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PDBsum entry 1l3s

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protein dna_rna ligands metals links
Transferase/DNA PDB id
1l3s
Jmol
Contents
Protein chain
580 a.a. *
DNA/RNA
Ligands
SUC ×2
SO4 ×5
Metals
_MG
Waters ×560
* Residue conservation analysis
PDB id:
1l3s
Name: Transferase/DNA
Title: Crystal structure of bacillus DNA polymerase i fragment complexed to 9 base pairs of duplex DNA.
Structure: 5'-d( Gp Cp Gp Ap Tp Cp Ap Cp G)-3'. Chain: b. Engineered: yes. Other_details: primer strand. 5'- d( Gp A Cp Gp Tp Ap Cp Gp Tp Gp Ap Tp Cp Gp Cp A)-3'. Chain: c. Engineered: yes. Other_details: template strand.
Source: Synthetic: yes. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: this protein was isolated from an as yet unnamed novel strain of bacillus stearothermophilus (see ref 2).
Biol. unit: Trimer (from PQS)
Resolution:
1.70Å     R-factor:   0.197     R-free:   0.227
Authors: S.J.Johnson,J.S.Taylor,L.S.Beese
Key ref:
S.J.Johnson et al. (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. PubMed id: 12649320 DOI: 10.1073/pnas.0630532100
Date:
01-Mar-02     Release date:   25-Mar-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P52026  (DPO1_GEOSE) -  DNA polymerase I
Seq:
Struc:
 
Seq:
Struc:
876 a.a.
580 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 67 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleobase-containing compound metabolic process   3 terms 
  Biochemical function     nucleic acid binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0630532100 Proc Natl Acad Sci U S A 100:3895-3900 (2003)
PubMed id: 12649320  
 
 
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
S.J.Johnson, J.S.Taylor, L.S.Beese.
 
  ABSTRACT  
 
DNA polymerases replicate DNA by adding nucleotides to a growing primer strand while avoiding frameshift and point mutations. Here we present a series of up to six successive replication events that were obtained by extension of a primed template directly in a crystal of the thermostable Bacillus DNA polymerase I. The 6-bp extension involves a 20-A translocation of the DNA duplex, representing the largest molecular movement observed in a protein crystal. In addition, we obtained the structure of a "closed" conformation of the enzyme with a bound triphosphate juxtaposed to a template and a dideoxy-terminated primer by constructing a point mutant that destroys a crystal lattice contact stabilizing the wild-type polymerase in an "open" conformation. Together, these observations allow many of the steps involved in DNA replication to be observed in the same enzyme at near atomic detail. The successive replication events observed directly by catalysis in the crystal confirm the general reaction sequence deduced from observations obtained by using several other polymerases and further refine critical aspects of the known reaction mechanism, and also allow us to propose new features that concern the regulated transfer of the template strand between a preinsertion site and an insertion site. We propose that such regulated transfer is an important element in the prevention of frameshift mutations in high-fidelity DNA polymerases. The ability to observe processive, high-fidelity replication directly in a crystal establishes this polymerase as a powerful model system for mechanistic studies in which the structural consequences of mismatches and DNA adducts are observed.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Active site superposition of open and closed BF structures. (A) The 11-bp open binary complex (yellow) and the closed ternary complex (blue) are shown in stereo view. The largest conformational differences occur in the fingers domain, including the O helix, O1 helix, and preinsertion site. The acceptor template base (n) occupies the preinsertion site in the open conformation and the insertion site in the closed conformation. (B) A close-up view of the preinsertion site. The locations of the conserved Tyr-714 are indicated.
Figure 3.
