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PDBsum entry 3ktq
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Transferase/DNA
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PDB id
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3ktq
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.7.7.7
- DNA-directed Dna polymerase.
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Reaction:
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DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
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DNA(n)
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+
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2'-deoxyribonucleoside 5'-triphosphate
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=
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DNA(n+1)
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+
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diphosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Embo J
17:7514-7525
(1998)
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PubMed id:
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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.
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Y.Li,
S.Korolev,
G.Waksman.
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ABSTRACT
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The crystal structures of two ternary complexes of the large fragment of Thermus
aquaticus DNA polymerase I (Klentaq1) with a primer/template DNA and
dideoxycytidine triphosphate, and that of a binary complex of the same enzyme
with a primer/template DNA, were determined to a resolution of 2.3, 2.3 and 2.5
A, respectively. One ternary complex structure differs markedly from the two
other structures by a large reorientation of the tip of the fingers domain. This
structure, designated 'closed', represents the ternary polymerase complex caught
in the act of incorporating a nucleotide. In the two other structures, the tip
of the fingers domain is rotated outward by 46 degrees ('open') in an
orientation similar to that of the apo form of Klentaq1. These structures
provide the first direct evidence in DNA polymerase I enzymes of a large
conformational change responsible for assembling an active ternary complex.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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Nat Struct Mol Biol,
19,
253-259.
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PDB codes:
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T.Nakamura,
Y.Zhao,
Y.Yamagata,
Y.J.Hua,
and
W.Yang
(2012).
Watching DNA polymerase η make a phosphodiester bond.
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Nature,
487,
196-201.
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PDB codes:
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J.P.Gill,
J.Wang,
and
D.P.Millar
(2011).
DNA polymerase activity at the single-molecule level.
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Biochem Soc Trans,
39,
595-599.
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R.Vasquez-Del Carpio,
T.D.Silverstein,
S.Lone,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2011).
Role of human DNA polymerase κ in extension opposite from a cis-syn thymine dimer.
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J Mol Biol,
408,
252-261.
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PDB code:
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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.
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Structure,
18,
83-93.
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PDB codes:
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A.K.Upadhyay,
T.T.Talele,
and
V.N.Pandey
(2010).
Impact of template overhang-binding region of HIV-1 RT on the binding and orientation of the duplex region of the template-primer.
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Mol Cell Biochem,
338,
19-33.
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C.M.Bailey,
and
K.S.Anderson
(2010).
A mechanistic view of human mitochondrial DNA polymerase gamma: providing insight into drug toxicity and mitochondrial disease.
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Biochim Biophys Acta,
1804,
1213-1222.
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F.Chen,
E.A.Gaucher,
N.A.Leal,
D.Hutter,
S.A.Havemann,
S.Govindarajan,
E.A.Ortlund,
and
S.A.Benner
(2010).
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection.
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Proc Natl Acad Sci U S A,
107,
1948-1953.
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G.Stengel,
M.Urban,
B.W.Purse,
and
R.D.Kuchta
(2010).
Incorporation of the fluorescent ribonucleotide analogue tCTP by T7 RNA polymerase.
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Anal Chem,
82,
1082-1089.
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G.Zhao,
and
Y.Guan
(2010).
Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions.
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Acta Biochim Biophys Sin (Shanghai),
42,
722-728.
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H.Zhang,
and
F.P.Guengerich
(2010).
Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W.
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J Mol Biol,
395,
1007-1018.
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J.D.Pata
(2010).
Structural diversity of the Y-family DNA polymerases.
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Biochim Biophys Acta,
1804,
1124-1135.
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J.D.Pata,
and
J.Jaeger
(2010).
Molecular machines and targeted molecular dynamics: DNA in motion.
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Structure,
18,
4-6.
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J.G.Song,
E.J.Kil,
S.S.Cho,
I.H.Kim,
and
S.T.Kwon
(2010).
An amino acid residue in the middle of the fingers subdomain is involved in Neq DNA polymerase processivity: enhanced processivity of engineered Neq DNA polymerase and its PCR application.
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Protein Eng Des Sel,
23,
835-842.
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K.A.Johnson
(2010).
The kinetic and chemical mechanism of high-fidelity DNA polymerases.
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Biochim Biophys Acta,
1804,
1041-1048.
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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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Proc Natl Acad Sci U S A,
107,
17980-17985.
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K.Singh,
B.Marchand,
K.A.Kirby,
E.Michailidis,
and
S.G.Sarafianos
(2010).
Structural Aspects of Drug Resistance and Inhibition of HIV-1 Reverse Transcriptase.
