PDBsum entry: 1waf

Nucleotidyltransferase

PDB-id

1waf


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Ligands

GMP ×2

* Residue conservation analysis

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PDB id:

1waf

Name:

Nucleotidyltransferase

Title:

DNA polymerase from bacteriophage rb69

Structure:

DNA polymerase. Chain: a, b. Synonym: t4 gp43. Engineered: yes

Source:

Enterobacteria phage rb69. Organism_taxid: 12353. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: Q38087 (DPOL_BPR69)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

903 a.a.

Struc:

903 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Enzyme class:

E.C.2.7.7.7 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1) (see diagram below)

Resolution:

3.20Å

R-factor:

0.198

R-free:

0.274

Authors:

J.Wang,A.K.M.A.Satter,C.C.Wang,J.D.Karam,W.H.Konigsberg, T.A.Steitz

Key ref:

J.Wang et al. (1997). Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.. Cell, 89, 1087-1099. [PubMed id: 9215631] [DOI: 10.1016/S0092-8674(00)80296-2]

Date:

13-Apr-97

Release date:

14-Jan-98

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Surface

Enzyme reaction for E.C.2.7.7.7

N deoxynucleoside triphosphate	=	N diphosphate	+	{DNA}(N)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Key reference

DOI no: 10.1016/S0092-8674(00)80296-2 Cell 89:1087-1099 (1997)

PubMed id: 9215631

Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.

J.Wang, A.K.Sattar, C.C.Wang, J.D.Karam, W.H.Konigsberg, T.A.Steitz.

ABSTRACT

The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a member of the eukaryotic pol alpha family of replicative DNA polymerases, shares some similarities with other polymerases but shows many differences. Although its palm domain has the same topology as other polymerases, except rat DNA polymerase beta, one of the three carboxylates required for nucleotidyl transfer is located on a different beta strand. The structures of the fingers and thumb domains are unrelated to all other known polymerase structures. The editing 3'-5' exonuclease domain of gp43 is homologous to that of E. coli DNA polymerase I but lies on the opposite side of the polymerase active site. An extended structure-based alignment of eukaryotic DNA polymerase sequences provides structural insights that should be applicable to most eukaryotic DNA polymerases.

Selected figure(s)

Figure 1.
Figure 1. Stereo Representation of a Portion of Two Electron-Density MapsThe experimental (blue at 1.5σ) and 2F[o]-F[c] (pink at 1.25σ) densities of RB69 gp43 at 2.8 Å resolution are superimposed on the refined model in the region around D621 in the polymerase catalytic site. Figure 8.
Figure 8. Solvent-Accessible Contact-Surface Representation of a Hypothetical Model for the Replication ComplexIncluded in the model are gp32, gp43, gp45, and a model-built DNA primer template bound with its 3′ terminus in the exonuclease active site. The protein coordinates used were from the crystal structures of T4 gp32 core ([62]), the β subunit of E. coli DNA polymerase III ( [39]), and RB69 gp43. The locations of the various domains and clefts are indicated by arrows.

The above figures are reprinted by permission from Cell Press: Cell (1997, 89, 1087-1099) copyright 1997.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19661923 B.Ibarra, Y.R.Chemla, S.Plyasunov, S.B.Smith, J.M.Lázaro, M.Salas, and C.Bustamante (2009).
Proofreading dynamics of a processive DNA polymerase.

EMBO J, 28, 2794-2802.

19033368 I.Rodríguez, J.M.Lázaro, M.Salas, and M.de Vega (2009).
Involvement of the TPR2 subdomain movement in the activities of phi29 DNA polymerase.

Nucleic Acids Res, 37, 193-203.

19282447 R.Fazlieva, C.S.Spittle, D.Morrissey, H.Hayashi, H.Yan, and Y.Matsumoto (2009).
Proofreading exonuclease activity of human DNA polymerase delta and its effects on lesion-bypass DNA synthesis.

Nucleic Acids Res, 37, 2854-2866.

