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PDBsum entry 1kln
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protein dna_rna metals links
Transferase/DNA PDB id
1kln

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
595 a.a. *
DNA/RNA
Metals
_ZN
* Residue conservation analysis
PDB id:
1kln
Name: Transferase/DNA
Title: DNA polymerase i klenow fragment (E.C.2.7.7.7) mutant/DNA complex
Structure: DNA (5'-d( Gp Cp Cp Tp Cp Gp Cp Gp Gp Cp Gp Gp C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Gp Cp Cp Gp Cp Gp Ap Gp Gp C)-3'). Chain: c. Engineered: yes. Protein (DNA polymerase i klenow fragment . Chain: a. Mutation: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562
Resolution:
3.20Å     R-factor:   0.230    
Authors: L.S.Beese,V.Derbyshire,T.A.Steitz
Key ref: L.S.Beese et al. (1993). Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science, 260, 352-355. PubMed id: 8469987 DOI: 10.1126/science.8469987
Date:
24-May-94     Release date:   30-Nov-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00582  (DPO1_ECOLI) -  DNA polymerase I from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		928 a.a.
595 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains
  G-C-C-T-C-G-C-G-G-C-G-G-C 13 bases
  G-C-C-G-C-G-A-G-G-C 10 bases

 Enzyme reactions 
   Enzyme class: 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
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1126/science.8469987 Science 260:352-355 (1993)
PubMed id: 8469987  
 
 
Structure of DNA polymerase I Klenow fragment bound to duplex DNA.
L.S.Beese, V.Derbyshire, T.A.Steitz.
 
  ABSTRACT  
 
Klenow fragment of Escherichia coli DNA polymerase I, which was cocrystallized with duplex DNA, positioned 11 base pairs of DNA in a groove that lies at right angles to the cleft that contains the polymerase active site and is adjacent to the 3' to 5' exonuclease domain. When the fragment bound DNA, a region previously referred to as the "disordered domain" became more ordered and moved along with two helices toward the 3' to 5' exonuclease domain to form the binding groove. A single-stranded, 3' extension of three nucleotides bound to the 3' to 5' exonuclease active site. Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polymerase catalytic site.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266819 K.Das, S.E.Martinez, J.D.Bauman, and E.Arnold (2012).
HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism.
  Nat Struct Mol Biol, 19, 253-259.
PDB codes: 3v4i 3v6d 3v81
21262835 K.M.Hastie, C.R.Kimberlin, M.A.Zandonatti, I.J.MacRae, and E.O.Saphire (2011).
Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 3' to 5' exonuclease activity essential for immune suppression.
  Proc Natl Acad Sci U S A, 108, 2396-2401.
PDB codes: 3q7b 3q7c
21185718 Y.W.Yin (2011).
Structural insight on processivity, human disease and antiviral drug toxicity.
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20706627 G.Pastor-Palacios, E.Azuara-Liceaga, and L.G.Brieba (2010).
A nuclear family A DNA polymerase from Entamoeba histolytica bypasses thymine glycol.
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20829187 G.Zhao, and Y.Guan (2010).
Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions.
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20231166 J.C.St John, J.Facucho-Oliveira, Y.Jiang, R.Kelly, and R.Salah (2010).
Mitochondrial DNA transmission, replication and inheritance: a journey from the gamete through the embryo and into offspring and embryonic stem cells.
  Hum Reprod Update, 16, 488-509.  
20921373 K.Datta, N.P.Johnson, and P.H.von Hippel (2010).
DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase.
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20357774 M.Mitchell, A.Gillis, M.Futahashi, H.Fujiwara, and E.Skordalakes (2010).
Structural basis for telomerase catalytic subunit TERT binding to RNA template and telomeric DNA.
  Nat Struct Mol Biol, 17, 513-518.
PDB code: 3kyl
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  J Nucleic Acids, 2010, 0.  
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POLG1 p.R722H mutation associated with multiple mtDNA deletions and a neurological phenotype.
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19773426 A.L.Mikheikin, H.K.Lin, P.Mehta, L.Jen-Jacobson, and M.A.Trakselis (2009).
A trimeric DNA polymerase complex increases the native replication processivity.
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19033368 I.Rodríguez, J.M.Lázaro, M.Salas, and M.de Vega (2009).
