DPOL_BPPH2
ID DPOL_BPPH2 Reviewed; 575 AA.
AC P03680; B3VMN6; Q38545;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=DNA polymerase;
DE EC=2.7.7.7 {ECO:0000269|PubMed:3863101};
DE EC=3.1.11.- {ECO:0000269|PubMed:2790959};
DE AltName: Full=Gene product 2 {ECO:0000305};
DE Short=gp2 {ECO:0000305};
DE AltName: Full=Protein p2 {ECO:0000305};
GN Name=2;
OS Bacillus phage phi29 (Bacteriophage phi-29).
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Salasmaviridae; Picovirinae; Salasvirus.
OX NCBI_TaxID=10756;
OH NCBI_TaxID=1423; Bacillus subtilis.
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=6809534; DOI=10.1016/0378-1119(82)90149-4;
RA Yoshikawa H., Ito J.;
RT "Nucleotide sequence of the major early region of bacteriophage phi 29.";
RL Gene 17:323-335(1982).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Villegas A.P., Lingohr E.J., Ceyssens P.-J., Kropinski A.M.;
RL Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-85.
RX PubMed=6292852; DOI=10.1093/nar/10.19.5785;
RA Escarmis C., Salas M.;
RT "Nucleotide sequence of the early genes 3 and 4 of bacteriophage phi 29.";
RL Nucleic Acids Res. 10:5785-5798(1982).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND MUTANT TEMPERATURE-SENSITIVE
RP TS2(24).
RX PubMed=2118623;
RA Blasco M.A., Blanco L., Pares E., Salas M., Bernad A.;
RT "Structural and functional analysis of temperature-sensitive mutants of the
RT phage phi 29 DNA polymerase.";
RL Nucleic Acids Res. 18:4763-4770(1990).
RN [5]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=3863101; DOI=10.1073/pnas.82.19.6404;
RA Blanco L., Salas M.;
RT "Replication of phage phi 29 DNA with purified terminal protein and DNA
RT polymerase: synthesis of full-length phi 29 DNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 82:6404-6408(1985).
RN [6]
RP FUNCTION.
RX PubMed=2498321; DOI=10.1016/s0021-9258(18)81883-x;
RA Blanco L., Bernad A., Lazaro J.M., Martin G., Garmendia C., Salas M.;
RT "Highly efficient DNA synthesis by the phage phi 29 DNA polymerase.
RT Symmetrical mode of DNA replication.";
RL J. Biol. Chem. 264:8935-8940(1989).
RN [7]
RP FUNCTION, AND MUTAGENESIS OF ASP-12; GLU-14 AND ASP-66.
RX PubMed=2790959; DOI=10.1016/0092-8674(89)90883-0;
RA Bernad A., Blanco L., Lazaro J.M., Martin G., Salas M.;
RT "A conserved 3'->5' exonuclease active site in prokaryotic and eukaryotic
RT DNA polymerases.";
RL Cell 59:219-228(1989).
RN [8]
RP MUTAGENESIS OF TYR-454; CYS-455; ASP-456; THR-457 AND ASP-458.
RX PubMed=2191296; DOI=10.1073/pnas.87.12.4610;
RA Bernad A., Lazaro J.M., Salas M., Blanco L.;
RT "The highly conserved amino acid sequence motif Tyr-Gly-Asp-Thr-Asp-Ser in
RT alpha-like DNA polymerases is required by phage phi 29 DNA polymerase for
RT protein-primed initiation and polymerization.";
RL Proc. Natl. Acad. Sci. U.S.A. 87:4610-4614(1990).
RN [9]
RP DOMAIN.
RX PubMed=1850426; DOI=10.1016/s0021-9258(20)89535-0;
RA Blasco M.A., Bernad A., Blanco L., Salas M.;
RT "Characterization and mapping of the pyrophosphorolytic activity of the
RT phage phi 29 DNA polymerase. Involvement of amino acid motifs highly
RT conserved in alpha-like DNA polymerases.";
RL J. Biol. Chem. 266:7904-7909(1991).
RN [10]
RP FUNCTION.
RX PubMed=1730646; DOI=10.1016/s0021-9258(18)48418-9;
RA Blanco L., Bernad A., Esteban J.A., Salas M.;
RT "DNA-independent deoxynucleotidylation of the phi 29 terminal protein by
RT the phi 29 DNA polymerase.";
RL J. Biol. Chem. 267:1225-1230(1992).
RN [11]
RP MUTAGENESIS OF ASP-12; GLU-14; ASP-66 AND ASP-169, AND COFACTOR.
RX PubMed=1310035; DOI=10.1021/bi00117a006;
RA Esteban J.A., Bernad A., Salas M., Blanco L.;
RT "Metal activation of synthetic and degradative activities of phi 29 DNA
RT polymerase, a model enzyme for protein-primed DNA replication.";
RL Biochemistry 31:350-359(1992).
RN [12]
RP FUNCTION.
RX PubMed=8428945; DOI=10.1016/s0021-9258(18)53833-3;
RA Esteban J.A., Salas M., Blanco L.;
RT "Fidelity of phi 29 DNA polymerase. Comparison between protein-primed
RT initiation and DNA polymerization.";
RL J. Biol. Chem. 268:2719-2726(1993).
RN [13]
RP MUTAGENESIS OF ASN-387; SER-388; GLY-391 AND PHE-393.
RX PubMed=8344956; DOI=10.1016/s0021-9258(19)85482-0;
RA Blasco M.A., Lazaro J.M., Blanco L., Salas M.;
RT "Phi 29 DNA polymerase active site. The conserved amino acid motif
RT 'Kx3NSxYG' is involved in template-primer binding and dNTP selection.";
RL J. Biol. Chem. 268:16763-16770(1993).
RN [14]
RP MUTAGENESIS OF ASP-249; SER-252; LEU-253 AND PRO-255.
RX PubMed=8226957; DOI=10.1016/s0021-9258(20)80499-2;
RA Blasco M.A., Lazaro J.M., Blanco L., Salas M.;
RT "Phi 29 DNA polymerase active site. Residue ASP249 of conserved amino acid
RT motif 'Dx2SLYP' is critical for synthetic activities.";
RL J. Biol. Chem. 268:24106-24113(1993).
RN [15]
RP MUTAGENESIS OF THR-434; ALA-437 AND ARG-438.
RX PubMed=7962004; DOI=10.1016/s0021-9258(18)43984-1;
RA Mendez J., Blanco L., Lazaro J.M., Salas M.;
RT "Primer-terminus stabilization at the phi 29 DNA polymerase active site.