18758444 A.J.Gillis, A.P.Schuller, and E.Skordalakes (2008).
Structure of the Tribolium castaneum telomerase catalytic subunit TERT.

Nature, 455, 633-637.

PDB codes: 3du5 3du6

18263611 C.A.Howell, C.M.Kondratick, and M.T.Washington (2008).
Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase zeta.

Nucleic Acids Res, 36, 1731-1740.

17959669 K.F.Bryant, and D.M.Coen (2008).
Inhibition of translation by a short element in the 5' leader of the herpes simplex virus 1 DNA polymerase transcript.

J Virol, 82, 77-85.

18393274 K.H.Tang, and M.D.Tsai (2008).
Structure and function of 2:1 DNA polymerase.DNA complexes.

J Cell Physiol, 216, 315-320.

17148482 E.Crespan, L.Alexandrova, A.Khandazhinskaya, M.Jasko, M.Kukhanova, G.Villani, U.Hübscher, S.Spadari, and G.Maga (2007).
Expanding the repertoire of DNA polymerase substrates: template-instructed incorporation of non-nucleoside triphosphate analogues by DNA polymerases beta and lambda.

Nucleic Acids Res, 35, 45-57.

17043128 G.M.Scott, A.Weinberg, W.D.Rawlinson, and S.Chou (2007).
Multidrug resistance conferred by novel DNA polymerase mutations in human cytomegalovirus isolates.

Antimicrob Agents Chemother, 51, 89-94.

17766250 H.Zhang, W.Cao, E.Zakharova, W.Konigsberg, and E.M.De La Cruz (2007).
Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates.

Nucleic Acids Res, 35, 6052-6062.

17098747 M.Hogg, P.Aller, W.Konigsberg, S.S.Wallace, and S.Doublié (2007).
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.

PDB code: 2dtu

17121822 S.A.Nick McElhinny, C.M.Stith, P.M.Burgers, and T.A.Kunkel (2007).
Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase delta.

J Biol Chem, 282, 2324-2332.

17071961 E.Longás, M.de Vega, J.M.Lázaro, and M.Salas (2006).
Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity.

Nucleic Acids Res, 34, 6051-6063.

16415021 E.P.Tchesnokov, C.Gilbert, G.Boivin, and M.Götte (2006).
Role of helix P of the human cytomegalovirus DNA polymerase in resistance and hypersusceptibility to the antiviral drug foscarnet.

J Virol, 80, 1440-1450.

17176463 E.V.Koonin (2006).
Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases.

Biol Direct, 1, 39.

16369485 F.J.Asturias, I.K.Cheung, N.Sabouri, O.Chilkova, D.Wepplo, and E.Johansson (2006).
Structure of Saccharomyces cerevisiae DNA polymerase epsilon by cryo-electron microscopy.

Nat Struct Mol Biol, 13, 35-43.

17067213 J.B.Sweasy, J.M.Lauper, and K.A.Eckert (2006).
DNA polymerases and human diseases.

Radiat Res, 166, 693-714.

16339886 K.Datta, A.J.Wowor, A.J.Richard, and V.J.LiCata (2006).
Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA.

Biophys J, 90, 1739-1751.

16687658 M.Hogg, W.Cooper, L.Reha-Krantz, and S.S.Wallace (2006).
Kinetics of error generation in homologous B-family DNA polymerases.

Nucleic Acids Res, 34, 2528-2535.

16757576 P.Pérez-Arnaiz, J.M.Lázaro, M.Salas, and M.de Vega (2006).
Involvement of phi29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication.

Nucleic Acids Res, 34, 3107-3115.

16344551 R.N.Venkatesan, J.J.Hsu, N.A.Lawrence, B.D.Preston, and L.A.Loeb (2006).
Mutator phenotypes caused by substitution at a conserved motif A residue in eukaryotic DNA polymerase delta.

J Biol Chem, 281, 4486-4494.

