ACTIVITY, AND FUNCTION.
PubMed=22630605; DOI=10.1021/bi300296q;
Xia S., Vashishtha A., Bulkley D., Eom S.H., Wang J., Konigsberg W.H.;
"Contribution of partial charge interactions and base stacking to the
efficiency of primer extension at and beyond abasic sites in DNA.";
Biochemistry 51:4922-4931(2012).
[29] {ECO:0000244|PDB:3UIQ}
X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) IN COMPLEX WITH CALCIUM, AND
COFACTOR.
PubMed=22238207; DOI=10.1002/pro.2026;
Xia S., Eom S.H., Konigsberg W.H., Wang J.;
"Bidentate and tridentate metal-ion coordination states within ternary
complexes of RB69 DNA polymerase.";
Protein Sci. 21:447-451(2012).
[30]
X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH CALCIUM AND
TTP, COFACTOR, MUTAGENESIS OF ASP-222 AND ASP-327, AND CATALYTIC
ACTIVITY.
PubMed=23214497; DOI=10.1021/ja3079048;
Xia S., Wang J., Konigsberg W.H.;
"DNA mismatch synthesis complexes provide insights into base
selectivity of a B family DNA polymerase.";
J. Am. Chem. Soc. 135:193-202(2013).
[31] {ECO:0000244|PDB:4J2A, ECO:0000244|PDB:4J2B, ECO:0000244|PDB:4J2E}
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 1-901 IN COMPLEX WITH ATP;
CALCIUM AND TTP, MUTAGENESIS OF LEU-415, AND COFACTOR.
PubMed=23921641; DOI=10.1093/nar/gkt674;
Xia S., Wood M., Bradley M.J., De La Cruz E.M., Konigsberg W.H.;
"Alteration in the cavity size adjacent to the active site of RB69 DNA
polymerase changes its conformational dynamics.";
Nucleic Acids Res. 41:9077-9089(2013).
[32] {ECO:0000244|PDB:4I9L, ECO:0000244|PDB:4I9Q, ECO:0000244|PDB:4KHN}
X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS), MUTAGENESIS OF ASP-714,
CATALYTIC ACTIVITY, AND COFACTOR.
PubMed=24116139; DOI=10.1371/journal.pone.0076700;
Jacewicz A., Trzemecka A., Guja K.E., Plochocka D., Yakubovskaya E.,
Bebenek A., Garcia-Diaz M.;
"A remote palm domain residue of RB69 DNA polymerase is critical for
enzyme activity and influences the conformation of the active site.";
PLoS ONE 8:76700-76700(2013).
[33] {ECO:0000244|PDB:4KHQ, ECO:0000244|PDB:4KHS, ECO:0000244|PDB:4KHU, ECO:0000244|PDB:4KHW, ECO:0000244|PDB:4KHY, ECO:0000244|PDB:4KI4, ECO:0000244|PDB:4KI6}
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH CALCIUM AND
TTP.
PubMed=24082122; DOI=10.1073/pnas.1309119110;
Clausen A.R., Murray M.S., Passer A.R., Pedersen L.C., Kunkel T.A.;
"Structure-function analysis of ribonucleotide bypass by B family DNA
replicases.";
Proc. Natl. Acad. Sci. U.S.A. 110:16802-16807(2013).
[34] {ECO:0000244|PDB:4M3R, ECO:0000244|PDB:4M3T, ECO:0000244|PDB:4M3U, ECO:0000244|PDB:4M3W, ECO:0000244|PDB:4M3X, ECO:0000244|PDB:4M3Y, ECO:0000244|PDB:4M3Z, ECO:0000244|PDB:4M41, ECO:0000244|PDB:4M42, ECO:0000244|PDB:4M45}
X-RAY CRYSTALLOGRAPHY (1.84 ANGSTROMS) IN COMPLEX WITH ATP AND
CALCIUM.
PubMed=24458997; DOI=10.1002/pro.2434;
Xia S., Konigsberg W.H.;
"Mispairs with Watson-Crick base-pair geometry observed in ternary
complexes of an RB69 DNA polymerase variant.";
Protein Sci. 23:508-513(2014).
-!- 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:17098747,
ECO:0000269|PubMed:18503083, ECO:0000269|PubMed:22571765,
ECO:0000269|PubMed:22616982}.
-!- CATALYTIC ACTIVITY: Deoxynucleoside triphosphate + DNA(n) =
diphosphate + DNA(n+1). {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}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:20166752, ECO:0000269|PubMed:22026756,
ECO:0000305|PubMed:11389835, ECO:0000305|PubMed:15057282,
ECO:0000305|PubMed:15057283, ECO:0000305|PubMed:17718515,
ECO:0000305|PubMed:18503083, ECO:0000305|PubMed:20166748,
ECO:0000305|PubMed:21158418, ECO:0000305|PubMed:21566148,
ECO:0000305|PubMed:21923197, ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:23214497, ECO:0000305|PubMed:23921641,
ECO:0000305|PubMed:24116139};
-!- 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 (By
similarity). Interacts with the polymerase clamp; this interaction
constitutes the polymerase holoenzyme (PubMed:10535734).
{ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:10535734}.
-!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity
(PubMed:9215631). The C-terminus contains the polymerase activity
and is involved in binding to the polymerase clamp protein
(PubMed:9215631). A beta hairpin structure is necessary for the
proofreading function of the polymerase (By similarity).
{ECO:0000255|HAMAP-Rule:MF_04100, ECO:0000269|PubMed:9215631}.
-!- SIMILARITY: Belongs to the DNA polymerase type-B family.
{ECO:0000255|HAMAP-Rule:MF_04100}.
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EMBL; U34036; AAA93077.1; -; Genomic_DNA.
EMBL; AY303349; AAP75958.1; -; Genomic_DNA.
RefSeq; NP_861746.1; NC_004928.1.
PDB; 1B1F; Model; -; R=387-892.
PDB; 1B8H; X-ray; 3.00 A; D=893-903.
PDB; 1CLQ; X-ray; 2.70 A; A=1-903.
PDB; 1IG9; X-ray; 2.60 A; A=1-903.
PDB; 1IH7; X-ray; 2.21 A; A=1-903.
PDB; 1Q9X; X-ray; 2.69 A; A/B/C/D=1-903.
PDB; 1Q9Y; X-ray; 2.80 A; A=1-903.
PDB; 1QE4; Model; -; F=1-903.
PDB; 1WAF; X-ray; 3.20 A; A/B=1-903.
PDB; 1WAG; Model; -; R=1-903.
PDB; 1WAH; Model; -; R=1-903.
PDB; 1WAI; Model; -; R=1-903.
PDB; 1WAJ; X-ray; 2.80 A; A=1-903.
PDB; 2ATQ; X-ray; 3.20 A; A=1-903.
PDB; 2DTU; X-ray; 2.37 A; A/B/C/D=1-902.
PDB; 2DY4; X-ray; 2.65 A; A/B/C/D=1-903.
PDB; 2OYQ; X-ray; 2.86 A; A/B/C/D=1-903.
PDB; 2OZM; X-ray; 2.86 A; A=1-903.
PDB; 2OZS; X-ray; 2.75 A; A=1-903.
PDB; 2P5G; X-ray; 2.80 A; A/B/C/D=1-903.
PDB; 2P5O; X-ray; 2.80 A; A/B/C/D=1-903.
PDB; 3CFO; X-ray; 2.60 A; A=1-903.
PDB; 3CFP; X-ray; 2.50 A; A=1-903.
PDB; 3CFR; X-ray; 2.40 A; A=1-903.
PDB; 3CQ8; X-ray; 2.50 A; A=1-903.
PDB; 3KD1; X-ray; 2.66 A; E=1-903.
PDB; 3KD5; X-ray; 2.69 A; E=1-903.
PDB; 3L8B; X-ray; 2.15 A; A/B=1-903.
PDB; 3LDS; X-ray; 3.00 A; A=1-903.
PDB; 3LZI; X-ray; 2.30 A; A=1-903.
PDB; 3LZJ; X-ray; 2.05 A; A=1-903.
PDB; 3NAE; X-ray; 2.00 A; A=1-903.
PDB; 3NCI; X-ray; 1.79 A; A=1-903.
PDB; 3NDK; X-ray; 2.00 A; A=1-903.
PDB; 3NE6; X-ray; 2.00 A; A=1-903.
PDB; 3NGI; X-ray; 1.89 A; A=1-903.
PDB; 3NHG; X-ray; 2.50 A; A=1-903.
PDB; 3QEI; X-ray; 2.18 A; A=1-903.
PDB; 3QEP; X-ray; 1.80 A; A=1-903.
PDB; 3QER; X-ray; 1.96 A; A=1-903.
PDB; 3QES; X-ray; 1.98 A; A=1-903.
PDB; 3QET; X-ray; 2.08 A; A=1-903.
PDB; 3QEV; X-ray; 1.77 A; A=1-903.
PDB; 3QEW; X-ray; 1.84 A; A=1-903.
PDB; 3QEX; X-ray; 1.73 A; A=1-903.
PDB; 3QNN; X-ray; 1.92 A; A=1-901.
PDB; 3QNO; X-ray; 1.88 A; A=1-901.
PDB; 3RMA; X-ray; 2.84 A; A/B/C/D=1-903.
PDB; 3RMB; X-ray; 2.65 A; A/B/C/D=1-903.
PDB; 3RMC; X-ray; 3.00 A; A/B/C/D=1-903.
PDB; 3RMD; X-ray; 2.98 A; A/B/C/D=1-903.
PDB; 3RWU; X-ray; 2.33 A; A=1-901.
PDB; 3S9H; X-ray; 1.95 A; A=1-903.
PDB; 3SCX; X-ray; 2.35 A; A=1-901.
PDB; 3SI6; X-ray; 1.85 A; A=1-901.
PDB; 3SJJ; X-ray; 2.38 A; A=1-901.
PDB; 3SNN; X-ray; 2.00 A; A=1-901.