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Discrimination between right and wrong purine dNTPs by DNA polymerase I from Bacillus stearothermophilus.
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Disease mutations in the human mitochondrial DNA polymerase thumb subdomain impart severe defects in mitochondrial DNA replication.
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19155277 W.A.Baase, D.Jose, B.C.Ponedel, P.H.von Hippel, and N.P.Johnson (2009).
DNA models of trinucleotide frameshift deletions: the formation of loops and bulges at the primer-template junction.
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  J Am Chem Soc, 130, 2336-2343.  
18652487 A.Sheriff, E.Motea, I.Lee, and A.J.Berdis (2008).
Mechanism and dynamics of translesion DNA synthesis catalyzed by the Escherichia coli Klenow fragment.
  Biochemistry, 47, 8527-8537.  
18429330 J.Gury, L.Zinger, L.Gielly, P.Taberlet, and R.A.Geremia (2008).
Exonuclease activity of proofreading DNA polymerases is at the origin of artifacts in molecular profiling studies.
  Electrophoresis, 29, 2437-2444.  
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Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.
  Nucleic Acids Res, 36, 705-711.  
18448432 P.Kukreti, K.Singh, A.Ketkar, and M.J.Modak (2008).
Identification of a new motif required for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I (Klenow fragment): the RRRY motif is necessary for the binding of single-stranded DNA substrate and the template strand of the mismatched duplex.
  J Biol Chem, 283, 17979-17990.  
19106298 R.J.Evans, D.R.Davies, J.M.Bullard, J.Christensen, L.S.Green, J.W.Guiles, J.D.Pata, W.K.Ribble, N.Janjic, and T.C.Jarvis (2008).
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PDB codes: 3f2b 3f2c 3f2d
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17996706 J.Jiang, E.G.Maes, A.B.Taylor, L.Wang, A.P.Hinck, E.M.Lafer, and R.Sousa (2007).
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PDB codes: 2qw9 2qwl 2qwm 2qwn 2qwo 2qwp 2qwq 2qwr
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Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore.
  Nat Nanotechnol, 2, 718-724.  
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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.  
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Mutation of Phe102 to Ser in the carboxyl terminal helix of Escherichia coli thioredoxin affects the stability and processivity of T7 DNA polymerase.
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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
16061181 P.J.Rothwell, V.Mitaksov, and G.Waksman (2005).
Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: implications for the molecular basis of fidelity in DNA polymerases.
  Mol Cell, 19, 345-355.  
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.  
15345530 I.Andricioaei, A.Goel, D.Herschbach, and M.Karplus (2004).
Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations.
  Biophys J, 87, 1478-1497.  
15189842 L.Yang, W.A.Beard, S.H.Wilson, S.Broyde, and T.Schlick (2004).
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  Biophys J, 86, 3392-3408.  
15496986 M.Seki, C.Masutani, L.W.Yang, A.Schuffert, S.Iwai, I.Bahar, and R.D.Wood (2004).
High-efficiency bypass of DNA damage by human DNA polymerase Q.
  EMBO J, 23, 4484-4494.  
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.  
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.  
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.  
14623953 C.A.Minetti, D.P.Remeta, H.Miller, C.A.Gelfand, G.E.Plum, A.P.Grollman, and K.J.Breslauer (2003).
The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies.
  Proc Natl Acad Sci U S A, 100, 14719-14724.  
12560493 D.Shinde, Y.Lai, F.Sun, and N.Arnheim (2003).
Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites.
  Nucleic Acids Res, 31, 974-980.  
14500822 K.Datta, and V.J.LiCata (2003).
Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA.
  Nucleic Acids Res, 31, 5590-5597.  
12573693 K.E.McGinness, and G.F.Joyce (2003).
In search of an RNA replicase ribozyme.
  Chem Biol, 10, 5.  
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.  
12655016 S.Park, M.Seetharaman, A.Ogdie, D.Ferguson, and N.Tretyakova (2003).
3'-Exonuclease resistance of DNA oligodeoxynucleotides containing O6-[4-oxo-4-(3-pyridyl)butyl]guanine.
  Nucleic Acids Res, 31, 1984-1994.  
12641455 Z.A.Doddridge, R.D.Bertram, C.J.Hayes, and P.Soultanas (2003).
Effects of vinylphosphonate internucleotide linkages on the cleavage specificity of exonuclease III and on the activity of DNA polymerase I.
