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PDBsum entry 1waj
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Nucleotidyltransferase PDB id
1waj

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
903 a.a. *
Ligands
5GP
Waters ×61
* Residue conservation analysis
PDB id:
1waj
Name: Nucleotidyltransferase
Title: DNA polymerase from bacteriophage rb69
Structure: DNA polymerase. Chain: a. Synonym: t4 gp43. Engineered: yes
Source: Enterobacteria phage rb69. Organism_taxid: 12353. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.80Å     R-factor:   0.210     R-free:   0.280
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q38087  (DPOL_BPR69) -  DNA-directed DNA polymerase from Escherichia phage RB69
Seq:
Struc: 		 
Seq:
Struc: 		903 a.a.
903 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
 + diphosphate
   Enzyme class 2: E.C.3.1.11.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added 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 Šresolution 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
21036870 D.A.Korona, K.G.Lecompte, and Z.F.Pursell (2011).
The high fidelity and unique error signature of human DNA polymerase epsilon.
  Nucleic Acids Res, 39, 1763-1773.  
21245343 K.Mayanagi, S.Kiyonari, H.Nishida, M.Saito, D.Kohda, Y.Ishino, T.Shirai, and K.Morikawa (2011).
Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.
  Proc Natl Acad Sci U S A, 108, 1845-1849.  
21168327 M.Mason, A.Schuller, and E.Skordalakes (2011).
Telomerase structure function.
  Curr Opin Struct Biol, 21, 92.  
21185718 Y.W.Yin (2011).
Structural insight on processivity, human disease and antiviral drug toxicity.
  Curr Opin Struct Biol, 21, 83-91.  
20152155 A.A.Golosov, J.J.Warren, L.S.Beese, and M.Karplus (2010).
The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis.
  Structure, 18, 83-93.
PDB codes: 3eyz 3ez5
20163964 E.Johansson, and S.A.Macneill (2010).
The eukaryotic replicative DNA polymerases take shape.
  Trends Biochem Sci, 35, 339-347.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20166748 M.Hogg, J.Rudnicki, J.Midkiff, L.Reha-Krantz, S.Doublié, and S.S.Wallace (2010).
Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.
  Biochemistry, 49, 2317-2325.
PDB code: 3lds
19665592 S.K.Perumal, H.Yue, Z.Hu, M.M.Spiering, and S.J.Benkovic (2010).
Single-molecule studies of DNA replisome function.
  Biochim Biophys Acta, 1804, 1094-1112.  
  21129204 T.C.Mueser, J.M.Hinerman, J.M.Devos, R.A.Boyer, and K.J.Williams (2010).
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives.
  Virol J, 7, 359.  
21108267 T.Ogino, K.Sato, and A.Matsuda (2010).
Incorporation of 2'-deoxy-2'-isonucleoside 5'-triphosphates (iNTPs) into DNA by A- and B-family DNA polymerases with different recognition mechanisms.
  Chembiochem, 11, 2597-2605.  
20334433 X.Meng, Y.Zhou, E.Y.Lee, M.Y.Lee, and D.N.Frick (2010).
The p12 subunit of human polymerase delta modulates the rate and fidelity of DNA synthesis.
  Biochemistry, 49, 3545-3554.  
21081096 Y.Li, and T.Schlick (2010).
Modeling DNA polymerase μ motions: subtle transitions before chemistry.
  Biophys J, 99, 3463-3472.  
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.  
19622750 E.P.Tchesnokov, A.Obikhod, R.F.Schinazi, and M.Götte (2009).
Engineering of a chimeric RB69 DNA polymerase sensitive to drugs targeting the cytomegalovirus enzyme.
  J Biol Chem, 284, 26439-26446.  
19522539 H.Zhang, J.Beckman, J.Wang, and W.Konigsberg (2009).
RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity.
  Biochemistry, 48, 6940-6950.  
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.  
19072331 J.N.Patro, M.Urban, and R.D.Kuchta (2009).
Role of the 2-amino group of purines during dNTP polymerization by human DNA polymerase alpha.
  Biochemistry, 48, 180-189.  
19348507 M.Trostler, A.Delier, J.Beckman, M.Urban, J.N.Patro, T.E.Spratt, L.S.Beese, and R.D.Kuchta (2009).
Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus.
  Biochemistry, 48, 4633-4641.  
19228037 M.Wang, H.R.Lee, and W.Konigsberg (2009).
Effect of A and B metal ion site occupancy on conformational changes in an RB69 DNA polymerase ternary complex.
  Biochemistry, 48, 2075-2086.  
19788334 N.A.Cavanaugh, K.A.Ramirez-Aguilar, M.Urban, and R.D.Kuchta (2009).
Herpes simplex virus-1 helicase-primase: roles of each subunit in DNA binding and phosphodiester bond formation.
  Biochemistry, 48, 10199-10207.  
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.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
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.  
18691598 R.A.Wing, S.Bailey, and T.A.Steitz (2008).
Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.
  J Mol Biol, 382, 859-869.
PDB code: 3e0d
17988102 A.P.Silverman, Q.Jiang, M.F.Goodman, and E.T.Kool (2007).
Steric and electrostatic effects in DNA synthesis by the SOS-induced DNA polymerases II and IV of Escherichia coli.
  Biochemistry, 46, 13874-13881.  
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.  
17209555 J.Beckman, K.Kincaid, M.Hocek, T.Spratt, J.Engels, R.Cosstick, and R.D.Kuchta (2007).