PDB; 3SPY; X-ray; 2.14 A; A=1-901.
PDB; 3SPZ; X-ray; 2.43 A; A=1-903.
PDB; 3SQ0; X-ray; 2.00 A; A=1-903.
PDB; 3SQ1; X-ray; 1.82 A; A=1-901.
PDB; 3SQ2; X-ray; 2.10 A; A=1-902.
PDB; 3SQ4; X-ray; 2.23 A; A=1-902.
PDB; 3SUN; X-ray; 2.42 A; A=1-895.
PDB; 3SUO; X-ray; 2.23 A; A=1-900.
PDB; 3SUP; X-ray; 2.32 A; A=1-903.
PDB; 3SUQ; X-ray; 3.15 A; A=1-897.
PDB; 3TAB; X-ray; 2.80 A; A/B/C/D=1-903.
PDB; 3TAE; X-ray; 2.71 A; A/B/C/D=1-903.
PDB; 3TAF; X-ray; 3.00 A; A/B/C/D=1-903.
PDB; 3TAG; X-ray; 2.95 A; A/B/C/D=1-903.
PDB; 3UIQ; X-ray; 1.88 A; A=1-903.
PDB; 4DTJ; X-ray; 1.90 A; A=1-901.
PDB; 4DTM; X-ray; 1.95 A; A=1-901.
PDB; 4DTN; X-ray; 1.96 A; A=1-903.
PDB; 4DTO; X-ray; 2.05 A; A=1-903.
PDB; 4DTP; X-ray; 2.05 A; A=1-903.
PDB; 4DTR; X-ray; 2.04 A; A=1-903.
PDB; 4DTS; X-ray; 1.96 A; A=1-903.
PDB; 4DTU; X-ray; 1.86 A; A=1-903.
PDB; 4DTX; X-ray; 1.84 A; A=1-903.
PDB; 4DU1; X-ray; 2.15 A; A=1-903.
PDB; 4DU3; X-ray; 2.02 A; A=1-903.
PDB; 4DU4; X-ray; 2.28 A; A=1-903.
PDB; 4E3S; X-ray; 2.04 A; A=1-903.
PDB; 4FJ5; X-ray; 2.05 A; A=1-903.
PDB; 4FJ7; X-ray; 1.90 A; A=1-903.
PDB; 4FJ8; X-ray; 2.19 A; A=1-903.
PDB; 4FJ9; X-ray; 1.97 A; A=1-903.
PDB; 4FJG; X-ray; 2.02 A; A=1-903.
PDB; 4FJH; X-ray; 2.11 A; A=1-903.
PDB; 4FJI; X-ray; 2.20 A; A=1-903.
PDB; 4FJJ; X-ray; 1.99 A; A=1-903.
PDB; 4FJK; X-ray; 2.00 A; A=1-903.
PDB; 4FJL; X-ray; 1.87 A; A=1-903.
PDB; 4FJM; X-ray; 2.02 A; A=1-903.
PDB; 4FJN; X-ray; 1.98 A; A=1-903.
PDB; 4FJX; X-ray; 2.11 A; A=1-903.
PDB; 4FK0; X-ray; 2.18 A; A=1-903.
PDB; 4FK2; X-ray; 1.98 A; A=1-903.
PDB; 4FK4; X-ray; 1.90 A; A=1-903.
PDB; 4I9L; X-ray; 2.60 A; A=1-903.
PDB; 4I9Q; X-ray; 2.30 A; A/B=1-903.
PDB; 4J2A; X-ray; 1.80 A; A=1-901.
PDB; 4J2B; X-ray; 2.04 A; A=1-901.
PDB; 4J2D; X-ray; 1.76 A; A=1-901.
PDB; 4J2E; X-ray; 2.02 A; A=1-901.
PDB; 4KHN; X-ray; 2.55 A; A/B=1-903.
PDB; 4KHQ; X-ray; 2.19 A; A=1-903.
PDB; 4KHS; X-ray; 2.12 A; A=1-903.
PDB; 4KHU; X-ray; 2.05 A; A=1-903.
PDB; 4KHW; X-ray; 2.37 A; A=1-903.
PDB; 4KHY; X-ray; 2.25 A; A=1-903.
PDB; 4KI4; X-ray; 2.45 A; A=1-903.
PDB; 4KI6; X-ray; 2.55 A; A=1-903.
PDB; 4M3R; X-ray; 2.07 A; A=1-903.
PDB; 4M3T; X-ray; 1.90 A; A=1-903.
PDB; 4M3U; X-ray; 2.07 A; A=1-903.
PDB; 4M3W; X-ray; 2.10 A; A=1-903.
PDB; 4M3X; X-ray; 2.20 A; A=1-903.
PDB; 4M3Y; X-ray; 1.86 A; A=1-903.
PDB; 4M3Z; X-ray; 1.84 A; A=1-903.
PDB; 4M41; X-ray; 2.15 A; A=1-903.
PDB; 4M42; X-ray; 2.04 A; A=1-903.
PDB; 4M45; X-ray; 1.89 A; A=1-903.