17176036 R.Radhakrishnan, K.Arora, Y.Wang, W.A.Beard, S.H.Wilson, and T.Schlick (2006).
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.

Biochemistry, 45, 15142-15156.

16705640 R.Shi, A.Azzi, C.Gilbert, G.Boivin, and S.X.Lin (2006).
Three-dimensional modeling of cytomegalovirus DNA polymerase and preliminary analysis of drug resistance.

Proteins, 64, 301-307.

16638752 S.Liu, J.D.Knafels, J.S.Chang, G.A.Waszak, E.T.Baldwin, M.R.Deibel, D.R.Thomsen, F.L.Homa, P.A.Wells, M.C.Tory, R.A.Poorman, H.Gao, X.Qiu, and A.P.Seddon (2006).
Crystal structure of the herpes simplex virus 1 DNA polymerase.

J Biol Chem, 281, 18193-18200.

PDB code: 2gv9

16881051 S.Sun, L.Geng, and Y.Shamoo (2006).
Structure and enzymatic properties of a chimeric bacteriophage RB69 DNA polymerase and single-stranded DNA binding protein with increased processivity.

Proteins, 65, 231-238.

PDB codes: 2a1k 2atq

16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.

EMBO J, 25, 3458-3468.

15647500 A.Bibillo, D.Lener, G.J.Klarmann, and S.F.Le Grice (2005).
Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase.

Nucleic Acids Res, 33, 171-181.

16043633 E.Crespan, S.Zanoli, A.Khandazhinskaya, I.Shevelev, M.Jasko, L.Alexandrova, M.Kukhanova, G.Blanca, G.Villani, U.Hübscher, S.Spadari, and G.Maga (2005).
Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases beta and lambda.

Nucleic Acids Res, 33, 4117-4127.

15845765 I.Rodríguez, J.M.Lázaro, L.Blanco, S.Kamtekar, A.J.Berman, J.Wang, T.A.Steitz, M.Salas, and M.de Vega (2005).
A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity.

Proc Natl Acad Sci U S A, 102, 6407-6412.

15608377 J.Wang, S.Kamtekar, A.J.Berman, and T.A.Steitz (2005).
Correction of X-ray intensities from single crystals containing lattice-translocation defects.

Acta Crystallogr D Biol Crystallogr, 61, 67-74.

PDB code: 1xi1

15830148 M.B.Miranda, M.Handermann, and G.Darai (2005).
DNA polymerase gene locus of Cercopithecine herpesvirus 1 is a suitable target for specific and rapid identification of viral infection by PCR technology.

Virus Genes, 30, 307-322.

15769292 T.M.Rose (2005).
CODEHOP-mediated PCR - a powerful technique for the identification and characterization of viral genomes.

Virol J, 2, 20.

15105145 A.M.Fillet, L.Auray, S.Alain, K.Gourlain, B.M.Imbert, F.Najioullah, G.Champier, S.Gouarin, J.Carquin, N.Houhou, I.Garrigue, A.Ducancelle, D.Thouvenot, and M.C.Mazeron (2004).
Natural polymorphism of cytomegalovirus DNA polymerase lies in two nonconserved regions located between domains delta-C and II and between domains III and I.

Antimicrob Agents Chemother, 48, 1865-1868.

15107492 C.L.Hendrickson, K.G.Devine, and S.A.Benner (2004).
Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine.

Nucleic Acids Res, 32, 2241-2250.

15057282 E.Freisinger, A.P.Grollman, H.Miller, and C.Kisker (2004).
Lesion (in)tolerance reveals insights into DNA replication fidelity.

EMBO J, 23, 1494-1505.

PDB codes: 1q9x 1q9y

15189144 L.S.Kaguni (2004).
DNA polymerase gamma, the mitochondrial replicase.

Annu Rev Biochem, 73, 293-320.

15189842 L.Yang, W.A.Beard, S.H.Wilson, S.Broyde, and T.Schlick (2004).
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

Biophys J, 86, 3392-3408.