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Viruses,
2,
606-638.
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P.Gong,
and
O.B.Peersen
(2010).
Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase.
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Proc Natl Acad Sci U S A,
107,
22505-22510.
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PDB codes:
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R.G.Federley,
and
L.J.Romano
(2010).
DNA polymerase: structural homology, conformational dynamics, and the effects of carcinogenic DNA adducts.
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J Nucleic Acids,
2010,
0.
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R.Kranaster,
and
A.Marx
(2010).
Engineered DNA polymerases in biotechnology.
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Chembiochem,
11,
2077-2084.
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R.Kranaster,
M.Drum,
N.Engel,
M.Weidmann,
F.T.Hufert,
and
A.Marx
(2010).
One-step RNA pathogen detection with reverse transcriptase activity of a mutated thermostable Thermus aquaticus DNA polymerase.
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Biotechnol J,
5,
224-231.
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S.K.Perumal,
H.Yue,
Z.Hu,
M.M.Spiering,
and
S.J.Benkovic
(2010).
Single-molecule studies of DNA replisome function.
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Biochim Biophys Acta,
1804,
1094-1112.
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S.Obeid,
A.Baccaro,
W.Welte,
K.Diederichs,
and
A.Marx
(2010).
Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase.
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Proc Natl Acad Sci U S A,
107,
21327-21331.
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PDB codes:
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S.Obeid,
N.Blatter,
R.Kranaster,
A.Schnur,
K.Diederichs,
W.Welte,
and
A.Marx
(2010).
Replication through an abasic DNA lesion: structural basis for adenine selectivity.
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EMBO J,
29,
1738-1747.
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PDB codes:
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T.D.Silverstein,
R.E.Johnson,
R.Jain,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2010).
Structural basis for the suppression of skin cancers by DNA polymerase eta.
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Nature,
465,
1039-1043.
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PDB codes:
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T.D.Silverstein,
R.Jain,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2010).
Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase η.
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Structure,
18,
1463-1470.
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PDB codes:
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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.
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Proc Natl Acad Sci U S A,
107,
715-720.
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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.
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PLoS Biol,
7,
e1000225.
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D.C.Tahmassebi,
and
D.P.Millar
(2009).
Fluorophore-quencher pair for monitoring protein motion.
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Biochem Biophys Res Commun,
380,
277-280.
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D.Loakes,
J.Gallego,
V.B.Pinheiro,
E.T.Kool,
and
P.Holliger
(2009).
Evolving a polymerase for hydrophobic base analogues.
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J Am Chem Soc,
131,
14827-14837.
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I.A.Pyshnaya,
O.A.Vinogradova,
M.R.Kabilov,
E.M.Ivanova,
and
D.V.Pyshnyi
(2009).
Bridged oligonucleotides as molecular probes for investigation of enzyme-substrate interaction and allele-specific analysis of DNA.
|
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Biochemistry (Mosc),
74,
1009-1020.
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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.
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Nucleic Acids Res,
37,
193-203.
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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.
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J Biol Chem,
284,
17180-17193.
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M.B.Kermekchiev,
L.I.Kirilova,
E.E.Vail,
and
W.M.Barnes
(2009).
Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples.
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Nucleic Acids Res,
37,
e40.
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M.K.Swan,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2009).
Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta.
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Nat Struct Mol Biol,
16,
979-986.
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PDB code:
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M.K.Swan,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2009).
Structure of the human Rev1-DNA-dNTP ternary complex.
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J Mol Biol,
390,
699-709.
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PDB code:
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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.
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ACS Nano,
3,
995.
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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.
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J Am Chem Soc,
131,
3772-3778.
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P.Sandin,
G.Stengel,
T.Ljungdahl,
K.Börjesson,
B.Macao,
and
L.M.Wilhelmsson
(2009).
Highly efficient incorporation of the fluorescent nucleotide analogs tC and tCO by Klenow fragment.
|
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Nucleic Acids Res,
37,
3924-3933.
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R.Vasquez-Del Carpio,
T.D.Silverstein,
S.Lone,
M.K.Swan,
J.R.Choudhury,
R.E.Johnson,
S.Prakash,
L.Prakash,
and
A.K.Aggarwal
(2009).
Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion.
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PLoS One,
4,
e5766.
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PDB codes:
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S.Balasubramanian,
F.Xu,
and
W.K.Olson
(2009).
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
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Biophys J,
96,
2245-2260.
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S.Ogata,
M.Takahashi,
N.Minakawa,
and
A.Matsuda
(2009).
Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo- ) DNA polymerase.