PDB; 5GNQ; X-ray; 2.10 A; A/B=1-903.
PDBsum; 1B1F; -.
PDBsum; 1B8H; -.
PDBsum; 1CLQ; -.
PDBsum; 1IG9; -.
PDBsum; 1IH7; -.
PDBsum; 1Q9X; -.
PDBsum; 1Q9Y; -.
PDBsum; 1QE4; -.
PDBsum; 1WAF; -.
PDBsum; 1WAG; -.
PDBsum; 1WAH; -.
PDBsum; 1WAI; -.
PDBsum; 1WAJ; -.
PDBsum; 2ATQ; -.
PDBsum; 2DTU; -.
PDBsum; 2DY4; -.
PDBsum; 2OYQ; -.
PDBsum; 2OZM; -.
PDBsum; 2OZS; -.
PDBsum; 2P5G; -.
PDBsum; 2P5O; -.
PDBsum; 3CFO; -.
PDBsum; 3CFP; -.
PDBsum; 3CFR; -.
PDBsum; 3CQ8; -.
PDBsum; 3KD1; -.
PDBsum; 3KD5; -.
PDBsum; 3L8B; -.
PDBsum; 3LDS; -.
PDBsum; 3LZI; -.
PDBsum; 3LZJ; -.
PDBsum; 3NAE; -.
PDBsum; 3NCI; -.
PDBsum; 3NDK; -.
PDBsum; 3NE6; -.
PDBsum; 3NGI; -.
PDBsum; 3NHG; -.
PDBsum; 3QEI; -.
PDBsum; 3QEP; -.
PDBsum; 3QER; -.
PDBsum; 3QES; -.
PDBsum; 3QET; -.
PDBsum; 3QEV; -.
PDBsum; 3QEW; -.
PDBsum; 3QEX; -.
PDBsum; 3QNN; -.
PDBsum; 3QNO; -.
PDBsum; 3RMA; -.
PDBsum; 3RMB; -.
PDBsum; 3RMC; -.
PDBsum; 3RMD; -.
PDBsum; 3RWU; -.
PDBsum; 3S9H; -.
PDBsum; 3SCX; -.
PDBsum; 3SI6; -.
PDBsum; 3SJJ; -.
PDBsum; 3SNN; -.
PDBsum; 3SPY; -.
PDBsum; 3SPZ; -.
PDBsum; 3SQ0; -.
PDBsum; 3SQ1; -.
PDBsum; 3SQ2; -.
PDBsum; 3SQ4; -.
PDBsum; 3SUN; -.
PDBsum; 3SUO; -.
PDBsum; 3SUP; -.
PDBsum; 3SUQ; -.
PDBsum; 3TAB; -.
PDBsum; 3TAE; -.
PDBsum; 3TAF; -.
PDBsum; 3TAG; -.
PDBsum; 3UIQ; -.
PDBsum; 4DTJ; -.
PDBsum; 4DTM; -.
PDBsum; 4DTN; -.
PDBsum; 4DTO; -.
PDBsum; 4DTP; -.
PDBsum; 4DTR; -.
PDBsum; 4DTS; -.
PDBsum; 4DTU; -.
PDBsum; 4DTX; -.
PDBsum; 4DU1; -.
PDBsum; 4DU3; -.
PDBsum; 4DU4; -.
PDBsum; 4E3S; -.
PDBsum; 4FJ5; -.
PDBsum; 4FJ7; -.
PDBsum; 4FJ8; -.
PDBsum; 4FJ9; -.
PDBsum; 4FJG; -.
PDBsum; 4FJH; -.
PDBsum; 4FJI; -.
PDBsum; 4FJJ; -.
PDBsum; 4FJK; -.
PDBsum; 4FJL; -.
PDBsum; 4FJM; -.
PDBsum; 4FJN; -.
PDBsum; 4FJX; -.
PDBsum; 4FK0; -.
PDBsum; 4FK2; -.
PDBsum; 4FK4; -.
PDBsum; 4I9L; -.
PDBsum; 4I9Q; -.
PDBsum; 4J2A; -.
PDBsum; 4J2B; -.
PDBsum; 4J2D; -.
PDBsum; 4J2E; -.
PDBsum; 4KHN; -.
PDBsum; 4KHQ; -.
PDBsum; 4KHS; -.
PDBsum; 4KHU; -.
PDBsum; 4KHW; -.
PDBsum; 4KHY; -.
PDBsum; 4KI4; -.
PDBsum; 4KI6; -.
PDBsum; 4M3R; -.
PDBsum; 4M3T; -.
PDBsum; 4M3U; -.
PDBsum; 4M3W; -.
PDBsum; 4M3X; -.
PDBsum; 4M3Y; -.
PDBsum; 4M3Z; -.
PDBsum; 4M41; -.
PDBsum; 4M42; -.
PDBsum; 4M45; -.
PDBsum; 5GNQ; -.
ProteinModelPortal; Q38087; -.
SMR; Q38087; -.
DrugBank; DB08245; 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-NITRO-1H-INDOLE.
DrugBank; DB02857; Guanosine.