15057283 M.Hogg, S.S.Wallace, and S.Doublié (2004).
Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.

EMBO J, 23, 1483-1493.

PDB codes: 1rv2 2p5o

15065652 T.A.Steitz, and Y.W.Yin (2004).
Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.

Philos Trans R Soc Lond B Biol Sci, 359, 17-23.

15082768 T.J.Moriarty, D.T.Marie-Egyptienne, and C.Autexier (2004).
Functional organization of repeat addition processivity and DNA synthesis determinants in the human telomerase multimer.

Mol Cell Biol, 24, 3720-3733.

15627374 V.M.Petrov, and J.D.Karam (2004).
Diversity of structure and function of DNA polymerase (gp43) of T4-related bacteriophages.

Biochemistry (Mosc), 69, 1213-1218.

14729920 V.Truniger, J.M.Lázaro, and M.Salas (2004).
Function of the C-terminus of phi29 DNA polymerase in DNA and terminal protein binding.

Nucleic Acids Res, 32, 361-370.

14704353 Y.Shen, X.F.Tang, H.Yokoyama, E.Matsui, and I.Matsui (2004).
A 21-amino acid peptide from the cysteine cluster II of the family D DNA polymerase from Pyrococcus horikoshii stimulates its nuclease activity which is Mre11-like and prefers manganese ion as the cofactor.

Nucleic Acids Res, 32, 158-168.

14694096 Y.T.Hwang, H.J.Zuccola, Q.Lu, and C.B.Hwang (2004).
A point mutation within conserved region VI of herpes simplex virus type 1 DNA polymerase confers altered drug sensitivity and enhances replication fidelity.

J Virol, 78, 650-657.

15485923 Y.Zhou, and T.S.Wang (2004).
A coordinated temporal interplay of nucleosome reorganization factor, sister chromatin cohesion factor, and DNA polymerase alpha facilitates DNA replication.

Mol Cell Biol, 24, 9568-9579.

12869690 A.Goel, R.D.Astumian, and D.Herschbach (2003).
Tuning and switching a DNA polymerase motor with mechanical tension.

Proc Natl Acad Sci U S A, 100, 9699-9704.

14527289 B.Grabowski, and Z.Kelman (2003).
Archeal DNA replication: eukaryal proteins in a bacterial context.

Annu Rev Microbiol, 57, 487-516.

12700227 E.Delagoutte, and P.H.Von Hippel (2003).
Function and assembly of the bacteriophage T4 DNA replication complex: interactions of the T4 polymerase with various model DNA constructs.

J Biol Chem, 278, 25435-25447.

12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.

Microbiol Mol Biol Rev, 67, 86.

12427736 F.T.Ishmael, M.A.Trakselis, and S.J.Benkovic (2003).
Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome.

J Biol Chem, 278, 3145-3152.

12829822 J.Bestman-Smith, and G.Boivin (2003).
Drug resistance patterns of recombinant herpes simplex virus DNA polymerase mutants generated with a set of overlapping cosmids and plasmids.

J Virol, 77, 7820-7829.

12637557 M.Ogawa, S.Limsirichaikul, A.Niimi, S.Iwai, S.Yoshida, and M.Suzuki (2003).
Distinct function of conserved amino acids in the fingers of Saccharomyces cerevisiae DNA polymerase alpha.

J Biol Chem, 278, 19071-19078.

14596616 O.Kornyushyna, and C.J.Burrows (2003).
Effect of the oxidized guanosine lesions spiroiminodihydantoin and guanidinohydantoin on proofreading by Escherichia coli DNA polymerase I (Klenow fragment) in different sequence contexts.

Biochemistry, 42, 13008-13018.

14504218 P.J.Gutiérrez, and T.S.Wang (2003).
Genomic instability induced by mutations in Saccharomyces cerevisiae POL1.

Genetics, 165, 65-81.

12649320 S.J.Johnson, J.S.Taylor, and L.S.Beese (2003).
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.

Proc Natl Acad Sci U S A, 100, 3895-3900.