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Nucleic Acids Res,
37,
5602-5609.
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T.D.Christian,
L.J.Romano,
and
D.Rueda
(2009).
Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution.
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Proc Natl Acad Sci U S A,
106,
21109-21114.
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T.E.Exner
(2009).
Insights into the high fidelity of a DNA polymerase I mutant.
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J Mol Model,
15,
1271-1280.
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V.Vooradi,
and
L.J.Romano
(2009).
Effect of N-2-acetylaminofluorene and 2-aminofluorene adducts on DNA binding and synthesis by yeast DNA polymerase eta.
|
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Biochemistry,
48,
4209-4216.
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W.A.Beard,
D.D.Shock,
V.K.Batra,
L.C.Pedersen,
and
S.H.Wilson
(2009).
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
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J Biol Chem,
284,
31680-31689.
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PDB codes:
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Y.C.Tsai,
Z.Jin,
and
K.A.Johnson
(2009).
Site-specific labeling of T7 DNA polymerase with a conformationally sensitive fluorophore and its use in detecting single-nucleotide polymorphisms.
|
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Anal Biochem,
384,
136-144.
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A.M.Leconte,
G.T.Hwang,
S.Matsuda,
P.Capek,
Y.Hari,
and
F.E.Romesberg
(2008).
Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet.
|
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J Am Chem Soc,
130,
2336-2343.
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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.
|
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Biochemistry,
47,
8527-8537.
|
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B.A.Sampoli Benítez,
K.Arora,
L.Balistreri,
and
T.Schlick
(2008).
Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation.
|
| |
J Mol Biol,
384,
1086-1097.
|
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D.F.Zamyatkin,
F.Parra,
J.M.Alonso,
D.A.Harki,
B.R.Peterson,
P.Grochulski,
and
K.K.Ng
(2008).
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.
|
| |
J Biol Chem,
283,
7705-7712.
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PDB codes:
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D.T.Nair,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
A.K.Aggarwal
(2008).
Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase.
|
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Structure,
16,
239-245.
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PDB code:
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G.T.Hwang,
and
F.E.Romesberg
(2008).
Unnatural substrate repertoire of A, B, and X family DNA polymerases.
|
| |
J Am Chem Soc,
130,
14872-14882.
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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.
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J.W.Beckman,
Q.Wang,
and
F.P.Guengerich
(2008).
Kinetic Analysis of Correct Nucleotide Insertion by a Y-family DNA Polymerase Reveals Conformational Changes Both Prior to and following Phosphodiester Bond Formation as Detected by Tryptophan Fluorescence.
|
| |
J Biol Chem,
283,
36711-36723.
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K.H.Tang,
and
M.D.Tsai
(2008).
Structure and function of 2:1 DNA polymerase.DNA complexes.
|
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J Cell Physiol,
216,
315-320.
|
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K.Li,
A.Brownley,
T.B.Stockwell,
K.Beeson,
T.C.McIntosh,
D.Busam,
S.Ferriera,
S.Murphy,
and
S.Levy
(2008).
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing.
|
| |
BMC Bioinformatics,
9,
191.
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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.
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| |
J Biol Chem,
283,
17979-17990.
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P.Thomen,
P.J.Lopez,
U.Bockelmann,
J.Guillerez,
M.Dreyfus,
and
F.Heslot
(2008).
T7 RNA polymerase studied by force measurements varying cofactor concentration.
|
| |
Biophys J,
95,
2423-2433.
|
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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.
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|
|
PDB code:
|
|
|
|
|
|
|
|
S.Chinnaswamy,
I.Yarbrough,
S.Palaninathan,
C.T.Kumar,
V.Vijayaraghavan,
B.Demeler,
S.M.Lemon,
J.C.Sacchettini,
and
C.C.Kao
(2008).
A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase.
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J Biol Chem,
283,
20535-20546.
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S.Sabbioneda,
A.M.Gourdin,
C.M.Green,
A.Zotter,
G.Giglia-Mari,
A.Houtsmuller,
W.Vermeulen,
and
A.R.Lehmann
(2008).
Effect of proliferating cell nuclear antigen ubiquitination and chromatin structure on the dynamic properties of the Y-family DNA polymerases.
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| |
Mol Biol Cell,
19,
5193-5202.
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V.K.Batra,
W.A.Beard,
D.D.Shock,
L.C.Pedersen,
and
S.H.Wilson
(2008).
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
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| |
Mol Cell,
30,
315-324.
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|
|
PDB codes:
|
|
|
|
|
|
|
|
W.J.Allen,
P.J.Rothwell,
and
G.Waksman
(2008).