Human DNA polymerase alpha uses a combination of positive and negative selectivity to polymerize purine dNTPs with high fidelity.
  Biochemistry, 46, 448-460.  
18496613 M.Garcia-Diaz, and K.Bebenek (2007).
Multiple functions of DNA polymerases.
  CRC Crit Rev Plant Sci, 26, 105-122.  
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.  
16959568 M.H.Lamers, R.E.Georgescu, S.G.Lee, M.O'Donnell, and J.Kuriyan (2006).
Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.
  Cell, 126, 881-892.
PDB codes: 2hnh 2hqa
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.  
16959569 S.Bailey, R.A.Wing, and T.A.Steitz (2006).
The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
  Cell, 126, 893-904.
PDB codes: 2hpi 2hpm
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.  
15109812 A.R.Pavlov, N.V.Pavlova, S.A.Kozyavkin, and A.I.Slesarev (2004).
Recent developments in the optimization of thermostable DNA polymerases for efficient applications.
  Trends Biotechnol, 22, 253-260.  
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.  
15130474 D.Das, and M.M.Georgiadis (2004).
The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.
  Structure, 12, 819-829.
PDB codes: 1rw3 4mh8
15122880 D.W.Gohara, J.J.Arnold, and C.E.Cameron (2004).
Poliovirus RNA-dependent RNA polymerase (3Dpol): kinetic, thermodynamic, and structural analysis of ribonucleotide selection.
  Biochemistry, 43, 5149-5158.  
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.  
15016374 Y.W.Yin, and T.A.Steitz (2004).
The structural mechanism of translocation and helicase activity in T7 RNA polymerase.
  Cell, 116, 393-404.
PDB codes: 1s76 1s77
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.  
11566124 W.A.Beard, and S.H.Wilson (2001).
DNA lesion bypass polymerases open up.
  Structure, 9, 759-764.  
  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.  
  20882113 J.C.Morales, and E.T.Kool (2000).
Varied Molecular Interactions at the Active Sites of Several DNA Polymerases: Nonpolar Nucleoside Isosteres as Probes.
  J Am Chem Soc, 122, 1001-1007.  
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.  
10712935 J.L.Keck, and J.M.Berger (2000).
DNA replication at high resolution.
  Chem Biol, 7, R63-R71.  
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.  
11074294 L.M.Mansky, and K.S.Cunningham (2000).
Virus mutators and antimutators: roles in evolution, pathogenesis and emergence.
  Trends Genet, 16, 512-517.  
10660290 M.M.Hingorani, and M.O'Donnell (2000).
Sliding clamps: a (tail)ored fit.
  Curr Biol, 10, R25-R29.  
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
10574802 H.Ago, T.Adachi, A.Yoshida, M.Yamamoto, N.Habuka, K.Yatsunami, and M.Miyano (1999).
Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus.
  Structure, 7, 1417-1426.
PDB code: 1quv
  10430556 I.K.Cann, and Y.Ishino (1999).
Archaeal DNA replication: identifying the pieces to solve a puzzle.
  Genetics, 152, 1249-1267.  
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
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.  
10368292 S.Doublié, M.R.Sawaya, and T.Ellenberger (1999).
An open and closed case for all polymerases.
  Structure, 7, R31-R35.  
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.  
10535734 Y.Shamoo, and T.A.Steitz (1999).
Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
  Cell, 99, 155-166.
PDB codes: 1b77 1b8h 1clq 1qe4
10545321 Y.Zhao, D.Jeruzalmi, I.Moarefi, L.Leighton, R.Lasken, and J.Kuriyan (1999).
Crystal structure of an archaebacterial DNA polymerase.
  Structure, 7, 1189-1199.
PDB codes: 1d5a 1qqc
9666335 A.G.Murzin (1998).
How far divergent evolution goes in proteins.
  Curr Opin Struct Biol, 8, 380-387.  
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.  
9519297 C.A.Brautigam, and T.A.Steitz (1998).
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.
  Curr Opin Struct Biol, 8, 54-63.  
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.  
9757823 K.Singh, and M.J.Modak (1998).
A unified DNA- and dNTP-binding mode for DNA polymerases.
  Trends Biochem Sci, 23, 277-281.  
  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.  
9914251 S.Doublié, and T.Ellenberger (1998).
The mechanism of action of T7 DNA polymerase.
  Curr Opin Struct Biol, 8, 704-712.  
9476890 T.A.Baker, and S.P.Bell (1998).
Polymerases and the replisome: machines within machines.
  Cell, 92, 295-305.  
9461069 T.A.Kunkel, and S.H.Wilson (1998).
DNA polymerases on the move.
  Nat Struct Biol, 5, 95-99.  
9519290 T.J.Richmond, and T.A.Steitz (1998).
Protein-nucleic acid interactions.
  Curr Opin Struct Biol, 8, 11-13.  
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.  
9519403 Z.Kelman, J.Hurwitz, and M.O'Donnell (1998).
Processivity of DNA polymerases: two mechanisms, one goal.
  Structure, 6, 121-125.  
9390554 J.Wang, J.A.Hartling, and J.M.Flanagan (1997).
The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis.
  Cell, 91, 447-456.
PDB code: 1tyf
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.

 

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