PDB codes: 1l3s 1l3t 1l3u 1l3v 1l5u 1lv5

12458197 S.Sun, and Y.Shamoo (2003).
Biochemical characterization of interactions between DNA polymerase and single-stranded DNA-binding protein in bacteriophage RB69.

J Biol Chem, 278, 3876-3881.

12805385 V.Truniger, J.M.Lázaro, M.de Vega, L.Blanco, and M.Salas (2003).
phi 29 DNA polymerase residue Leu384, highly conserved in motif B of eukaryotic type DNA replicases, is involved in nucleotide insertion fidelity.

J Biol Chem, 278, 33482-33491.

12454051 A.Bebenek, G.T.Carver, H.K.Dressman, F.A.Kadyrov, J.K.Haseman, V.Petrov, W.H.Konigsberg, J.D.Karam, and J.W.Drake (2002).
Dissecting the fidelity of bacteriophage RB69 DNA polymerase: site-specific modulation of fidelity by polymerase accessory proteins.

Genetics, 162, 1003-1018.

11976309 C.Desplats, C.Dez, F.Tétart, H.Eleaume, and H.M.Krisch (2002).
Snapshot of the genome of the pseudo-T-even bacteriophage RB49.

J Bacteriol, 184, 2789-2804.

12140316 G.Villani, N.Tanguy Le Gac, L.Wasungu, D.Burnouf, R.P.Fuchs, and P.E.Boehmer (2002).
Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase.

Nucleic Acids Res, 30, 3323-3332.

12162740 G.Yang, M.Franklin, J.Li, T.C.Lin, and W.Konigsberg (2002).
A conserved Tyr residue is required for sugar selectivity in a Pol alpha DNA polymerase.

Biochemistry, 41, 10256-10261.

11988770 I.V.Shevelev, and U.Hübscher (2002).
The 3' 5' exonucleases.

Nat Rev Mol Cell Biol, 3, 364-376.

11788711 K.S.Makarova, L.Aravind, N.V.Grishin, I.B.Rogozin, and E.V.Koonin (2002).
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

Nucleic Acids Res, 30, 482-496.

11823435 M.Delarue, J.B.Boulé, J.Lescar, N.Expert-Bezançon, N.Jourdan, N.Sukumar, F.Rougeon, and C.Papanicolaou (2002).
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.

EMBO J, 21, 427-439.

PDB codes: 1jms 1kdh 1kej

12415291 M.J.Fogg, L.H.Pearl, and B.A.Connolly (2002).
Structural basis for uracil recognition by archaeal family B DNA polymerases.

Nat Struct Biol, 9, 922-927.

12210533 P.Cramer (2002).
Common structural features of nucleic acid polymerases.

Bioessays, 24, 724-729.

12447445 P.Szabó, I.Scheuring, T.Czárán, and E.Szathmáry (2002).
In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity.

Nature, 420, 340-343.

11884636 R.Eisenbrandt, J.M.Lázaro, M.Salas, and M.de Vega (2002).
Phi29 DNA polymerase residues Tyr59, His61 and Phe69 of the highly conserved ExoII motif are essential for interaction with the terminal protein.

Nucleic Acids Res, 30, 1379-1386.

12087102 V.M.Petrov, S.S.Ng, and J.D.Karam (2002).
Protein determinants of RNA binding by DNA polymerase of the T4-related bacteriophage RB69.

J Biol Chem, 277, 33041-33048.

11917008 V.Truniger, J.M.Lázaro, F.J.Esteban, L.Blanco, and M.Salas (2002).
A positively charged residue of phi29 DNA polymerase, highly conserved in DNA polymerases from families A and B, is involved in binding the incoming nucleotide.

Nucleic Acids Res, 30, 1483-1492.

11284703 E.Delagoutte, and P.H.von Hippel (2001).
Molecular mechanisms of the functional coupling of the helicase (gp41) and polymerase (gp43) of bacteriophage T4 within the DNA replication fork.