RT Mutational analysis of conserved motif TX2GR.";
RL J. Biol. Chem. 269:30030-30038(1994).
RN [16]
RP MUTAGENESIS OF TYR-254 AND TYR-390.
RX PubMed=8537389; DOI=10.1074/jbc.270.52.31235;
RA Saturno J., Blanco L., Salas M., Esteban J.A.;
RT "A novel kinetic analysis to calculate nucleotide affinity of proofreading
RT DNA polymerases. Application to phi 29 DNA polymerase fidelity mutants.";
RL J. Biol. Chem. 270:31235-31243(1995).
RN [17]
RP MUTAGENESIS OF LYS-498 AND TYR-500.
RX PubMed=7852344; DOI=10.1074/jbc.270.6.2735;
RA Blasco M.A., Mendez J., Lazaro J.M., Blanco L., Salas M.;
RT "Primer terminus stabilization at the phi 29 DNA polymerase active site.
RT Mutational analysis of conserved motif KXY.";
RL J. Biol. Chem. 270:2735-2740(1995).
RN [18]
RP DOMAIN.
RX PubMed=8621470; DOI=10.1074/jbc.271.15.8509;
RA Blanco L., Salas M.;
RT "Relating structure to function in phi29 DNA polymerase.";
RL J. Biol. Chem. 271:8509-8512(1996).
RN [19]
RP MUTAGENESIS OF ARG-223; TYR-226; TYR-226; ARG-227; ARG-227; GLY-228;
RP GLY-228; GLY-229; GLY-229; PHE-230; PHE-230 AND PHE-230, AND DOMAIN.
RX PubMed=8670845; DOI=10.1002/j.1460-2075.1996.tb00709.x;
RA Truniger V., Lazaro J.M., Salas M., Blanco L.;
RT "A DNA binding motif coordinating synthesis and degradation in proofreading
RT DNA polymerases.";
RL EMBO J. 15:3430-3441(1996).
RN [20]
RP MUTAGENESIS OF THR-15 AND ASN-62.
RX PubMed=8605889;
RA de Vega M., Lazaro J.M., Salas M., Blanco L.;
RT "Primer-terminus stabilization at the 3'-5' exonuclease active site of
RT phi29 DNA polymerase. Involvement of two amino acid residues highly
RT conserved in proofreading DNA polymerases.";
RL EMBO J. 15:1182-1192(1996).
RN [21]
RP FUNCTION.
RX PubMed=9171364; DOI=10.1093/emboj/16.9.2519;
RA Mendez J., Blanco L., Salas M.;
RT "Protein-primed DNA replication: a transition between two modes of priming
RT by a unique DNA polymerase.";
RL EMBO J. 16:2519-2527(1997).
RN [22]
RP MUTAGENESIS OF LYS-143.
RX PubMed=9231901; DOI=10.1006/jmbi.1997.1093;
RA de Vega M., Ilyina T., Lazaro J.M., Salas M., Blanco L.;
RT "An invariant lysine residue is involved in catalysis at the 3'-5'
RT exonuclease active site of eukaryotic-type DNA polymerases.";
RL J. Mol. Biol. 270:65-78(1997).
RN [23]
RP MUTAGENESIS OF LYS-383.
RX PubMed=9199402; DOI=10.1006/jmbi.1997.1053;
RA Saturno J., Lazaro J.M., Esteban F.J., Blanco L., Salas M.;
RT "Phi29 DNA polymerase residue Lys383, invariant at motif B of DNA-dependent
RT polymerases, is involved in dNTP binding.";
RL J. Mol. Biol. 269:313-325(1997).
RN [24]
RP MUTAGENESIS OF PHE-65; SER-122 AND LEU-123.
RX PubMed=9642062; DOI=10.1006/jmbi.1998.1805;
RA de Vega M., Lazaro J.M., Salas M., Blanco L.;
RT "Mutational analysis of phi29 DNA polymerase residues acting as ssDNA
RT ligands for 3'-5' exonucleolysis.";
RL J. Mol. Biol. 279:807-822(1998).
RN [25]
RP MUTAGENESIS OF PHE-65; SER-122 AND LEU-123.
RX PubMed=9786901; DOI=10.1074/jbc.273.44.28966;
RA de Vega M., Blanco L., Salas M.;
RT "phi29 DNA polymerase residue Ser122, a single-stranded DNA ligand for 3'-
RT 5' exonucleolysis, is required to interact with the terminal protein.";
RL J. Biol. Chem. 273:28966-28977(1998).
RN [26]
RP MUTAGENESIS OF ASP-456, AND COFACTOR.
RX PubMed=9784372; DOI=10.1006/jmbi.1998.2121;
RA Saturno J., Lazaro J.M., Blanco L., Salas M.;
RT "Role of the first aspartate residue of the 'YxDTDS' motif of phi29 DNA
RT polymerase as a metal ligand during both TP-primed and DNA-primed DNA
RT synthesis.";
RL J. Mol. Biol. 283:633-642(1998).
RN [27]
RP DOMAIN.
RX PubMed=9614939; DOI=10.1006/jmbi.1998.1724;
RA Truniger V., Lazaro J.M., Salas M., Blanco L.;
RT "Phi 29 DNA polymerase requires the N-terminal domain to bind terminal
RT protein and DNA primer substrates.";
RL J. Mol. Biol. 278:741-755(1998).
RN [28]
RP MUTAGENESIS OF ARG-223; TYR-226; ARG-227; GLY-228; GLY-229; PHE-230 AND
RP PHE-230, DOMAIN, AND INTERACTION WITH THE PRIMER TERMINAL PROTEIN.
RX PubMed=9931249; DOI=10.1006/jmbi.1998.2477;
RA Truniger V., Blanco L., Salas M.;
RT "Role of the 'YxGG/A' motif of Phi29 DNA polymerase in protein-primed
RT replication.";
RL J. Mol. Biol. 286:57-69(1999).
RN [29]
RP MUTAGENESIS OF TYR-254.
RX PubMed=10388570; DOI=10.1006/jmbi.1999.2900;
RA Bonnin A., Lazaro J.M., Blanco L., Salas M.;
RT "A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-
RT type phi29 DNA polymerase.";
RL J. Mol. Biol. 290:241-251(1999).
RN [30]
RP FUNCTION.
RX PubMed=10493855; DOI=10.1006/jmbi.1999.3052;
RA de Vega M., Blanco L., Salas M.;
RT "Processive proofreading and the spatial relationship between polymerase
RT and exonuclease active sites of bacteriophage phi29 DNA polymerase.";
RL J. Mol. Biol. 292:39-51(1999).