  Biochemistry, 42, 3239-3246.  
12473094 A.V.Cherepanov, and S.de Vries (2002).
Dynamic mechanism of nick recognition by DNA ligase.
  Eur J Biochem, 269, 5993-5999.  
12364611 S.W.Yang, M.Astatke, J.Potter, and D.K.Chatterjee (2002).
Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides.
  Nucleic Acids Res, 30, 4314-4320.  
11900537 W.C.Lam, E.H.Thompson, O.Potapova, X.C.Sun, C.M.Joyce, and D.P.Millar (2002).
3'-5' exonuclease of Klenow fragment: role of amino acid residues within the single-stranded DNA binding region in exonucleolysis and duplex DNA melting.
  Biochemistry, 41, 3943-3951.  
11238937 C.M.Kondratick, M.T.Washington, S.Prakash, and L.Prakash (2001).
Acidic residues critical for the activity and biological function of yeast DNA polymerase eta.
  Mol Cell Biol, 21, 2018-2025.  
11504869 C.Rocher, R.Dalibart, T.Letellier, G.Précigoux, and P.Lestienne (2001).
Initiation of DNA replication by DNA polymerases from primers forming a triple helix.
  Nucleic Acids Res, 29, 3320-3326.  
11525166 M.C.Merckel, I.P.Fabrichniy, A.Salminen, N.Kalkkinen, A.A.Baykov, R.Lahti, and A.Goldman (2001).
Crystal structure of Streptococcus mutans pyrophosphatase: a new fold for an old mechanism.
  Structure, 9, 289-297.
PDB code: 1i74
11504881 N.Murata-Kamiya, and H.Kamiya (2001).
Methylglyoxal, an endogenous aldehyde, crosslinks DNA polymerase and the substrate DNA.
  Nucleic Acids Res, 29, 3433-3438.  
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.  
11557814 S.Taladriz, T.Hanke, M.J.Ramiro, M.García-Díaz, M.García De Lacoba, L.Blanco, and V.Larraga (2001).
Nuclear DNA polymerase beta from Leishmania infantum. Cloning, molecular analysis and developmental regulation.
  Nucleic Acids Res, 29, 3822-3834.  
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.  
11258875 T.E.Spratt (2001).
Identification of hydrogen bonds between Escherichia coli DNA polymerase I (Klenow fragment) and the minor groove of DNA by amino acid substitution of the polymerase and atomic substitution of the DNA.
  Biochemistry, 40, 2647-2652.  
11050232 B.Maier, D.Bensimon, and V.Croquette (2000).
Replication by a single DNA polymerase of a stretched single-stranded DNA.
  Proc Natl Acad Sci U S A, 97, 12002-12007.  
11063578 C.I.Wooddell, and R.R.Burgess (2000).
Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity cross-linking.
  Biochemistry, 39, 13405-13421.  
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
10704212 J.C.Morales, and E.T.Kool (2000).
Importance of terminal base pair hydrogen-bonding in 3'-end proofreading by the Klenow fragment of DNA polymerase I.
  Biochemistry, 39, 2626-2632.  
11041863 J.C.Morales, and E.T.Kool (2000).
Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases.
  Biochemistry, 39, 12979-12988.  
  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.  
10630996 L.Dzantiev, and L.J.Romano (2000).
A conformational change in E. coli DNA polymerase I (Klenow fragment) is induced in the presence of a dNTP complementary to the template base in the active site.
  Biochemistry, 39, 356-361.  
10819981 L.Dzantiev, and L.J.Romano (2000).
Differential effects of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts on the conformational change in the structure of DNA polymerase I (Klenow fragment).
  Biochemistry, 39, 5139-5145.  
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.  
10047577 J.Jäger, and J.D.Pata (1999).
Getting a grip: polymerases and their substrate complexes.
  Curr Opin Struct Biol, 9, 21-28.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10322129 S.G.Sarafianos, K.Das, J.Ding, P.L.Boyer, S.H.Hughes, and E.Arnold (1999).
Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site.
  Chem Biol, 6, R137-R146.  
10052936 W.C.Lam, E.J.Van der Schans, L.C.Sowers, and D.P.Millar (1999).
Interaction of DNA polymerase I (Klenow fragment) with DNA substrates containing extrahelical bases: implications for proofreading of frameshift errors during DNA synthesis.