Fig. 3. Conformational interlocks during DNA synthesis. A schematic overview of the polymerase active site (A) and atomic coordinates (B) derived from the open and closed BF structures represent a complete round of DNA synthesis. The conformational changes described here are presented in animated form in Movie 1, which is published as supporting information on the PNAS web site. The reaction cycle starts with the acceptor template base (n, red) bound at the template preinsertion site (between the O and O1 helices; green shading); Tyr-714 blocks access to the insertion site (blue shading) and stacks with the n-1 base pair at the postinsertion site (gray shading). Formation of the closed conformation involves rearrangement of the O and O1 helices, which simultaneously blocks the template preinsertion site and unblocks the insertion site. These rearrangements move the acceptor template base (n) to the insertion site, where it pairs with an incoming dNTP (green). Nucleotide incorporation occurs on formation of a cognate base pair and proper assembly of the catalytic site (orange shading). The cycle is completed with translocation of the DNA by one base pair position. The polymerase resets to the open conformation in preparation for the next round of DNA synthesis.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
21190057 J.S.Fraser, and C.J.Jackson (2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
  Cell Mol Life Sci, 68, 1829-1841.  
21321236 M.L.Gleghorn, E.K.Davydova, R.Basu, L.B.Rothman-Denes, and K.S.Murakami (2011).
X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.
  Proc Natl Acad Sci U S A, 108, 3566-3571.
PDB codes: 3q0a 3q22 3q23 3q24
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
19665596 C.M.Joyce (2010).
Techniques used to study the DNA polymerase reaction pathway.
  Biochim Biophys Acta, 1804, 1032-1040.  
20371498 D.Zhi, M.Shatsky, and S.E.Brenner (2010).
Alignment-free local structural search by writhe decomposition.
  Bioinformatics, 26, 1176-1184.  
20067253 G.Stengel, M.Urban, B.W.Purse, and R.D.Kuchta (2010).
Incorporation of the fluorescent ribonucleotide analogue tCTP by T7 RNA polymerase.
  Anal Chem, 82, 1082-1089.  
20123134 J.D.Pata (2010).
Structural diversity of the Y-family DNA polymerases.
  Biochim Biophys Acta, 1804, 1124-1135.  
20152146 J.D.Pata, and J.Jaeger (2010).
Molecular machines and targeted molecular dynamics: DNA in motion.
  Structure, 18, 4-6.  
20078153 J.Hafner, and W.Zheng (2010).
Optimal modeling of atomic fluctuations in protein crystal structures for weak crystal contact interactions.
  J Chem Phys, 132, 014111.  
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.
  Proc Natl Acad Sci U S A, 107, 17980-17985.  
20111609 M.Yokoyama, H.Mori, and H.Sato (2010).
Allosteric regulation of HIV-1 reverse transcriptase by ATP for nucleotide selection.
  PLoS One, 5, e8867.  
21148772 P.Gong, and O.B.Peersen (2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
  Proc Natl Acad Sci U S A, 107, 22505-22510.
PDB codes: 3ol6 3ol7 3ol8 3ol9 3ola 3olb
  20847947 R.G.Federley, and L.J.Romano (2010).
DNA polymerase: structural homology, conformational dynamics, and the effects of carcinogenic DNA adducts.
  J Nucleic Acids, 2010, 0.  
20162624 R.Venkatramani, and R.Radhakrishnan (2010).
Computational delineation of the catalytic step of a high-fidelity DNA polymerase.
  Protein Sci, 19, 815-825.  
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.  
20080740 Y.Santoso, C.M.Joyce, O.Potapova, L.Le Reste, J.Hohlbein, J.P.Torella, N.D.Grindley, and A.N.Kapanidis (2010).
Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
  Proc Natl Acad Sci U S A, 107, 715-720.  
20575136 Y.Santoso, J.P.Torella, and A.N.Kapanidis (2010).
Characterizing single-molecule FRET dynamics with probability distribution analysis.
  Chemphyschem, 11, 2209-2219.  
19151724 C.Castro, E.D.Smidansky, J.J.Arnold, K.R.Maksimchuk, I.Moustafa, A.Uchida, M.Götte, W.Konigsberg, and C.E.Cameron (2009).
Nucleic acid polymerases use a general acid for nucleotidyl transfer.
  Nat Struct Mol Biol, 16, 212-218.  
19859523 C.Xu, B.A.Maxwell, J.A.Brown, L.Zhang, and Z.Suo (2009).
Global conformational dynamics of a Y-family DNA polymerase during catalysis.