RN [31]
RP MUTAGENESIS OF LYS-392.
RX PubMed=12054770; DOI=10.1016/s0022-2836(02)00022-0;
RA Truniger V., Lazaro J.M., Blanco L., Salas M.;
RT "A highly conserved lysine residue in phi29 DNA polymerase is important for
RT correct binding of the templating nucleotide during initiation of phi29 DNA
RT replication.";
RL J. Mol. Biol. 318:83-96(2002).
RN [32]
RP INTERACTION WITH THE PRIMER TERMINAL PROTEIN, AND MUTAGENESIS OF TYR-59;
RP HIS-61 AND PHE-69.
RX PubMed=11884636; DOI=10.1093/nar/30.6.1379;
RA Eisenbrandt R., Lazaro J.M., Salas M., de Vega M.;
RT "Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly
RT conserved ExoII motif are essential for interaction with the terminal
RT protein.";
RL Nucleic Acids Res. 30:1379-1386(2002).
RN [33]
RP MUTAGENESIS OF ILE-364 AND LYS-371.
RX PubMed=11917008; DOI=10.1093/nar/30.7.1483;
RA Truniger V., Lazaro J.M., Esteban F.J., Blanco L., Salas M.;
RT "A positively charged residue of phi29 DNA polymerase, highly conserved in
RT DNA polymerases from families A and B, is involved in binding the incoming
RT nucleotide.";
RL Nucleic Acids Res. 30:1483-1492(2002).
RN [34]
RP MUTAGENESIS OF LEU-384.
RX PubMed=12805385; DOI=10.1074/jbc.m303052200;
RA Truniger V., Lazaro J.M., de Vega M., Blanco L., Salas M.;
RT "phi 29 DNA polymerase residue Leu384, highly conserved in motif B of
RT eukaryotic type DNA replicases, is involved in nucleotide insertion
RT fidelity.";
RL J. Biol. Chem. 278:33482-33491(2003).
RN [35]
RP MUTAGENESIS OF PHE-128.
RX PubMed=12473453; DOI=10.1016/s0022-2836(02)01130-0;
RA Rodriguez I., Lazaro J.M., Salas M., de Vega M.;
RT "phi29 DNA polymerase residue Phe128 of the highly conserved (S/T)Lx(2)h
RT motif is required for a stable and functional interaction with the terminal
RT protein.";
RL J. Mol. Biol. 325:85-97(2003).
RN [36]
RP MUTAGENESIS OF LYS-366 AND LYS-379.
RX PubMed=14672657; DOI=10.1016/j.jmb.2003.10.024;
RA Truniger V., Lazaro J.M., Salas M.;
RT "Two positively charged residues of phi29 DNA polymerase, conserved in
RT protein-primed DNA polymerases, are involved in stabilisation of the
RT incoming nucleotide.";
RL J. Mol. Biol. 335:481-494(2004).
RN [37]
RP DOMAIN.
RX PubMed=14729920; DOI=10.1093/nar/gkh184;
RA Truniger V., Lazaro J.M., Salas M.;
RT "Function of the C-terminus of phi29 DNA polymerase in DNA and terminal
RT protein binding.";
RL Nucleic Acids Res. 32:361-370(2004).
RN [38]
RP DOMAIN, AND MUTAGENESIS OF ARG-187; THR-189; SER-192; LYS-196; PHE-198 AND
RP LYS-206.
RX PubMed=15777661; DOI=10.1016/j.gene.2004.12.041;
RA Truniger V., Bonnin A., Lazaro J.M., de Vega M., Salas M.;
RT "Involvement of the 'linker' region between the exonuclease and
RT polymerization domains of phi29 DNA polymerase in DNA and TP binding.";
RL Gene 348:89-99(2005).
RN [39]
RP DOMAIN.
RX PubMed=15845765; DOI=10.1073/pnas.0500597102;
RA Rodriguez I., Lazaro J.M., Blanco L., Kamtekar S., Berman A.J., Wang J.,
RA Steitz T.A., Salas M., de Vega M.;
RT "A specific subdomain in phi29 DNA polymerase confers both processivity and
RT strand-displacement capacity.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:6407-6412(2005).
RN [40]
RP MUTAGENESIS OF TYR-390.
RX PubMed=17652324; DOI=10.1093/nar/gkm545;
RA de Vega M., Salas M.;
RT "A highly conserved Tyrosine residue of family B DNA polymerases
RT contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-
RT deoxyguanosine.";
RL Nucleic Acids Res. 35:5096-5107(2007).
RN [41]
RP FUNCTION.
RX PubMed=19011105; DOI=10.1073/pnas.0809882105;
RA Longas E., Villar L., Lazaro J.M., de Vega M., Salas M.;
RT "Phage phi29 and Nf terminal protein-priming domain specifies the internal
RT template nucleotide to initiate DNA replication.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:18290-18295(2008).
RN [42]
RP MUTAGENESIS OF TYR-148.
RX PubMed=19576228; DOI=10.1016/j.jmb.2009.06.068;
RA Perez-Arnaiz P., Lazaro J.M., Salas M., de Vega M.;
RT "Functional importance of bacteriophage phi29 DNA polymerase residue Tyr148
RT in primer-terminus stabilisation at the 3'-5' exonuclease active site.";
RL J. Mol. Biol. 391:797-807(2009).
RN [43]
RP DOMAIN.
RX PubMed=19033368; DOI=10.1093/nar/gkn928;
RA Rodriguez I., Lazaro J.M., Salas M., de Vega M.;
RT "Involvement of the TPR2 subdomain movement in the activities of phi29 DNA
RT polymerase.";
RL Nucleic Acids Res. 37:193-203(2009).
RN [44]
RP MUTAGENESIS OF VAL-250.
RX PubMed=19883660; DOI=10.1016/j.jmb.2009.10.061;
RA Perez-Arnaiz P., Lazaro J.M., Salas M., de Vega M.;
RT "phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP
RT complex ligand and in protein-primed initiation.";
RL J. Mol. Biol. 395:223-233(2010).
RN [45]
RP INTERACTION WITH THE PRIMER TERMINAL PROTEIN.
RX PubMed=22210885; DOI=10.1093/nar/gkr1283;
RA del Prado A., Villar L., de Vega M., Salas M.;
RT "Involvement of residues of the Phi29 terminal protein intermediate and
RT priming domains in the formation of a stable and functional heterodimer
RT with the replicative DNA polymerase.";
RL Nucleic Acids Res. 40:3886-3897(2012).
RN [46]
RP MUTAGENESIS OF LYS-529.