DrugBank; DB01972; Guanosine-5'-Monophosphate.
GeneID; 1494172; -.
KEGG; vg:1494172; -.
KO; K18942; -.
OrthoDB; VOG0900001M; -.
SABIO-RK; Q38087; -.
EvolutionaryTrace; Q38087; -.
Proteomes; UP000000876; 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:0006260; P:DNA replication; IEA:UniProtKB-KW.
GO; GO:0039693; P:viral DNA genome 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 1 903 DNA-directed DNA polymerase.
/FTId=PRO_0000046547.
REGION 103 340 3'-5'exonuclease. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:9215631}.
REGION 248 264 Beta hairpin. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:17098747}.
REGION 380 903 Polymerase. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:9215631}.
REGION 414 416 Substrate binding. {ECO:0000244|PDB:1IG9,
ECO:0000244|PDB:3CFP,
ECO:0000244|PDB:3CFR,
ECO:0000244|PDB:3CQ8,
ECO:0000244|PDB:3LZJ,
ECO:0000244|PDB:3NGI,
ECO:0000244|PDB:3NHG,
ECO:0000244|PDB:3QEP,
ECO:0000244|PDB:3QET,
ECO:0000244|PDB:3QNO,
ECO:0000244|PDB:3RWU,
ECO:0000244|PDB:3SQ2,
ECO:0000244|PDB:3SQ4,
ECO:0000244|PDB:3SUN,
ECO:0000244|PDB:3SUO,
ECO:0000244|PDB:4DTJ,
ECO:0000244|PDB:4DTX,
ECO:0000244|PDB:4FJ9,
ECO:0000244|PDB:4FJJ,
ECO:0000244|PDB:4FJN,
ECO:0000244|PDB:4FK2,
ECO:0000244|PDB:4J2A,
ECO:0000244|PDB:4J2B,
ECO:0000244|PDB:4J2D,
ECO:0000244|PDB:4J2E,
ECO:0000244|PDB:4KHS,
ECO:0000244|PDB:4KHU,
ECO:0000244|PDB:4KHW,
ECO:0000244|PDB:4KHY,
ECO:0000244|PDB:4KI4,
ECO:0000244|PDB:4KI6,
ECO:0000244|PDB:4M3R,
ECO:0000244|PDB:4M3T,
ECO:0000244|PDB:4M3U,
ECO:0000244|PDB:4M3W,
ECO:0000244|PDB:4M3X,
ECO:0000244|PDB:4M3Y,
ECO:0000244|PDB:4M3Z,
ECO:0000244|PDB:4M41,
ECO:0000244|PDB:4M42,
ECO:0000244|PDB:4M45, ECO:0000255|HAMAP-
Rule:MF_04100}.
REGION 705 708 Binding of DNA in B-conformation.
{ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:11389835,
ECO:0000269|PubMed:24116139}.
REGION 897 903 Interaction with the polymerase clamp.
{ECO:0000255|HAMAP-Rule:MF_04100}.
METAL 114 114 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
METAL 116 116 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100}.
METAL 222 222 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000305|PubMed:23214497}.
METAL 327 327 Magnesium 1; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000305|PubMed:23214497}.
METAL 327 327 Magnesium 2; catalytic; for 3'-5'
exonuclease activity. {ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000305|PubMed:23214497}.
METAL 411 411 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000244|PDB:2OZM,
ECO:0000244|PDB:2OZS,
ECO:0000244|PDB:3KD5,
ECO:0000244|PDB:3SI6,
ECO:0000244|PDB:3SNN,
ECO:0000244|PDB:3SPY, ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:15057283,
ECO:0000269|PubMed:17718515,
ECO:0000269|PubMed:21566148,
ECO:0000269|PubMed:21923197,
ECO:0000269|PubMed:22026756,
ECO:0000305|PubMed:11389835,
ECO:0000305|PubMed:15057282,
ECO:0000305|PubMed:18503083,
ECO:0000305|PubMed:20166748,
ECO:0000305|PubMed:21158418,
ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:23214497,
ECO:0000305|PubMed:23921641,
ECO:0000305|PubMed:24116139}.
METAL 411 411 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000244|PDB:2OZM,
ECO:0000244|PDB:2OZS,
ECO:0000244|PDB:3KD5,
ECO:0000244|PDB:3SI6,
ECO:0000244|PDB:3SNN,
ECO:0000244|PDB:3SPY, ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:15057283,
ECO:0000269|PubMed:17718515,
ECO:0000269|PubMed:21566148,
ECO:0000269|PubMed:21923197,
ECO:0000269|PubMed:22026756,
ECO:0000305|PubMed:11389835,
ECO:0000305|PubMed:15057282,
ECO:0000305|PubMed:18503083,
ECO:0000305|PubMed:20166748,
ECO:0000305|PubMed:21158418,
ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:23214497,
ECO:0000305|PubMed:23921641,
ECO:0000305|PubMed:24116139}.
METAL 412 412 Magnesium 4; catalytic; via carbonyl
oxygen; for polymerase activity.