  Biochemistry, 38, 2661-2668.  
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
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.  
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.  
9485318 H.S.Misra, P.K.Pandey, M.J.Modak, R.Vinayak, and V.N.Pandey (1998).
Polyamide nucleic acid-DNA chimera lacking the phosphate backbone are novel primers for polymerase reaction catalyzed by DNA polymerases.
  Biochemistry, 37, 1917-1925.  
9757823 K.Singh, and M.J.Modak (1998).
A unified DNA- and dNTP-binding mode for DNA polymerases.
  Trends Biochem Sci, 23, 277-281.  
9741847 L.Holm, and C.Sander (1998).
Dictionary of recurrent domains in protein structures.
  Proteins, 33, 88-96.  
  9560367 M.F.Goodman, and K.D.Fygenson (1998).
DNA polymerase fidelity: from genetics toward a biochemical understanding.
  Genetics, 148, 1475-1482.  
9858758 R.Strick, and C.W.Knopf (1998).
DNA binding properties and processive proofreading of herpes simplex virus type 1 DNA polymerase.
  Biochim Biophys Acta, 1388, 315-324.  
9914251 S.Doublié, and T.Ellenberger (1998).
The mechanism of action of T7 DNA polymerase.
  Curr Opin Struct Biol, 8, 704-712.  
9461069 T.A.Kunkel, and S.H.Wilson (1998).
DNA polymerases on the move.
  Nat Struct Biol, 5, 95-99.  
9485315 T.E.Carver, and D.P.Millar (1998).
Recognition of sequence-directed DNA structure by the Klenow fragment of DNA polymerase I.
  Biochemistry, 37, 1898-1904.  
9484221 W.C.Lam, E.J.Van der Schans, C.M.Joyce, and D.P.Millar (1998).
Effects of mutations on the partitioning of DNA substrates between the polymerase and 3'-5' exonuclease sites of DNA polymerase I (Klenow fragment).
  Biochemistry, 37, 1513-1522.  
9485450 W.S.Furey, C.M.Joyce, M.A.Osborne, D.Klenerman, J.A.Peliska, and S.Balasubramanian (1998).
Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment.
  Biochemistry, 37, 2979-2990.  
9808040 Y.C.Yuan, R.H.Whitson, Q.Liu, K.Itakura, and Y.Chen (1998).
A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
  Nat Struct Biol, 5, 959-964.
PDB code: 1bmy
9857206 Y.Li, S.Korolev, and G.Waksman (1998).
Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.
  EMBO J, 17, 7514-7525.
PDB codes: 2ktq 3ktq 4ktq
9519403 Z.Kelman, J.Hurwitz, and M.O'Donnell (1998).
Processivity of DNA polymerases: two mechanisms, one goal.
  Structure, 6, 121-125.  
9154923 C.L.Gibb, W.Cheng, V.N.Morozov, and N.R.Kallenbach (1997).
Effect of nuclear protein HMG1 on in vitro slippage synthesis of the tandem repeat dTG x dCA.
  Biochemistry, 36, 5418-5424.  
9050827 C.M.Joyce (1997).
Choosing the right sugar: how polymerases select a nucleotide substrate.
  Proc Natl Acad Sci U S A, 94, 1619-1622.  
9012809 E.Bedford, S.Tabor, and C.C.Richardson (1997).
The thioredoxin binding domain of bacteriophage T7 DNA polymerase confers processivity on Escherichia coli DNA polymerase I.
  Proc Natl Acad Sci U S A, 94, 479-484.  
9241229 I.S.Mian (1997).
Comparative sequence analysis of ribonucleases HII, III, II PH and D.
  Nucleic Acids Res, 25, 3187-3195.  
9354757 J.Ding, S.H.Hughes, and E.Arnold (1997).
Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer.
  Biopolymers, 44, 125-138.  
9309225 J.L.Hansen, A.M.Long, and S.C.Schultz (1997).
Structure of the RNA-dependent RNA polymerase of poliovirus.
  Structure, 5, 1109-1122.
PDB code: 1rdr
9016716 J.R.Kiefer, C.Mao, C.J.Hansen, S.L.Basehore, H.H.Hogrefe, J.C.Braman, and L.S.Beese (1997).
Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
  Structure, 5, 95.