RX PubMed=24023769; DOI=10.1371/journal.pone.0072765;
RA del Prado A., Lazaro J.M., Villar L., Salas M., de Vega M.;
RT "Dual role of phi29 DNA polymerase Lys529 in stabilisation of the DNA
RT priming-terminus and the terminal protein-priming residue at the
RT polymerisation site.";
RL PLoS ONE 8:E72765-E72765(2013).
RN [47]
RP MUTAGENESIS OF TYR-226 AND TYR-390.
RX PubMed=24464581; DOI=10.1074/jbc.m113.535666;
RA Dahl J.M., Wang H., Lazaro J.M., Salas M., Lieberman K.R.;
RT "Dynamics of translocation and substrate binding in individual complexes
RT formed with active site mutants of {phi}29 DNA polymerase.";
RL J. Biol. Chem. 289:6350-6361(2014).
RN [48] {ECO:0007744|PDB:1XHX, ECO:0007744|PDB:1XHZ}
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS).
RX PubMed=15546620; DOI=10.1016/j.molcel.2004.10.019;
RA Kamtekar S., Berman A.J., Wang J., Lazaro J.M., de Vega M., Blanco L.,
RA Salas M., Steitz T.A.;
RT "Insights into strand displacement and processivity from the crystal
RT structure of the protein-primed DNA polymerase of bacteriophage phi29.";
RL Mol. Cell 16:609-618(2004).
RN [49] {ECO:0007744|PDB:1XI1}
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, AND
RP COFACTOR.
RX PubMed=15608377; DOI=10.1107/s0907444904026721;
RA Wang J., Kamtekar S., Berman A.J., Steitz T.A.;
RT "Correction of X-ray intensities from single crystals containing lattice-
RT translocation defects.";
RL Acta Crystallogr. D 61:67-74(2005).
RN [50] {ECO:0007744|PDB:2EX3}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS).
RX PubMed=16511564; DOI=10.1038/sj.emboj.7601027;
RA Kamtekar S., Berman A.J., Wang J., Lazaro J.M., de Vega M., Blanco L.,
RA Salas M., Steitz T.A.;
RT "The phi29 DNA polymerase:protein-primer structure suggests a model for the
RT initiation to elongation transition.";
RL EMBO J. 25:1335-1343(2006).
RN [51] {ECO:0007744|PDB:2PY5, ECO:0007744|PDB:2PYJ, ECO:0007744|PDB:2PYL, ECO:0007744|PDB:2PZS}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH MANGANESE AND TTP,
RP AND COFACTOR.
RX PubMed=17611604; DOI=10.1038/sj.emboj.7601780;
RA Berman A.J., Kamtekar S., Goodman J.L., Lazaro J.M., de Vega M., Blanco L.,
RA Salas M., Steitz T.A.;
RT "Structures of phi29 DNA polymerase complexed with substrate: the mechanism
RT of translocation in B-family polymerases.";
RL EMBO J. 26:3494-3505(2007).
CC -!- FUNCTION: Polymerase responsible for protein-primed viral DNA
CC replication by strand displacement with high processivity and fidelity
CC (PubMed:3863101) (PubMed:2498321). To start replication, the DNA
CC polymerase forms a heterodimer with a free primer terminal protein
CC (TP), recognizes the replication origins at both 5' ends of the linear
CC chromosome, and initiates replication using as primer the OH-group of
CC Ser-232 of the TP (PubMed:22210885). This polymerase possesses three
CC enzymatic activities: DNA synthesis (polymerase), primer terminal
CC protein (TP) deoxynucleotidylation, which is the formation of a
CC covalent linkage (phosphoester) between the hydroxyl group of a
CC specific serine residue in TP and 5'-dAMP, a reaction directed by the
CC second T at the 3' end, and 3' to 5' exonuclease activity
CC (PubMed:2790959). Exonuclease activity has a proofreading purpose
CC (PubMed:2790959). DNA polymerase edits the polymerization errors using
CC an intramolecular pathway as the primer terminus travels from one
CC active site to the other without dissociation from the DNA
CC (PubMed:10493855). DNA polymerization catalyzed by the DNA polymerase
CC is a highly accurate process, but the protein-primed initiation is a
CC quite inaccurate reaction (PubMed:8428945). Since the polymerase
CC initiates the replication on the second thymine, the TP-dAMP initiation
CC product translocates backwards to recover the template information of
CC the first nucleotide (sliding back-mechanism) (PubMed:19011105).
CC {ECO:0000269|PubMed:10493855, ECO:0000269|PubMed:1730646,
CC ECO:0000269|PubMed:19011105, ECO:0000269|PubMed:22210885,
CC ECO:0000269|PubMed:2498321, ECO:0000269|PubMed:2790959,
CC ECO:0000269|PubMed:3863101, ECO:0000269|PubMed:8428945,
CC ECO:0000269|PubMed:9171364}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC Evidence={ECO:0000269|PubMed:3863101};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:1310035, ECO:0000269|PubMed:15608377,
CC ECO:0000269|PubMed:17611604, ECO:0000269|PubMed:9784372};
CC -!- SUBUNIT: Interacts with the primer terminal protein; this interaction
CC allows the initiation of TP-primed DNA replication at both viral DNA
CC ends. Interacts with DNA. {ECO:0000269|PubMed:11884636,
CC ECO:0000269|PubMed:22210885, ECO:0000269|PubMed:9931249}.
CC -!- DOMAIN: The N-terminus contains the 3'-5' exonuclease activity and
CC strand displacement ability (PubMed:8621470). The conserved motif
CC YxGG/A located between the 3'-5' exonuclease and polymerization domains
CC is important for DNA-binding, coordination between DNA synthesis and
CC degradation and for the formation of a stable complex between TP and
CC the DNA polymerase (PubMed:8670845, PubMed:9931249, PubMed:15777661).
CC The C-terminus is involved in the protein-primed initiation, DNA
CC polymerization and pyrophosphorolytic activities (PubMed:8621470,
CC PubMed:1850426). The YCDTD motif is essential for the
CC pyrophosphorolytic activity (PubMed:1850426). The TPR2 region is
CC necessary for the strand displacement coupled to DNA synthesis and
CC probably also for allowing the TP priming domain to move out from the
CC polymerase during transition from initiation to elongation
CC (PubMed:15845765, PubMed:19033368). {ECO:0000269|PubMed:15845765,
CC ECO:0000269|PubMed:1850426, ECO:0000269|PubMed:19033368,
CC ECO:0000269|PubMed:8621470, ECO:0000269|PubMed:9614939,
CC ECO:0000269|PubMed:9931249}.