  PLoS Biol, 7, e1000225.  
19411253 K.Datta, N.P.Johnson, V.J.LiCata, and P.H.von Hippel (2009).
Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases.
  J Biol Chem, 284, 17180-17193.  
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.  
19338283 N.A.Wilson, R.Abu-Shumays, B.Gyarfas, H.Wang, K.R.Lieberman, M.Akeson, and W.B.Dunbar (2009).
Electronic control of DNA polymerase binding and unbinding to single DNA molecules.
  ACS Nano, 3, 995.  
19275265 N.Hurt, H.Wang, M.Akeson, and K.R.Lieberman (2009).
Specific nucleotide binding and rebinding to individual DNA polymerase complexes captured on a nanopore.
  J Am Chem Soc, 131, 3772-3778.  
19364137 P.Xu, L.Oum, Y.C.Lee, N.E.Geacintov, and S.Broyde (2009).
Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase.
  Biochemistry, 48, 4677-4690.  
18399510 J.Cramer, G.Rangam, A.Marx, and T.Restle (2008).
Varied active-site constraints in the klenow fragment of E. coli DNA polymerase I and the lesion-bypass Dbh DNA polymerase.
  Chembiochem, 9, 1243-1250.  
18369368 K.Bebenek, M.Garcia-Diaz, M.C.Foley, L.C.Pedersen, T.Schlick, and T.A.Kunkel (2008).
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.
  EMBO Rep, 9, 459-464.
PDB codes: 3c5f 3c5g
  18268843 K.K.Ng, J.J.Arnold, and C.E.Cameron (2008).
Structure-function relationships among RNA-dependent RNA polymerases.
  Curr Top Microbiol Immunol, 320, 137-156.  
19006151 M.Renders, R.Lievrouw, M.Krecmerová, A.Holý, and P.Herdewijn (2008).
Enzymatic polymerization of phosphonate nucleosides.
  Chembiochem, 9, 2883-2888.  
18058909 R.Venkatramani, and R.Radhakrishnan (2008).
Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermophilus.
  Proteins, 71, 1360-1372.  
18352668 R.Venkatramani, and R.Radhakrishnan (2008).
Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase.
  Phys Rev Lett, 100, 088102.  
18407502 S.Broyde, L.Wang, O.Rechkoblit, N.E.Geacintov, and D.J.Patel (2008).
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
  Trends Biochem Sci, 33, 209-219.  
17223130 A.A.Thompson, R.A.Albertini, and O.B.Peersen (2007).
Stabilization of poliovirus polymerase by NTP binding and fingers-thumb interactions.
  J Mol Biol, 366, 1459-1474.
PDB codes: 2ily 2ilz 2im0 2im1 2im2 2im3
17611604 A.J.Berman, S.Kamtekar, J.L.Goodman, J.M.Lázaro, M.de Vega, L.Blanco, M.Salas, and T.A.Steitz (2007).
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.
  EMBO J, 26, 3494-3505.
PDB codes: 2py5 2pyj 2pyl 2pzs
17517631 C.Ferrer-Orta, A.Arias, R.Pérez-Luque, C.Escarmís, E.Domingo, and N.Verdaguer (2007).
Sequential structures provide insights into the fidelity of RNA replication.
  Proc Natl Acad Sci U S A, 104, 9463-9468.
PDB codes: 2e9r 2e9t 2e9z 2ec0
17785419 C.H.Tsai, J.Chen, and J.W.Szostak (2007).
Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template.
  Proc Natl Acad Sci U S A, 104, 14598-14603.  
17640918 G.Luo, M.Wang, W.H.Konigsberg, and X.S.Xie (2007).
Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase.
  Proc Natl Acad Sci U S A, 104, 12610-12615.  
17317572 N.Z.Rudinger, R.Kranaster, and A.Marx (2007).
Hydrophobic amino acid and single-atom substitutions increase DNA polymerase selectivity.
  Chem Biol, 14, 185-194.  
17400246 P.R.Meyer, W.Rutvisuttinunt, S.E.Matsuura, A.G.So, and W.A.Scott (2007).
Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer-template controlled by binding deoxynucleoside triphosphates or foscarnet.