PDB codes: 1bdp 1xwl
9215631 J.Wang, A.K.Sattar, C.C.Wang, J.D.Karam, W.H.Konigsberg, and T.A.Steitz (1997).
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.
  Cell, 89, 1087-1099.
PDB codes: 1waf 1wag 1wah 1wai 1waj
9164459 K.Bebenek, W.A.Beard, T.A.Darden, L.Li, R.Prasad, B.A.Luton, D.G.Gorenstein, S.H.Wilson, and T.A.Kunkel (1997).
A minor groove binding track in reverse transcriptase.
  Nat Struct Biol, 4, 194-197.  
9108059 K.Shiba, Y.Takahashi, and T.Noda (1997).
Creation of libraries with long ORFs by polymerization of a microgene.
  Proc Natl Acad Sci U S A, 94, 3805-3810.  
9396823 M.J.Moser, W.R.Holley, A.Chatterjee, and I.S.Mian (1997).
The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.
  Nucleic Acids Res, 25, 5110-5118.  
9047336 M.T.Hess, U.Schwitter, M.Petretta, B.Giese, and H.Naegeli (1997).
DNA synthesis arrest at C4'-modified deoxyribose residues.
  Biochemistry, 36, 2332-2337.  
9047333 T.Akiyama, and M.E.Hogan (1997).
Structural analysis of DNA bending induced by tethered triple helix forming oligonucleotides.
  Biochemistry, 36, 2307-2315.  
9341220 T.E.Spratt (1997).
Klenow fragment-DNA interaction required for the incorporation of nucleotides opposite guanine and O6-methylguanine.
  Biochemistry, 36, 13292-13297.  
9153415 W.Tong, C.D.Lu, S.K.Sharma, S.Matsuura, A.G.So, and W.A.Scott (1997).
Nucleotide-induced stable complex formation by HIV-1 reverse transcriptase.
  Biochemistry, 36, 5749-5757.  
8679529 B.G.Werneburg, J.Ahn, X.Zhong, R.J.Hondal, V.S.Kraynov, and M.D.Tsai (1996).
DNA polymerase beta: pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity.
  Biochemistry, 35, 7041-7050.  
8794744 B.M.Moore, R.K.Jalluri, and M.B.Doughty (1996).
DNA polymerase photoprobe 2-[(4-azidophenacyl)thio]-2'-deoxyadenosine 5'-triphosphate labels an Escherichia coli DNA polymerase I Klenow fragment substrate binding site.
  Biochemistry, 35, 11642-11651.  
8703921 F.M.Pisani, G.Manco, V.Carratore, and M.Rossi (1996).
Domain organization and DNA-induced conformational changes of an archaeal family B DNA polymerase.
  Biochemistry, 35, 9158-9166.  
8628681 F.Ye, J.A.Carrodeguas, and D.F.Bogenhagen (1996).
The gamma subfamily of DNA polymerases: cloning of a developmentally regulated cDNA encoding Xenopus laevis mitochondrial DNA polymerase gamma.
  Nucleic Acids Res, 24, 1481-1488.  
8841118 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
  Biochemistry, 35, 12742-12761.
PDB codes: 9icm 9icw 9icx 9icy
8646784 K.K.Leuther, D.A.Bushnell, and R.D.Kornberg (1996).
Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation.
  Cell, 85, 773-779.  
8807868 M.W.Frey, S.T.Frey, W.D.Horrocks, B.F.Kaboord, and S.J.Benkovic (1996).
Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase by lanthanide(III) luminescence spectroscopy.
  Chem Biol, 3, 393-403.  
  8816490 P.V.Harris, O.M.Mazina, E.A.Leonhardt, R.B.Case, J.B.Boyd, and K.C.Burtis (1996).
Molecular cloning of Drosophila mus308, a gene involved in DNA cross-link repair with homology to prokaryotic DNA polymerase I genes.
  Mol Cell Biol, 16, 5764-5771.  
8871404 R.Sousa (1996).
Structural and mechanistic relationships between nucleic acid polymerases.
  Trends Biochem Sci, 21, 186-190.  
8918794 S.Prasartkaew, N.M.Zijlstra, P.Wilairat, J.P.Overdulve, and E.de Vries (1996).
Molecular cloning of a Plasmodium falciparum gene interrupted by 15 introns encoding a functional primase 53 kDa subunit as demonstrated by expression in a baculovirus system.