CC -!- MISCELLANEOUS: This DNA polymerase requires a protein as a primer.
CC {ECO:0000269|PubMed:16511564}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ACE96023.1; Type=Erroneous initiation; Note=Truncated N-terminus.;
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DR EMBL; V01155; CAA24480.1; -; Genomic_DNA.
DR EMBL; X53370; CAA37450.1; -; Genomic_DNA.
DR EMBL; EU771092; ACE96023.1; ALT_INIT; Genomic_DNA.
DR EMBL; X53371; CAA37451.1; -; Genomic_DNA.
DR PIR; A04282; ERBP29.
DR RefSeq; YP_002004529.1; NC_011048.1.
DR PDB; 1XHX; X-ray; 2.35 A; A/B/C/D=1-575.
DR PDB; 1XHZ; X-ray; 2.70 A; A/B/C/D=1-575.
DR PDB; 1XI1; X-ray; 2.20 A; A/B=1-575.
DR PDB; 2EX3; X-ray; 3.00 A; A/C/E/G/I/K=1-575.
DR PDB; 2PY5; X-ray; 1.60 A; A/B=1-575.
DR PDB; 2PYJ; X-ray; 2.03 A; A/B=1-575.
DR PDB; 2PYL; X-ray; 2.20 A; A=1-575.
DR PDB; 2PZS; X-ray; 2.60 A; A/B/C/D=1-575.
DR PDBsum; 1XHX; -.
DR PDBsum; 1XHZ; -.
DR PDBsum; 1XI1; -.
DR PDBsum; 2EX3; -.
DR PDBsum; 2PY5; -.
DR PDBsum; 2PYJ; -.
DR PDBsum; 2PYL; -.
DR PDBsum; 2PZS; -.
DR SMR; P03680; -.
DR PRIDE; P03680; -.
DR GeneID; 6446511; -.
DR KEGG; vg:6446511; -.
DR BRENDA; 2.7.7.7; 723.
DR EvolutionaryTrace; P03680; -.
DR Proteomes; UP000001207; Genome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0001882; F:nucleoside binding; IEA:InterPro.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0039693; P:viral DNA genome replication; IDA:UniProtKB.
DR Gene3D; 3.30.420.10; -; 1.
DR Gene3D; 3.90.1600.10; -; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR004868; DNA-dir_DNA_pol_B_mt/vir.
DR InterPro; IPR014416; DNA-dir_DNA_polB_phi29_vir.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR Pfam; PF03175; DNA_pol_B_2; 1.
DR PIRSF; PIRSF004178; Dpol_Bac_phage; 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 Early protein; Exonuclease; Hydrolase; Magnesium; Metal-binding; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW Transferase; Viral DNA replication.
FT CHAIN 1..575
FT /note="DNA polymerase"
FT /id="PRO_0000046542"
FT REGION 1..191
FT /note="3'-5' exonuclease and strand displacement
FT activities"
FT /evidence="ECO:0000269|PubMed:8621470"
FT REGION 192..229
FT /note="Involved in DNA-binding, coordination between DNA
FT synthesis and degradation and TP interaction"
FT /evidence="ECO:0000269|PubMed:15777661,
FT ECO:0000269|PubMed:8670845, ECO:0000269|PubMed:9931249"
FT REGION 230..562
FT /note="Initiation, polymerization and pyrophosphorolytic
FT activities"
FT /evidence="ECO:0000269|PubMed:8621470"
FT REGION 398..420
FT /note="TPR2"
FT /evidence="ECO:0000269|PubMed:15845765"
FT REGION 563..575
FT /note="Involved in DNA-binding and TP interaction"
FT /evidence="ECO:0000269|PubMed:14729920"
FT MOTIF 454..458
FT /note="YCDTD"
FT /evidence="ECO:0000269|PubMed:1850426"
FT BINDING 145
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:1XI1"
FT BINDING 169
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:1XI1"
FT BINDING 249
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:8226957,
FT ECO:0007744|PDB:2PYJ"
FT BINDING 250
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:19883660,
FT ECO:0007744|PDB:2PYJ"
FT BINDING 254
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0007744|PDB:2PYL"
FT BINDING 371
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0007744|PDB:2PYL"
FT BINDING 383
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0007744|PDB:2PYL"
FT BINDING 456
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:9784372"
FT BINDING 458
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0007744|PDB:2PYJ"
FT BINDING 458
FT /ligand="TTP"
FT /ligand_id="ChEBI:CHEBI:63527"
FT /evidence="ECO:0007744|PDB:2PYL"
FT SITE 12
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:2790959,
FT ECO:0000269|PubMed:8344956"
FT SITE 14
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:2790959,
FT ECO:0000269|PubMed:8344956"
FT SITE 15
FT /note="Involved in proofreading function by stabilization
FT of the frayed primer-terminus at the 3'-5' exonuclease
FT active site"
FT /evidence="ECO:0000269|PubMed:8605889"
FT SITE 59
FT /note="Interaction with the primer terminal protein"
FT /evidence="ECO:0000269|PubMed:11884636"
FT SITE 61
FT /note="Interaction with the primer terminal protein"
FT /evidence="ECO:0000269|PubMed:11884636"
FT SITE 62
FT /note="Involved in proofreading function by stabilization
FT of the frayed primer-terminus at the 3'-5' exonuclease
FT active site"
FT /evidence="ECO:0000269|PubMed:8605889"
FT SITE 65
FT /note="Binds ssDNA; Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:9786901"
FT SITE 66
FT /note="Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:2790959,
FT ECO:0000269|PubMed:8344956"
FT SITE 69
FT /note="Interaction with the primer terminal protein"
FT /evidence="ECO:0000269|PubMed:11884636"
FT SITE 93
FT /note="Involved in binding template-primer structures"
FT /evidence="ECO:0000269|PubMed:8344956"
FT SITE 122
FT /note="Binds ssDNA; Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:9786901"
FT SITE 123
FT /note="Binds ssDNA; Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:9786901"
FT SITE 148
FT /note="Involved in the stabilization of the frayed 3'
FT terminus at the exonuclease active site"
FT /evidence="ECO:0000269|PubMed:19576228"
FT SITE 252
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:8226957"
FT SITE 254
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000269|PubMed:8537389"
FT SITE 356
FT /note="Binds ssDNA; Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:8605889"
FT SITE 364
FT /note="Involved in the binding of DNA and dNTP"
FT /evidence="ECO:0000269|PubMed:11917008"
FT SITE 366
FT /note="Stabilization of the incoming nucleotide"
FT /evidence="ECO:0000269|PubMed:14672657"
FT SITE 371
FT /note="Interacts with the phosphate groups of the incoming
FT nucleotide"
FT /evidence="ECO:0000269|PubMed:11917008"
FT SITE 379
FT /note="Stabilization of the incoming nucleotide"
FT /evidence="ECO:0000269|PubMed:14672657"
FT SITE 383
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000269|PubMed:9199402"
FT SITE 384
FT /note="Probably involved in positioning the templating