{ECO:0000244|PDB:2OZM,
ECO:0000244|PDB:2OZS,
ECO:0000244|PDB:3KD5,
ECO:0000244|PDB:3SI6,
ECO:0000244|PDB:3SNN,
ECO:0000244|PDB:3SPY, ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:17718515,
ECO:0000269|PubMed:21566148,
ECO:0000269|PubMed:21923197,
ECO:0000305|PubMed:18503083,
ECO:0000305|PubMed:23214497,
ECO:0000305|PubMed:23921641}.
METAL 623 623 Magnesium 3; catalytic; for polymerase
activity. {ECO:0000244|PDB:2OZM,
ECO:0000244|PDB:2OZS,
ECO:0000244|PDB:3KD5,
ECO:0000244|PDB:3SI6,
ECO:0000244|PDB:3SNN,
ECO:0000244|PDB:3SPY, ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:15057283,
ECO:0000269|PubMed:17718515,
ECO:0000269|PubMed:20166748,
ECO:0000269|PubMed:20166752,
ECO:0000269|PubMed:21566148,
ECO:0000269|PubMed:21923197,
ECO:0000269|PubMed:22026756,
ECO:0000305|PubMed:11389835,
ECO:0000305|PubMed:15057282,
ECO:0000305|PubMed:18503083,
ECO:0000305|PubMed:21158418,
ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:23214497,
ECO:0000305|PubMed:23921641,
ECO:0000305|PubMed:24116139}.
METAL 623 623 Magnesium 4; catalytic; for polymerase
activity. {ECO:0000244|PDB:2OZM,
ECO:0000244|PDB:2OZS,
ECO:0000244|PDB:3KD5,
ECO:0000244|PDB:3SI6,
ECO:0000244|PDB:3SNN,
ECO:0000244|PDB:3SPY, ECO:0000255|HAMAP-
Rule:MF_04100,
ECO:0000269|PubMed:15057283,
ECO:0000269|PubMed:17718515,
ECO:0000269|PubMed:20166748,
ECO:0000269|PubMed:20166752,
ECO:0000269|PubMed:21566148,
ECO:0000269|PubMed:21923197,
ECO:0000269|PubMed:22026756,
ECO:0000305|PubMed:11389835,
ECO:0000305|PubMed:15057282,
ECO:0000305|PubMed:18503083,
ECO:0000305|PubMed:21158418,
ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:23214497,
ECO:0000305|PubMed:23921641,
ECO:0000305|PubMed:24116139}.
BINDING 482 482 Substrate. {ECO:0000244|PDB:1IG9,
ECO:0000244|PDB:3CFP,
ECO:0000244|PDB:3CFR,
ECO:0000244|PDB:3CQ8,
ECO:0000244|PDB:3LZJ,
ECO:0000244|PDB:3NGI,
ECO:0000244|PDB:3NHG,
ECO:0000244|PDB:3QEP,
ECO:0000244|PDB:3QET,
ECO:0000244|PDB:3QNO,
ECO:0000244|PDB:3RWU,
ECO:0000244|PDB:3SQ2,
ECO:0000244|PDB:3SQ4,
ECO:0000244|PDB:3SUN,
ECO:0000244|PDB:3SUO,
ECO:0000244|PDB:4DTJ,
ECO:0000244|PDB:4DTX,
ECO:0000244|PDB:4FJ9,
ECO:0000244|PDB:4FJJ,
ECO:0000244|PDB:4FJN,
ECO:0000244|PDB:4FK2,
ECO:0000244|PDB:4J2A,
ECO:0000244|PDB:4J2B,
ECO:0000244|PDB:4J2D,
ECO:0000244|PDB:4J2E,
ECO:0000244|PDB:4KHS,
ECO:0000244|PDB:4KHU,
ECO:0000244|PDB:4KHW,
ECO:0000244|PDB:4KHY,
ECO:0000244|PDB:4KI4,
ECO:0000244|PDB:4KI6,
ECO:0000244|PDB:4M3R,
ECO:0000244|PDB:4M3T,
ECO:0000244|PDB:4M3U,
ECO:0000244|PDB:4M3W,
ECO:0000244|PDB:4M3X,
ECO:0000244|PDB:4M3Y,
ECO:0000244|PDB:4M3Z,
ECO:0000244|PDB:4M41,
ECO:0000244|PDB:4M42,
ECO:0000244|PDB:4M45, ECO:0000255|HAMAP-
Rule:MF_04100}.