  J Mol Biol, 369, 41-54.  
17576677 P.Xu, L.Oum, L.S.Beese, N.E.Geacintov, and S.Broyde (2007).
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
  Nucleic Acids Res, 35, 4275-4288.  
18654412 S.Benner, R.J.Chen, N.A.Wilson, R.Abu-Shumays, N.Hurt, K.R.Lieberman, D.W.Deamer, W.B.Dunbar, and M.Akeson (2007).
Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore.
  Nat Nanotechnol, 2, 718-724.  
17217958 S.Meneni, F.Liang, and B.P.Cho (2007).
Examination of the long-range effects of aminofluorene-induced conformational heterogeneity and its relevance to the mechanism of translesional DNA synthesis.
  J Mol Biol, 366, 1387-1400.  
17052459 E.Kashkina, M.Anikin, F.Brueckner, R.T.Pomerantz, W.T.McAllister, P.Cramer, and D.Temiakov (2006).
Template misalignment in multisubunit RNA polymerases and transcription fidelity.
  Mol Cell, 24, 257-266.  
17179038 J.J.Warren, L.J.Forsberg, and L.S.Beese (2006).
The structural basis for the mutagenicity of O(6)-methyl-guanine lesions.
  Proc Natl Acad Sci U S A, 103, 19701-19706.
PDB codes: 2hhq 2hhs 2hht 2hhu 2hhv 2hhw 2hhx 2hvh 2hvi 2hw3
16707660 L.V.Gening, S.A.Klincheva, A.Reshetnjak, A.P.Grollman, and H.Miller (2006).
RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa.
  Nucleic Acids Res, 34, 2579-2586.  
16439207 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, and T.A.Kunkel (2006).
Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase.
  Cell, 124, 331-342.
PDB codes: 2bcq 2bcr 2bcs 2bcu 2bcv
16545956 M.Garcia-Diaz, and T.A.Kunkel (2006).
Mechanism of a genetic glissando: structural biology of indel mutations.
  Trends Biochem Sci, 31, 206-214.  
16411765 O.Potapova, C.Chan, A.M.DeLucia, S.A.Helquist, E.T.Kool, N.D.Grindley, and C.M.Joyce (2006).
DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics.
  Biochemistry, 45, 890-898.  
16379496 O.Rechkoblit, L.Malinina, Y.Cheng, V.Kuryavyi, S.Broyde, N.E.Geacintov, and D.J.Patel (2006).
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.
  PLoS Biol, 4, e11.
PDB codes: 2asd 2asj 2asl 2atl 2au0
17052458 R.T.Pomerantz, D.Temiakov, M.Anikin, D.G.Vassylyev, and W.T.McAllister (2006).
A mechanism of nucleotide misincorporation during transcription due to template-strand misalignment.
  Mol Cell, 24, 245-255.  
16838276 S.Vichier-Guerre, S.Ferris, N.Auberger, K.Mahiddine, and J.L.Jestin (2006).
A population of thermostable reverse transcriptases evolved from Thermus aquaticus DNA polymerase I by phage display.
  Angew Chem Int Ed Engl, 45, 6133-6137.  
16900098 T.A.Steitz (2006).
Visualizing polynucleotide polymerase machines at work.
  EMBO J, 25, 3458-3468.  
16615916 V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, and S.H.Wilson (2006).
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
  Structure, 14, 757-766.
PDB codes: 2fmp 2fmq 2fms
16129597 D.Bourgeois, and A.Royant (2005).
Advances in kinetic protein crystallography.
  Curr Opin Struct Biol, 15, 538-547.  
15863620 J.Florián, M.F.Goodman, and A.Warshel (2005).
Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases.
  Proc Natl Acad Sci U S A, 102, 6819-6824.  
15608652 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, and L.C.Pedersen (2005).
A closed conformation for the Pol lambda catalytic cycle.
  Nat Struct Mol Biol, 12, 97-98.