Biochemistry, 40, 4459-4477.

11459977 M.A.Trakselis, S.C.Alley, E.Abel-Santos, and S.J.Benkovic (2001).
Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer.

Proc Natl Acad Sci U S A, 98, 8368-8375.

11178285 M.Albà (2001).
Replicative DNA polymerases.

Genome Biol, 2, REVIEWS3002.

11333228 M.I.Hadjimarcou, R.J.Kokoska, T.D.Petes, and L.J.Reha-Krantz (2001).
Identification of a mutant DNA polymerase delta in Saccharomyces cerevisiae with an antimutator phenotype for frameshift mutations.

Genetics, 158, 177-186.

11395406 S.J.Benkovic, A.M.Valentine, and F.Salinas (2001).
Replisome-mediated DNA replication.

Annu Rev Biochem, 70, 181-208.

11353079 S.Ramanathan, K.V.Chary, and B.J.Rao (2001).
Incoming nucleotide binds to Klenow ternary complex leading to stable physical sequestration of preceding dNTP on DNA.

Nucleic Acids Res, 29, 2097-2105.

11467934 T.C.Lin, C.X.Wang, C.M.Joyce, and W.H.Konigsberg (2001).
3'-5' Exonucleolytic activity of DNA polymerases: structural features that allow kinetic discrimination between ribo- and deoxyribonucleotide residues.

Biochemistry, 40, 8749-8755.

11560886 Y.I.Pavlov, P.V.Shcherbakova, and T.A.Kunkel (2001).
In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta.

Genetics, 159, 47-64.

11095675 A.R.Pavlov, and J.D.Karam (2000).
Nucleotide-sequence-specific and non-specific interactions of T4 DNA polymerase with its own mRNA.

Nucleic Acids Res, 28, 4657-4664.

10775636 E.R.Schultz, G.W.Rankin, M.P.Blanc, B.W.Raden, C.C.Tsai, and T.M.Rose (2000).
Characterization of two divergent lineages of macaque rhadinoviruses related to Kaposi's sarcoma-associated herpesvirus.

J Virol, 74, 4919-4928.

10860983 F.Salinas, and S.J.Benkovic (2000).
Characterization of bacteriophage T4-coordinated leading- and lagging-strand synthesis on a minicircle substrate.

Proc Natl Acad Sci U S A, 97, 7196-7201.

10617626 G.J.Klarmann, R.A.Smith, R.F.Schinazi, T.W.North, and B.D.Preston (2000).
Site-specific incorporation of nucleoside analogs by HIV-1 reverse transcriptase and the template grip mutant P157S. Template interactions influence substrate recognition at the polymerase active site.

J Biol Chem, 275, 359-366.

10944102 G.Martin, W.Keller, and S.Doublié (2000).
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP.

EMBO J, 19, 4193-4203.

PDB code: 1f5a

11090167 H.Liu, J.H.Naismith, and R.T.Hay (2000).
Identification of conserved residues contributing to the activities of adenovirus DNA polymerase.

J Virol, 74, 11681-11689.

10681506 J.J.Arnold, and C.E.Cameron (2000).
Poliovirus RNA-dependent RNA polymerase (3D(pol)). Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub).

J Biol Chem, 275, 5329-5336.

11024170 K.Böhlke, F.M.Pisani, C.E.Vorgias, B.Frey, H.Sobek, M.Rossi, and G.Antranikian (2000).
PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.

Nucleic Acids Res, 28, 3910-3917.

11041840 K.Vastmans, S.Pochet, A.Peys, L.Kerremans, A.Van Aerschot, C.Hendrix, P.Marlière, and P.Herdewijn (2000).
Enzymatic incorporation in DNA of 1,5-anhydrohexitol nucleotides.

Biochemistry, 39, 12757-12765.

11092939 N.Sukumar, J.B.Boulé, N.Expert-Bezançon, N.Jourdan, J.Lescar, F.Rougeon, C.Papanicolaou, and M.Delarue (2000).
Crystallization of the catalytic domain of murine terminal deoxynucleotidyl transferase.