BINDING 560 560 Substrate. {ECO:0000244|PDB:1IG9,
ECO:0000244|PDB:3CFP,
ECO:0000244|PDB:3CFR,
ECO:0000244|PDB:3CQ8,
ECO:0000244|PDB:3LZJ,
ECO:0000244|PDB:3NGI,
ECO:0000244|PDB:3NHG,
ECO:0000244|PDB:3QEP,
ECO:0000244|PDB:3QET,
ECO:0000244|PDB:3QNO,
ECO:0000244|PDB:3RWU,
ECO:0000244|PDB:3SQ2,
ECO:0000244|PDB:3SQ4,
ECO:0000244|PDB:3SUN,
ECO:0000244|PDB:3SUO,
ECO:0000244|PDB:4DTJ,
ECO:0000244|PDB:4DTX,
ECO:0000244|PDB:4FJJ,
ECO:0000244|PDB:4FJN,
ECO:0000244|PDB:4FK2,
ECO:0000244|PDB:4J2A,
ECO:0000244|PDB:4J2B,
ECO:0000244|PDB:4J2D,
ECO:0000244|PDB:4J2E,
ECO:0000244|PDB:4KHS,
ECO:0000244|PDB:4KHU,
ECO:0000244|PDB:4KHW,
ECO:0000244|PDB:4KHY,
ECO:0000244|PDB:4KI4,
ECO:0000244|PDB:4KI6,
ECO:0000244|PDB:4M3R,
ECO:0000244|PDB:4M3T,
ECO:0000244|PDB:4M3U,
ECO:0000244|PDB:4M3W,
ECO:0000244|PDB:4M3X,
ECO:0000244|PDB:4M3Y,
ECO:0000244|PDB:4M3Z,
ECO:0000244|PDB:4M41,
ECO:0000244|PDB:4M42,
ECO:0000244|PDB:4M45, ECO:0000255|HAMAP-
Rule:MF_04100}.
SITE 621 621 Optimization of metal coordination by the
polymerase active site.
{ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000305|PubMed:15057283,
ECO:0000305|PubMed:20166752,
ECO:0000305|PubMed:22571765,
ECO:0000305|PubMed:24116139}.
SITE 706 706 Optimization of metal coordination by the
polymerase active site.
{ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:15057283,
ECO:0000269|PubMed:22571765}.
SITE 714 714 Essential for viral replication.
{ECO:0000255|HAMAP-Rule:MF_04100,
ECO:0000269|PubMed:24116139}.
MUTAGEN 222 222 D->A: Complete loss of 3'-5' exonuclease
activity. {ECO:0000269|PubMed:23214497}.
MUTAGEN 327 327 D->A: Complete loss of 3'-5' exonuclease
activity. {ECO:0000269|PubMed:23214497}.
MUTAGEN 415 415 L->A,G: Decreases base selectivity by
several hundred fold.
{ECO:0000269|PubMed:23921641}.
MUTAGEN 415 415 L->G,F: Increased misinsertion, increased
mismatch extension and inefficient
proofreading.
{ECO:0000269|PubMed:18503083}.
MUTAGEN 415 415 L->M: No effect on base selectivity.
{ECO:0000269|PubMed:23921641}.
MUTAGEN 561 561 L->A: No effect on the ability to
recognize damaged DNA. Increase in
probability of nucleotide incorporation.
{ECO:0000269|PubMed:20166748}.
MUTAGEN 565 565 S->G: Increased incorporation efficiency
of correct dNMPs; when associated with A-
567. {ECO:0000269|PubMed:21216248}.
MUTAGEN 567 567 Y->A: Inserts both dCMP and dAMP opposite
8-oxoG rapidly and with equal efficiency.
100-fold increase of dAMP and dGMP when
situated opposite guanidinohydantoin.
Increased incorporation efficiency of
correct dNMPs; when associated with G-
565. {ECO:0000269|PubMed:20411947,
ECO:0000269|PubMed:21216248,
ECO:0000269|PubMed:22616982}.
MUTAGEN 621 621 D->A: Drastic decrease in the efficiency
of incorporation of dGMP.
{ECO:0000269|PubMed:22571765}.
MUTAGEN 706 706 K->A: Almost complete loss of polymerase
activity. {ECO:0000269|PubMed:22571765}.
MUTAGEN 714 714 D->A: Complete loss of viral replication.
{ECO:0000269|PubMed:24116139}.
STRAND 4 11 {ECO:0000244|PDB:3QEX}.
STRAND 14 20 {ECO:0000244|PDB:3QEX}.
STRAND 22 24 {ECO:0000244|PDB:1WAJ}.
STRAND 26 31 {ECO:0000244|PDB:3QEX}.
STRAND 36 40 {ECO:0000244|PDB:3QEX}.
STRAND 43 45 {ECO:0000244|PDB:4DTU}.
STRAND 48 51 {ECO:0000244|PDB:3QEX}.
STRAND 56 61 {ECO:0000244|PDB:3QEX}.
HELIX 65 78 {ECO:0000244|PDB:3QEX}.
STRAND 82 84 {ECO:0000244|PDB:1WAJ}.
HELIX 88 96 {ECO:0000244|PDB:3QEX}.
HELIX 105 107 {ECO:0000244|PDB:3QEX}.
STRAND 110 116 {ECO:0000244|PDB:3QEX}.
STRAND 120 123 {ECO:0000244|PDB:3SQ1}.
TURN 126 128 {ECO:0000244|PDB:3QEX}.
STRAND 135 140 {ECO:0000244|PDB:3QEX}.
TURN 141 144 {ECO:0000244|PDB:3QEX}.
STRAND 145 151 {ECO:0000244|PDB:3QEX}.
STRAND 152 156 {ECO:0000244|PDB:2ATQ}.