FT nucleotide at the polymerization active site and in
FT controlling nucleotide insertion fidelity"
FT /evidence="ECO:0000269|PubMed:12805385"
FT SITE 387
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:8344956"
FT SITE 390
FT /note="Probably involved in nucleotide binding selection"
FT /evidence="ECO:0000269|PubMed:8537389"
FT SITE 391
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:8344956"
FT SITE 420
FT /note="Binds ssDNA; Essential for 3'-5' exonucleolysis"
FT /evidence="ECO:0000269|PubMed:8605889"
FT SITE 434
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:7962004"
FT SITE 438
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:7962004"
FT SITE 498
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:7852344"
FT SITE 500
FT /note="Probably involved in binding template-primer
FT structures"
FT /evidence="ECO:0000269|PubMed:7852344"
FT SITE 529
FT /note="Stabilizes the primer-terminus at the polymerization
FT active site and contributes to the coordination between the
FT exonuclease and polymerazation activities"
FT /evidence="ECO:0000269|PubMed:24023769"
FT VARIANT 176
FT /note="A -> R (in mutant TS2(24))"
FT VARIANT 355
FT /note="A -> V (in mutant TS2(24))"
FT MUTAGEN 12
FT /note="D->A: Strong loss of 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:1310035,
FT ECO:0000269|PubMed:2790959"
FT MUTAGEN 14
FT /note="E->A: Strong loss of 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:1310035,
FT ECO:0000269|PubMed:2790959"
FT MUTAGEN 15
FT /note="T->I: 95% loss of ssDNA-binding. Decreased in
FT fidelity of DNA replication."
FT /evidence="ECO:0000269|PubMed:8605889"
FT MUTAGEN 59
FT /note="Y->F: Almost no effect on replication activity.
FT About 20% loss of TP-DNA initiation, 20% loss of TP-DNA
FT replication and 10% loss of TP-DNA amplification. Complete
FT loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 59
FT /note="Y->L: 3 fold decrease in replication activity. About
FT 80% loss of TP-DNA initiation, 70% loss of TP-DNA
FT replication and 97% loss of TP-DNA amplification. Complete
FT loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 59
FT /note="Y->R: 3 fold decrease in replication activity. About
FT 75% loss of TP-DNA initiation, complete loss of TP-DNA
FT replication and complete loss of TP-DNA amplification."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 61
FT /note="H->L: 5 fold decrease in replication activity. About
FT 85% loss of TP-DNA initiation, 80% loss of TP-DNA
FT replication and complete loss of TP-DNA amplification.
FT Complete loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 61
FT /note="H->R: 100 fold decrease in replication activity.
FT Complete loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 62
FT /note="N->D,H: 88% loss of ssDNA-binding. Decreased in
FT fidelity of DNA replication."
FT /evidence="ECO:0000269|PubMed:8605889"
FT MUTAGEN 65
FT /note="F->S: Loss of capacity to interact with a DNA
FT primer/template structure."
FT /evidence="ECO:0000269|PubMed:9786901"
FT MUTAGEN 66
FT /note="D->A: Strong loss of 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:1310035,
FT ECO:0000269|PubMed:2790959"
FT MUTAGEN 69
FT /note="F->S: 2 fold decrease in replication activity. About
FT 50% loss of TP-DNA initiation, 40% loss of TP-DNA
FT replication and 60% loss of TP-DNA amplification. Complete
FT loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 69
FT /note="F->Y: 2 fold decrease in replication activity. About
FT 80% loss of TP-DNA initiation, 50% loss of TP-DNA
FT replication and almost 95% loss of TP-DNA. Complete loss of
FT interaction with TP amplification."
FT /evidence="ECO:0000269|PubMed:11884636"
FT MUTAGEN 122
FT /note="S->T: Loss of capacity to interact with a DNA
FT primer/template structure."
FT /evidence="ECO:0000269|PubMed:9786901"
FT MUTAGEN 123
FT /note="L->N: Loss of capacity to interact with a DNA
FT primer/template structure."
FT /evidence="ECO:0000269|PubMed:9786901"
FT MUTAGEN 128
FT /note="F->A: Slight loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:12473453"
FT MUTAGEN 128
FT /note="F->Y: Almost complete loss of interaction with TP."
FT /evidence="ECO:0000269|PubMed:12473453"
FT MUTAGEN 143
FT /note="K->I,R: Strong loss of 3'-5' exonuclease,
FT proofreading and strand-displacement activities."
FT /evidence="ECO:0000269|PubMed:9231901"
FT MUTAGEN 148
FT /note="Y->A: Reduced capacity to stabilize the binding of
FT the primer terminus at the 3'-5' exonuclease active site."
FT /evidence="ECO:0000269|PubMed:19576228"
FT MUTAGEN 169
FT /note="D->A: Strong loss of 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:1310035"
FT MUTAGEN 187
FT /note="R->K: No effect on DNA-binding, TP binding and
FT replication/amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 189
FT /note="T->A: No effect on DNA-binding, TP binding and
FT replication/amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 192
FT /note="S->I: Loss of DNA-binding. Reduced TP binding. 25%
FT loss of replication and almost complete loss of
FT amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 192
FT /note="S->N: Loss of DNA-binding. No effect on TP binding.
FT 50% loss of replication/amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 196
FT /note="K->I: Loss of DNA-binding. Reduced TP binding. 25%
FT loss of replication and almost complete loss of
FT amplification. 6-fold reduced 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 196
FT /note="K->R: Slight loss of DNA-binding. No loss of
FT replication and amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 198
FT /note="F->V: Loss of DNA-binding. Reduced TP binding. 25%
FT loss of replication and almost complete loss of
FT amplification. 6-fold reduced 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 206
FT /note="K->I: No effect on DNA-binding. Reduced TP binding.
FT 70% loss of replication and 20% loss of amplification."
FT /evidence="ECO:0000269|PubMed:15777661"
FT MUTAGEN 223
FT /note="R->I: Favored exonucleolysis (low pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 226
FT /note="Y->F: Favored polymerization (high pol/exo ratio).