PDB codes: 1xsl 1xsn 1xsp
16140780 R.Chen, M.Yokoyama, H.Sato, C.Reilly, and L.M.Mansky (2005).
Human immunodeficiency virus mutagenesis during antiviral therapy: impact of drug-resistant reverse transcriptase and nucleoside and nonnucleoside reverse transcriptase inhibitors on human immunodeficiency virus type 1 mutation frequencies.
  J Virol, 79, 12045-12057.  
16084394 V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, and S.H.Wilson (2005).
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
  Structure, 13, 1225-1233.
PDB codes: 1zjm 1zjn
16094452 Z.F.Burton, M.Feig, X.Q.Gong, C.Zhang, Y.A.Nedialkov, and Y.Xiong (2005).
NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.
  Biochem Cell Biol, 83, 486-496.  
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
15016373 D.Temiakov, V.Patlan, M.Anikin, W.T.McAllister, S.Yokoyama, and D.G.Vassylyev (2004).
Structural basis for substrate selection by t7 RNA polymerase.
  Cell, 116, 381-391.
PDB code: 1s0v
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.  
15322558 G.W.Hsu, M.Ober, T.Carell, and L.S.Beese (2004).
Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase.
  Nature, 431, 217-221.
PDB codes: 1u45 1u47 1u48 1u49 1u4b
15507687 K.Arora, and T.Schlick (2004).
In silico evidence for DNA polymerase-beta's substrate-induced conformational change.
  Biophys J, 87, 3088-3099.  
15296738 K.S.Gajiwala, and C.Pinko (2004).
Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal.
  Structure, 12, 1449-1459.
PDB codes: 1ta8 1tae
15297882 L.G.Brieba, B.F.Eichman, R.J.Kokoska, S.Doublié, T.A.Kunkel, and T.Ellenberger (2004).
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
  EMBO J, 23, 3452-3461.
PDB codes: 1t8e 1tk0 1tk5 1tk8 1tkd
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
15093841 M.Karplus, and Y.Q.Gao (2004).
Biomolecular motors: the F1-ATPase paradigm.
  Curr Opin Struct Biol, 14, 250-259.  
15515078 M.Strerath, J.Gaster, and A.Marx (2004).
Recognition of remote mismatches by DNA polymerases.
  Chembiochem, 5, 1585-1588.  
15326591 R.L.Crowther, D.P.Remeta, C.A.Minetti, D.Das, S.P.Montano, and M.M.Georgiadis (2004).
Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase.
  Proteins, 57, 15-26.
PDB code: 1nnd
15016367 R.Landick (2004).
Active-site dynamics in RNA polymerases.
  Cell, 116, 351-353.  
15069184 R.Radhakrishnan, and T.Schlick (2004).
Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.
  Proc Natl Acad Sci U S A, 101, 5970-5975.  
15528277 S.Dutta, Y.Li, D.Johnson, L.Dzantiev, C.C.Richardson, L.J.Romano, and T.Ellenberger (2004).
Crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
  Proc Natl Acad Sci U S A, 101, 16186-16191.
PDB codes: 1x9m 1x9s 1x9w
15470496 S.Fujii, and R.P.Fuchs (2004).
Defining the position of the switches between replicative and bypass DNA polymerases.
  EMBO J, 23, 4342-4352.  
15035983 S.J.Johnson, and L.S.Beese (2004).
Structures of mismatch replication errors observed in a DNA polymerase.
  Cell, 116, 803-816.
PDB codes: 1njw 1njx 1njy 1njz 1nk0 1nk4 1nk5 1nk6 1nk7 1nk8 1nk9 1nkb 1nkc 1nke
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.  
15102443 T.A.Steitz (2004).
The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase.
  Curr Opin Struct Biol, 14, 4-9.  
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
12853630 A.M.DeLucia, N.D.Grindley, and C.M.Joyce (2003).
An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides.
  Nucleic Acids Res, 31, 4129-4137.  
12930945 L.Tsujikawa, M.Weinfield, and L.J.Reha-Krantz (2003).
Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I.
  Nucleic Acids Res, 31, 4965-4972.  
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.  
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.