  Nucleic Acids Res, 24, 3934-3941.  
  8670845 V.Truniger, J.M.Lázaro, M.Salas, and L.Blanco (1996).
A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases.
  EMBO J, 15, 3430-3441.  
8521466 A.Polyakov, E.Severinova, and S.A.Darst (1995).
Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme.
  Cell, 83, 365-373.  
  7592405 C.M.Joyce, and T.A.Steitz (1995).
Polymerase structures and function: variations on a theme?
  J Bacteriol, 177, 6321-6329.  
7539708 E.Arnold, J.Ding, S.H.Hughes, and Z.Hostomsky (1995).
Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates.
  Curr Opin Struct Biol, 5, 27-38.  
7669351 M.Salas, R.Freire, M.S.Soengas, J.A.Esteban, J.Méndez, A.Bravo, M.Serrano, M.A.Blasco, J.M.Lázaro, and L.Blanco (1995).
Protein-nucleic acid interactions in bacteriophage phi 29 DNA replication.
  FEMS Microbiol Rev, 17, 73-82.  
7476180 P.L.deHaseth, and J.D.Helmann (1995).
Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA.
  Mol Microbiol, 16, 817-824.  
7568114 S.Korolev, M.Nayal, W.M.Barnes, E.Di Cera, and G.Waksman (1995).
Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.
  Proc Natl Acad Sci U S A, 92, 9264-9268.
PDB code: 1ktq
7603992 S.Tabor, and C.C.Richardson (1995).
A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides.
  Proc Natl Acad Sci U S A, 92, 6339-6343.  
8539242 U.K.Urs, D.J.Sharkey, T.S.Peat, W.A.Hendrickson, and K.Murthy (1995).
Characterization of crystals of the thermostable DNA polymerase I from Thermus aquaticus.
  Proteins, 23, 111-114.  
  7988575 A.J.King, and P.C.van der Vliet (1994).
A precursor terminal protein-trinucleotide intermediate during initiation of adenovirus DNA replication: regeneration of molecular ends in vitro by a jumping back mechanism.
  EMBO J, 13, 5786-5792.  
7514786 D.B.Olsen, S.S.Carroll, J.C.Culberson, J.A.Shafer, and L.C.Kuo (1994).
Effect of template secondary structure on the inhibition of HIV-1 reverse transcriptase by a pyridinone non-nucleoside inhibitor.
  Nucleic Acids Res, 22, 1437-1443.  
7506421 D.E.Shippen, E.H.Blackburn, and C.M.Price (1994).
DNA bound by the Oxytricha telomere protein is accessible to telomerase and other DNA polymerases.
  Proc Natl Acad Sci U S A, 91, 405-409.  
  8113181 E.Angov, and R.D.Camerini-Otero (1994).
The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization.
  J Bacteriol, 176, 1405-1412.  
8065939 H.Yu, J.Chao, D.Patek, R.Mujumdar, S.Mujumdar, and A.S.Waggoner (1994).
Cyanine dye dUTP analogs for enzymatic labeling of DNA probes.
  Nucleic Acids Res, 22, 3226-3232.  
  8035492 J.Gottlieb, and M.D.Challberg (1994).
Interaction of herpes simplex virus type 1 DNA polymerase and the UL42 accessory protein with a model primer template.
  J Virol, 68, 4937-4945.  
7529124 J.Jäger, S.J.Smerdon, J.Wang, D.C.Boisvert, and T.A.Steitz (1994).
Comparison of three different crystal forms shows HIV-1 reverse transcriptase displays an internal swivel motion.
  Structure, 2, 869-876.  
7938011 T.E.Carver, R.A.Hochstrasser, and D.P.Millar (1994).
Proofreading DNA: recognition of aberrant DNA termini by the Klenow fragment of DNA polymerase I.
  Proc Natl Acad Sci U S A, 91, 10670-10674.  
7816603 W.Zhu, and J.Ito (1994).
Family A and family B DNA polymerases are structurally related: evolutionary implications.
  Nucleic Acids Res, 22, 5177-5183.  
8265361 V.Derbyshire, M.Astatke, and C.M.Joyce (1993).
Re-engineering the polymerase domain of Klenow fragment and evaluation of overproduction and purification strategies.
  Nucleic Acids Res, 21, 5439-5448.  
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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