HELIX 164 168 {ECO:0000244|PDB:3QEX}.
HELIX 171 173 {ECO:0000244|PDB:3QEX}.
TURN 176 179 {ECO:0000244|PDB:2ATQ}.
HELIX 180 183 {ECO:0000244|PDB:3QEX}.
STRAND 186 193 {ECO:0000244|PDB:3QEX}.
HELIX 194 207 {ECO:0000244|PDB:3QEX}.
STRAND 211 214 {ECO:0000244|PDB:3QEX}.
TURN 218 221 {ECO:0000244|PDB:3QEX}.
HELIX 222 234 {ECO:0000244|PDB:3QEX}.
HELIX 236 239 {ECO:0000244|PDB:3QEX}.
HELIX 240 242 {ECO:0000244|PDB:3QEX}.
STRAND 248 255 {ECO:0000244|PDB:3QEX}.
STRAND 258 265 {ECO:0000244|PDB:3QEX}.
STRAND 269 272 {ECO:0000244|PDB:1IH7}.
HELIX 273 280 {ECO:0000244|PDB:3QEX}.
HELIX 290 298 {ECO:0000244|PDB:3QEX}.
HELIX 309 311 {ECO:0000244|PDB:3QEX}.
HELIX 312 338 {ECO:0000244|PDB:3QEX}.
HELIX 340 351 {ECO:0000244|PDB:3QEX}.
HELIX 355 359 {ECO:0000244|PDB:3QEX}.
HELIX 361 374 {ECO:0000244|PDB:3QEX}.
TURN 375 377 {ECO:0000244|PDB:3QEX}.
STRAND 402 404 {ECO:0000244|PDB:3RWU}.
STRAND 405 412 {ECO:0000244|PDB:3QEX}.
HELIX 415 423 {ECO:0000244|PDB:3QEX}.
HELIX 427 429 {ECO:0000244|PDB:3QEX}.
STRAND 430 433 {ECO:0000244|PDB:3QEX}.
HELIX 439 443 {ECO:0000244|PDB:3QEX}.
STRAND 452 456 {ECO:0000244|PDB:3QEX}.
STRAND 460 463 {ECO:0000244|PDB:3QEX}.
STRAND 465 467 {ECO:0000244|PDB:3QEV}.
HELIX 470 502 {ECO:0000244|PDB:3QEX}.
STRAND 503 505 {ECO:0000244|PDB:4I9L}.
STRAND 507 509 {ECO:0000244|PDB:3QEV}.
STRAND 518 520 {ECO:0000244|PDB:2DY4}.
HELIX 524 530 {ECO:0000244|PDB:3QEX}.
STRAND 531 533 {ECO:0000244|PDB:3RMB}.
HELIX 535 569 {ECO:0000244|PDB:3QEX}.
HELIX 580 609 {ECO:0000244|PDB:3QEX}.
STRAND 617 621 {ECO:0000244|PDB:3QEX}.
STRAND 624 628 {ECO:0000244|PDB:3QEX}.
HELIX 630 636 {ECO:0000244|PDB:3QEX}.
HELIX 638 640 {ECO:0000244|PDB:3QEX}.
HELIX 644 657 {ECO:0000244|PDB:3QEX}.
HELIX 659 673 {ECO:0000244|PDB:3QEX}.
STRAND 683 689 {ECO:0000244|PDB:3QEX}.
STRAND 693 695 {ECO:0000244|PDB:1WAJ}.
STRAND 700 704 {ECO:0000244|PDB:3QEX}.
STRAND 707 715 {ECO:0000244|PDB:3QEX}.
STRAND 718 730 {ECO:0000244|PDB:3QEX}.
HELIX 731 733 {ECO:0000244|PDB:3QEX}.
HELIX 739 754 {ECO:0000244|PDB:3QEX}.
HELIX 757 770 {ECO:0000244|PDB:3QEX}.
HELIX 771 773 {ECO:0000244|PDB:3QEX}.
HELIX 776 779 {ECO:0000244|PDB:3QEX}.
STRAND 781 784 {ECO:0000244|PDB:3QEX}.
HELIX 789 791 {ECO:0000244|PDB:3QEX}.
STRAND 792 797 {ECO:0000244|PDB:3LZJ}.
HELIX 803 814 {ECO:0000244|PDB:3QEX}.
TURN 815 817 {ECO:0000244|PDB:3QEX}.
STRAND 819 821 {ECO:0000244|PDB:3QEX}.
STRAND 828 835 {ECO:0000244|PDB:3QEX}.
STRAND 837 839 {ECO:0000244|PDB:3RMC}.
STRAND 842 849 {ECO:0000244|PDB:3QEX}.
HELIX 856 865 {ECO:0000244|PDB:3QEX}.
HELIX 868 875 {ECO:0000244|PDB:3QEX}.
HELIX 877 887 {ECO:0000244|PDB:3QEX}.
STRAND 891 894 {ECO:0000244|PDB:2DTU}.
HELIX 897 900 {ECO:0000244|PDB:3QEX}.
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


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