FT decrease in forward and reverse rates of translocation.
FT Increased affinity for dNTP and for pyrophosphate in the
FT pre-translocation state."
FT /evidence="ECO:0000269|PubMed:24464581,
FT ECO:0000269|PubMed:8670845, ECO:0000269|PubMed:9931249"
FT MUTAGEN 226
FT /note="Y->S: Favored exonucleolysis. Complete loss of
FT polymerization."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 227
FT /note="R->I: Favored exonucleolysis (low pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 227
FT /note="R->K: No effect on the pol/exo ratio."
FT /evidence="ECO:0000269|PubMed:9931249"
FT MUTAGEN 228
FT /note="G->A: Favored polymerization (high pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 229
FT /note="G->A: Favored exonucleolysis (low pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 229
FT /note="G->D: Favored exonucleolysis. Complete loss of
FT polymerization."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 230
FT /note="F->A: Favored polymerization (high pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 230
FT /note="F->S: Favored exonucleolysis (low pol/exo ratio)."
FT /evidence="ECO:0000269|PubMed:8670845,
FT ECO:0000269|PubMed:9931249"
FT MUTAGEN 230
FT /note="F->Y: No effect on the pol/exo ratio."
FT /evidence="ECO:0000269|PubMed:9931249"
FT MUTAGEN 249
FT /note="D->E: Complete loss of DNA polymerase activity.
FT Slight decrease in template-primer binding. No effect on 3'
FT to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:8226957"
FT MUTAGEN 250
FT /note="V->A: No effect on TP-DNA replication."
FT /evidence="ECO:0000269|PubMed:19883660"
FT MUTAGEN 250
FT /note="V->F: Complete loss of TP-DNA replication."
FT /evidence="ECO:0000269|PubMed:19883660"
FT MUTAGEN 251
FT /note="N->D: No effect on TP-DNA replication."
FT /evidence="ECO:0000269|PubMed:19883660"
FT MUTAGEN 252
FT /note="S->G: 40% loss of DNA polymerase activity. No effect
FT on translocation or stabilization of the incorporated
FT nucIeotide. No effect on 3' to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:8226957"
FT MUTAGEN 252
FT /note="S->R: Complete loss of DNA polymerase activity.
FT Drastic loss of template-primer binding. No effect on 3' to
FT 5' exonucleolysis and interaction with the TP primer."
FT /evidence="ECO:0000269|PubMed:8226957"
FT MUTAGEN 253
FT /note="L->V: 30% loss of DNA polymerase activity. No effect
FT on translocation or stabilization of the incorporated
FT nucIeotide. No effect on 3' to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:8226957"
FT MUTAGEN 254
FT /note="Y->F: Decreased dNTP binding affinity. 10-fold
FT reduced affinity for the correct nucleotide."
FT /evidence="ECO:0000269|PubMed:8537389"
FT MUTAGEN 254
FT /note="Y->V: Loss of discrimination for rNTPs over dNTPs."
FT /evidence="ECO:0000269|PubMed:10388570"
FT MUTAGEN 255
FT /note="P->S: 30% loss of DNA polymerase activity. No effect
FT on translocation or stabilization of the incorporated
FT nucIeotide. No effect on 3' to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:8226957"
FT MUTAGEN 364
FT /note="I->Q: Partial loss of hability to stably bind the
FT DNA substrate."
FT /evidence="ECO:0000269|PubMed:11917008"
FT MUTAGEN 364
FT /note="I->R: Complete loss of hability to stably bind the
FT DNA substrate."
FT /evidence="ECO:0000269|PubMed:11917008"
FT MUTAGEN 366
FT /note="K->T: Slight decrease in DNA-binding capacity. No
FT effect on polymerisation activity, except that it is
FT reduced in the absence of a DNA template. Reduced affinity
FT for the initiating nucleotide. 3 fold reduction of the
FT initiation activity in the presence of p6."
FT /evidence="ECO:0000269|PubMed:14672657"
FT MUTAGEN 371
FT /note="K->T: Strong decrease in the affinity for dNTPs and
FT pyrophosphorolytic activity. No effect on exonucleolysis."
FT /evidence="ECO:0000269|PubMed:11917008"
FT MUTAGEN 379
FT /note="K->T: Slight increase in DNA-binding capacity.
FT Reduced affinity for the initiating nucleotide."
FT /evidence="ECO:0000269|PubMed:14672657"
FT MUTAGEN 383
FT /note="K->P: Complete loss of incorporation of dNTP
FT substrates using either DNA or TP as primer. No effect on
FT 3' to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:9199402"
FT MUTAGEN 383
FT /note="K->R: Strong loss of ability to use dNTPs in both
FT processive and non-processive DNA synthesis. Impaired
FT progression from protein-primed initiation to DNA
FT elongation. No effect on 3' to 5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:9199402"
FT MUTAGEN 384
FT /note="L->R: Reduced nucleotide insertion fidelity during
FT DNA-primed polymerization and protein-primed initiation. No
FT effect on the affinity for the different dNTPs."
FT /evidence="ECO:0000269|PubMed:12805385"
FT MUTAGEN 387
FT /note="N->Y: 3-fold higher Km value for dATP and more than
FT 11-fold lower Vmax value than the wild-type enzyme in the
FT initiation reaction. Impaired in enzyme-DNA translocation."
FT /evidence="ECO:0000269|PubMed:8344956"
FT MUTAGEN 388
FT /note="S->G: No effect on initiation and polymerization
FT activities. Increased efficiency of dNTP incorporation in
FT non-templated reactions."
FT /evidence="ECO:0000269|PubMed:8344956"
FT MUTAGEN 390
FT /note="Y->F: Decreased dNTP binding affinity in the post-
FT translocation state. 4.6-fold reduced affinity for the
FT correct nucleotide."
FT /evidence="ECO:0000269|PubMed:24464581,
FT ECO:0000269|PubMed:8537389"
FT MUTAGEN 390
FT /note="Y->S: Decreased dNTP binding affinity. 14-fold
FT reduced affinity for the correct nucleotide. Loss of
FT discrimination against dA insertion opposite 8oxodG."
FT /evidence="ECO:0000269|PubMed:17652324,
FT ECO:0000269|PubMed:8537389"
FT MUTAGEN 391
FT /note="G->D: Complete loss of template-primer binding."
FT /evidence="ECO:0000269|PubMed:8344956"
FT MUTAGEN 392
FT /note="K->Q: 50% loss of exonuclease activity. 80% loss of
FT processivity. No effect on DNA polymerase/DNA complex
FT formation."