Acta Crystallogr D Biol Crystallogr, 56, 1662-1664.

10805772 P.H.Patel, and L.A.Loeb (2000).
DNA polymerase active site is highly mutable: evolutionary consequences.

Proc Natl Acad Sci U S A, 97, 5095-5100.

10666444 S.J.Evans, M.J.Fogg, A.Mamone, M.Davis, L.H.Pearl, and B.A.Connolly (2000).
Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus.

Nucleic Acids Res, 28, 1059-1066.

10966467 T.A.Kunkel, and K.Bebenek (2000).
DNA replication fidelity.

Annu Rev Biochem, 69, 497-529.

10455197 E.Elisseeva, S.S.Mandal, and L.J.Reha-Krantz (1999).
Mutational and pH studies of the 3' --> 5' exonuclease activity of bacteriophage T4 DNA polymerase.

J Biol Chem, 274, 25151-25158.

10600732 G.M.Cheetham, and T.A.Steitz (1999).
Structure of a transcribing T7 RNA polymerase initiation complex.

Science, 286, 2305-2309.

PDB code: 1qln

10430556 I.K.Cann, and Y.Ishino (1999).
Archaeal DNA replication: identifying the pieces to solve a puzzle.

Genetics, 152, 1249-1267.

10097083 K.P.Hopfner, A.Eichinger, R.A.Engh, F.Laue, W.Ankenbauer, R.Huber, and B.Angerer (1999).
Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.

Proc Natl Acad Sci U S A, 96, 3600-3605.

PDB code: 1tgo

9892653 L.Huang, K.K.Ishii, H.Zuccola, A.M.Gehring, C.B.Hwang, J.Hogle, and D.M.Coen (1999).
The enzymological basis for resistance of herpesvirus DNA polymerase mutants to acyclovir: relationship to the structure of alpha-like DNA polymerases.

Proc Natl Acad Sci U S A, 96, 447-452.

PDB code: 1b1f

10430892 M.A.Greagg, M.J.Fogg, G.Panayotou, S.J.Evans, B.A.Connolly, and L.H.Pearl (1999).
A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil.

Proc Natl Acad Sci U S A, 96, 9045-9050.

10428796 R.Dua, D.L.Levy, and J.L.Campbell (1999).
Analysis of the essential functions of the C-terminal protein/protein interaction domain of Saccharomyces cerevisiae pol epsilon and its unexpected ability to support growth in the absence of the DNA polymerase domain.

J Biol Chem, 274, 22283-22288.

10455110 S.C.Alley, A.D.Jones, P.Soumillion, and S.J.Benkovic (1999).
The carboxyl terminus of the bacteriophage T4 DNA polymerase contacts its sliding clamp at the subunit interface.

J Biol Chem, 274, 24485-24489.

10464285 S.N.Sarkar, A.Ghosh, H.W.Wang, S.S.Sung, and G.C.Sen (1999).
The nature of the catalytic domain of 2'-5'-oligoadenylate synthetases.

J Biol Chem, 274, 25535-25542.

10364165 T.A.Steitz (1999).
DNA polymerases: structural diversity and common mechanisms.

J Biol Chem, 274, 17395-17398.

10523676 T.Mizuno, K.Yamagishi, H.Miyazawa, and F.Hanaoka (1999).
Molecular architecture of the mouse DNA polymerase alpha-primase complex.

Mol Cell Biol, 19, 7886-7896.

10409611 W.P.Osheroff, W.A.Beard, S.H.Wilson, and T.A.Kunkel (1999).
Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove.

J Biol Chem, 274, 20749-20752.

9736701 A.J.Berdis, and S.J.Benkovic (1998).
Simultaneous formation of functional leading and lagging strand holoenzyme complexes on a small, defined DNA substrate.

Proc Natl Acad Sci U S A, 95, 11128-11133.