An intramolecular FRET system monitors fingers subdomain opening in Klentaq1.
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Protein Sci,
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401-408.
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W.Rutvisuttinunt,
P.R.Meyer,
and
W.A.Scott
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Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer-template.
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PLoS ONE,
3,
e3561.
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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.
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| |
EMBO J,
26,
3494-3505.
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PDB codes:
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A.Jacewicz,
K.Makiela,
A.Kierzek,
J.W.Drake,
and
A.Bebenek
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The roles of Tyr391 and Tyr619 in RB69 DNA polymerase replication fidelity.
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J Mol Biol,
368,
18-29.
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C.Castro,
E.Smidansky,
K.R.Maksimchuk,
J.J.Arnold,
V.S.Korneeva,
M.Götte,
W.Konigsberg,
and
C.E.Cameron
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Two proton transfers in the transition state for nucleotidyl transfer catalyzed by RNA- and DNA-dependent RNA and DNA polymerases.
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Proc Natl Acad Sci U S A,
104,
4267-4272.
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E.Loh,
J.Choe,
and
L.A.Loeb
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Highly tolerated amino acid substitutions increase the fidelity of Escherichia coli DNA polymerase I.
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J Biol Chem,
282,
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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.
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Proc Natl Acad Sci U S A,
104,
12610-12615.
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H.Kirsten,
D.Teupser,
J.Weissfuss,
G.Wolfram,
F.Emmrich,
and
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Robustness of single-base extension against mismatches at the site of primer attachment in a clinical assay.
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J Mol Med,
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361-369.
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H.Zhang,
W.Cao,
E.Zakharova,
W.Konigsberg,
and
E.M.De La Cruz
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Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates.
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Nucleic Acids Res,
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I.Bougie,
and
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Characterization of the RNA binding energetics of the Candida albicans poly(A) polymerase.
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Yeast,
24,
431-446.
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K.Singh,
A.Srivastava,
S.S.Patel,
and
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Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA.
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J Biol Chem,
282,
10594-10604.
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M.E.Arana,
K.Takata,
M.Garcia-Diaz,
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and
T.A.Kunkel
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A unique error signature for human DNA polymerase nu.
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DNA Repair (Amst),
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213-223.
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M.Strerath,
C.Gloeckner,
D.Liu,
A.Schnur,
and
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Directed DNA polymerase evolution: effects of mutations in motif C on the mismatch-extension selectivity of thermus aquaticus DNA polymerase.
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| |
Chembiochem,
8,
395-401.
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M.de Vega,
and
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A highly conserved Tyrosine residue of family B DNA polymerases contributes to dictate translesion synthesis past 8-oxo-7,8-dihydro-2'-deoxyguanosine.
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Nucleic Acids Res,
35,
5096-5107.
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N.Z.Rudinger,
R.Kranaster,
and
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Hydrophobic amino acid and single-atom substitutions increase DNA polymerase selectivity.
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| |
Chem Biol,
14,
185-194.
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O.Koroleva,
N.Makharashvili,
C.T.Courcelle,
J.Courcelle,
and
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Structural conservation of RecF and Rad50: implications for DNA recognition and RecF function.
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| |
EMBO J,
26,
867-877.
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|
|
PDB code:
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|
|
|
|
|
|
|
P.J.Rothwell,
and
G.Waksman
(2007).
A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1.
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J Biol Chem,
282,
28884-28892.
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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.
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J Mol Biol,
369,
41-54.
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P.Xu,
L.Oum,
L.S.Beese,
N.E.Geacintov,
and
S.Broyde
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Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
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Nucleic Acids Res,
35,
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R.A.Perlow-Poehnelt,
I.Likhterov,
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D.A.Scicchitano,
N.E.Geacintov,
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Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase.
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J Biol Chem,
282,
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R.Takeuchi,
S.Kimura,
A.Saotome,
and
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Biochemical properties of a plastidial DNA polymerase of rice.
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Plant Mol Biol,
64,
601-611.
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S.Benner,
R.J.Chen,
N.A.Wilson,
R.Abu-Shumays,
N.Hurt,
K.R.Lieberman,
D.W.Deamer,
W.B.Dunbar,
and
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Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore.
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Nat Nanotechnol,
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718-724.
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S.Lone,
S.A.Townson,
S.N.Uljon,
R.E.Johnson,
A.Brahma,
D.T.Nair,
S.Prakash,
L.Prakash,
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Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass.
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Mol Cell,
25,
601-614.
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S.Melissis,
N.E.Labrou,
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One-step purification of Taq DNA polymerase using nucleotide-mimetic affinity chromatography.