FT /evidence="ECO:0000269|PubMed:12054770"
FT MUTAGEN 392
FT /note="K->R: 90% loss of exonuclease activity. 80% loss of
FT processivity. No effect on DNA polymerase/DNA complex
FT formation."
FT /evidence="ECO:0000269|PubMed:12054770"
FT MUTAGEN 393
FT /note="F->Y: Severe decrease in initial binding to
FT template-primer DNA molecules."
FT /evidence="ECO:0000269|PubMed:8344956"
FT MUTAGEN 434
FT /note="T->N: Complete loss of TP-dAMP formation. Almost
FT complete loss of DNA polymerization."
FT /evidence="ECO:0000269|PubMed:7962004"
FT MUTAGEN 437
FT /note="A->G: No effect on TP-dAMP formation. 20% loss of
FT DNA polymerization."
FT /evidence="ECO:0000269|PubMed:7962004"
FT MUTAGEN 438
FT /note="R->I: Complete loss of TP-dAMP formation. Almost
FT complete loss of DNA polymerization."
FT /evidence="ECO:0000269|PubMed:7962004"
FT MUTAGEN 438
FT /note="R->K: Complete loss of TP-dAMP formation. 30% loss
FT of DNA polymerization."
FT /evidence="ECO:0000269|PubMed:7962004"
FT MUTAGEN 454
FT /note="Y->F: No effect on the formation of the covalent
FT complex between the TP and 5'-dAMP. Loss of replication of
FT a p3-DNA complex or a primed M13 DNA. Increased 3'-5'
FT exonucleolysis."
FT /evidence="ECO:0000269|PubMed:2191296"
FT MUTAGEN 455
FT /note="C->G: 65% loss of formation of the covalent complex
FT between the TP and 5'-dAMP. Increased 3'-5'
FT exonucleolysis."
FT /evidence="ECO:0000269|PubMed:2191296"
FT MUTAGEN 456
FT /note="D->G: 50% loss of synthetic activities, TP-primed
FT initiation and DNA-primed polymerization. When
FT polymerization requires an efficient translocation along
FT the template, catalytic efficiency is strongly reduced. 90%
FT loss of formation of the covalent complex between the TP
FT and 5'-dAMP. Increased 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:2191296,
FT ECO:0000269|PubMed:9784372"
FT MUTAGEN 457
FT /note="T->P: Complete loss of initiation and polymerization
FT activities. Severe loss of protein-priming activity.
FT Increased 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:2191296"
FT MUTAGEN 458
FT /note="D->G: Complete loss of initiation and polymerization
FT activities. Severe loss of protein-priming activity.
FT Increased 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:2191296"
FT MUTAGEN 498
FT /note="K->R: Strong decrease in DNA polymerization
FT activity. Loss of binding to a primer-template DNA.
FT Increased 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:7852344"
FT MUTAGEN 498
FT /note="K->T: Strong decrease in initiation and DNA
FT polymerization activities. Loss of binding to a primer-
FT template DNA. Increased 3'-5' exonucleolysis."
FT /evidence="ECO:0000269|PubMed:7852344"
FT MUTAGEN 500
FT /note="Y->S: Strong decrease in DNA polymerization activity
FT and interaction with primer-template DNA. Increased 3'-5'
FT exonucleolysis."
FT /evidence="ECO:0000269|PubMed:7852344"
FT MUTAGEN 529
FT /note="K->A: Increased exonuclease activity and loss of
FT primer elongation. Deficient in nucleotide incorporation."
FT /evidence="ECO:0000269|PubMed:24023769"
FT MUTAGEN 529
FT /note="K->E: Increased exonuclease activity and complete
FT loss of primer elongation."
FT /evidence="ECO:0000269|PubMed:24023769"
FT CONFLICT 492
FT /note="A -> V (in Ref. 4; CAA37450)"
FT /evidence="ECO:0000305"
FT STRAND 8..15
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:2PYL"
FT STRAND 24..33
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 44..54
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 57..62
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 63..76
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 89..95
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 100..110
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 113..121
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 122..125
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 130..136
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:2PYL"
FT HELIX 160..182
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 190..202
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 204..210
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 216..223
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 238..242
FT /evidence="ECO:0007829|PDB:1XI1"
FT STRAND 244..250
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 253..260
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 263..274
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 283..294
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:2PYL"
FT STRAND 324..329
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 330..339
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 340..357
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 361..373
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 376..387
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 390..393
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 401..406
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 410..416
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 427..447
FT /evidence="ECO:0007829|PDB:2PY5"
FT TURN 448..451
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 452..456
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 459..466
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 469..474
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 477..479
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 482..496
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 499..509
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 512..515
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 518..520
FT /evidence="ECO:0007829|PDB:2PYJ"
FT STRAND 522..530
FT /evidence="ECO:0007829|PDB:2PY5"
FT HELIX 535..538
FT /evidence="ECO:0007829|PDB:2PY5"
FT TURN 543..545
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 551..561
FT /evidence="ECO:0007829|PDB:2PY5"
FT STRAND 564..573
FT /evidence="ECO:0007829|PDB:2PY5"
SQ SEQUENCE 575 AA; 66714 MW; 856EEB6B04A7E268 CRC64;
MKHMPRKMYS CDFETTTKVE DCRVWAYGYM NIEDHSEYKI GNSLDEFMAW VLKVQADLYF
HNLKFDGAFI INWLERNGFK WSADGLPNTY NTIISRMGQW YMIDICLGYK GKRKIHTVIY
DSLKKLPFPV KKIAKDFKLT VLKGDIDYHK ERPVGYKITP EEYAYIKNDI QIIAEALLIQ
FKQGLDRMTA GSDSLKGFKD IITTKKFKKV FPTLSLGLDK EVRYAYRGGF TWLNDRFKEK
EIGEGMVFDV NSLYPAQMYS RLLPYGEPIV FEGKYVWDED YPLHIQHIRC EFELKEGYIP
TIQIKRSRFY KGNEYLKSSG GEIADLWLSN VDLELMKEHY DLYNVEYISG LKFKATTGLF
KDFIDKWTYI KTTSEGAIKQ LAKLMLNSLY GKFASNPDVT GKVPYLKENG ALGFRLGEEE
TKDPVYTPMG VFITAWARYT TITAAQACYD RIIYCDTDSI HLTGTEIPDV IKDIVDPKKL
GYWAHESTFK RAKYLRQKTY IQDIYMKEVD GKLVEGSPDD YTDIKFSVKC AGMTDKIKKE
VTFENFKVGF SRKMKPKPVQ VPGGVVLVDD TFTIK