9670025 D.Jeruzalmi, and T.A.Steitz (1998).
Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

EMBO J, 17, 4101-4113.

PDB code: 1aro

9469832 E.J.Parker, C.H.Botting, A.Webster, and R.T.Hay (1998).
Adenovirus DNA polymerase: domain organisation and interaction with preterminal protein.

Nucleic Acids Res, 26, 1240-1247.

9778379 F.M.Pisani, M.De Felice, and M.Rossi (1998).
Amino acid residues involved in determining the processivity of the 3'-5' exonuclease activity in a family B DNA polymerase from the thermoacidophilic archaeon Sulfolobus solfataricus.

Biochemistry, 37, 15005-15012.

9774655 G.Mass, T.Nethanel, and G.Kaufmann (1998).
The middle subunit of replication protein A contacts growing RNA-DNA primers in replicating simian virus 40 chromosomes.

Mol Cell Biol, 18, 6399-6407.

9928485 G.Mosig (1998).
Recombination and recombination-dependent DNA replication in bacteriophage T4.

Annu Rev Genet, 32, 379-413.

9733733 J.M.Lanchy, G.Keith, S.F.Le Grice, B.Ehresmann, C.Ehresmann, and R.Marquet (1998).
Contacts between reverse transcriptase and the primer strand govern the transition from initiation to elongation of HIV-1 reverse transcription.

J Biol Chem, 273, 24425-24432.

9560380 L.A.Smith, and J.W.Drake (1998).
Aspects of the ultraviolet photobiology of some T-even bacteriophages.

Genetics, 148, 1611-1618.

9722519 L.J.Reha-Krantz, L.A.Marquez, E.Elisseeva, R.P.Baker, L.B.Bloom, H.B.Dunford, and M.F.Goodman (1998).
The proofreading pathway of bacteriophage T4 DNA polymerase.

J Biol Chem, 273, 22969-22976.

9560374 L.J.Reha-Krantz (1998).
Regulation of DNA polymerase exonucleolytic proofreading activity: studies of bacteriophage T4 "antimutator" DNA polymerases.

Genetics, 148, 1551-1557.

9555879 L.S.Yeh, T.Hsu, and J.D.Karam (1998).
Divergence of a DNA replication gene cluster in the T4-related bacteriophage RB69.

J Bacteriol, 180, 2005-2013.

9520378 M.Astatke, K.Ng, N.D.Grindley, and C.M.Joyce (1998).
A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides.

Proc Natl Acad Sci U S A, 95, 3402-3407.

9560367 M.F.Goodman, and K.D.Fygenson (1998).
DNA polymerase fidelity: from genetics toward a biochemical understanding.

Genetics, 148, 1475-1482.

9786901 M.de Vega, L.Blanco, and M.Salas (1998).
phi29 DNA polymerase residue Ser122, a single-stranded DNA ligand for 3'-5' exonucleolysis, is required to interact with the terminal protein.

J Biol Chem, 273, 28966-28977.

9560372 N.G.Nossal (1998).
A new look at old mutants of T4 DNA polymerase.

Genetics, 148, 1535-1538.

9485358 P.L.Opresko, J.B.Sweasy, and K.A.Eckert (1998).
The mutator form of polymerase beta with amino acid substitution at tyrosine 265 in the hinge region displays an increase in both base substitution and frame shift errors.

Biochemistry, 37, 2111-2119.

9778349 P.Wu, N.Nossal, and S.J.Benkovic (1998).
Kinetic characterization of a bacteriophage T4 antimutator DNA polymerase.

Biochemistry, 37, 14748-14755.

9560377 R.M.Schaaper (1998).
Antimutator mutants in bacteriophage T4 and Escherichia coli.

Genetics, 148, 1579-1585.

9461069 T.A.Kunkel, and S.H.Wilson (1998).
DNA polymerases on the move.

Nat Struct Biol, 5, 95-99.

10333564 Y.Ishino, and I.K.Cann (1998).
The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?

Genes Genet Syst, 73, 323-336.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.