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Biotechnol J,
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T.L.Yap,
T.Xu,
Y.L.Chen,
H.Malet,
M.P.Egloff,
B.Canard,
S.G.Vasudevan,
and
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Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution.
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| |
J Virol,
81,
4753-4765.
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PDB codes:
|
|
|
|
|
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|
|
Y.Wang,
S.Reddy,
W.A.Beard,
S.H.Wilson,
and
T.Schlick
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Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.
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Biophys J,
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A.M.DeLucia,
S.Chaudhuri,
O.Potapova,
N.D.Grindley,
and
C.M.Joyce
(2006).
The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases.
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| |
J Biol Chem,
281,
27286-27291.
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B.A.Sampoli Benítez,
K.Arora,
and
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In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism.
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Biophys J,
90,
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C.T.Ranjith-Kumar,
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Recombinant viral RdRps can initiate RNA synthesis from circular templates.
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| |
RNA,
12,
303-312.
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K.Datta,
A.J.Wowor,
A.J.Richard,
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V.J.LiCata
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Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA.
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Biophys J,
90,
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K.Takata,
T.Shimizu,
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Human DNA polymerase N (POLN) is a low fidelity enzyme capable of error-free bypass of 5S-thymine glycol.
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J Biol Chem,
281,
23445-23455.
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L.Fan,
A.S.Arvai,
P.K.Cooper,
S.Iwai,
F.Hanaoka,
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Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair.
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| |
Mol Cell,
22,
27-37.
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PDB codes:
|
|
|
|
|
|
|
|
M.H.Lamers,
R.E.Georgescu,
S.G.Lee,
M.O'Donnell,
and
J.Kuriyan
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Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.
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| |
Cell,
126,
881-892.
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PDB codes:
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|
|
|
|
|
|
|
M.Olejniczak,
and
W.J.Krzyzosiak
(2006).
Genotyping of simple sequence repeats--factors implicated in shadow band generation revisited.
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Electrophoresis,
27,
3724-3734.
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O.Potapova,
C.Chan,
A.M.DeLucia,
S.A.Helquist,
E.T.Kool,
N.D.Grindley,
and
C.M.Joyce
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DNA polymerase catalysis in the absence of Watson-Crick hydrogen bonds: analysis by single-turnover kinetics.
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| |
Biochemistry,
45,
890-898.
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P.Pérez-Arnaiz,
J.M.Lázaro,
M.Salas,
and
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(2006).
Involvement of phi29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication.
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Nucleic Acids Res,
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R.Radhakrishnan,
and
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Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta.
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Biochem Biophys Res Commun,
350,
521-529.
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S.F.Holmes,
T.J.Santangelo,
C.K.Cunningham,
J.W.Roberts,
and
D.A.Erie
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Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity.
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J Biol Chem,
281,
18677-18683.
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S.Matsuda,
A.A.Henry,
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Optimization of unnatural base pair packing for polymerase recognition.
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J Am Chem Soc,
128,
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S.Vichier-Guerre,
S.Ferris,
N.Auberger,
K.Mahiddine,
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A population of thermostable reverse transcriptases evolved from Thermus aquaticus DNA polymerase I by phage display.
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Angew Chem Int Ed Engl,
45,
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T.A.Steitz
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Visualizing polynucleotide polymerase machines at work.
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EMBO J,
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T.W.Kim,
L.G.Brieba,
T.Ellenberger,
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Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs.
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J Biol Chem,
281,
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V.K.Batra,
W.A.Beard,
D.D.Shock,
J.M.Krahn,
L.C.Pedersen,
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Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
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Structure,
14,
757-766.
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PDB codes:
|
|
|
|
|
|
|
|
V.S.Anand,
and
S.S.Patel
(2006).
Transient state kinetics of transcription elongation by T7 RNA polymerase.
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J Biol Chem,
281,
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W.Zheng,
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Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.
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Proc Natl Acad Sci U S A,
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A.M.Leconte,
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Polymerase evolution: efforts toward expansion of the genetic code.
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J Am Chem Soc,
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A.Vaisman,
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Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.
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EMBO J,
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PDB codes:
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|
D.T.Nair,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
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(2005).
Rev1 employs a novel mechanism of DNA synthesis using a protein template.
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| |
Science,
309,
2219-2222.
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PDB code:
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|
|
|
|
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|
D.T.Nair,
R.E.Johnson,
L.Prakash,
S.Prakash,
and
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Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair.
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Structure,
13,
1569-1577.
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PDB code:
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G.Stengel,
and
W.Knoll
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Surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions.
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Nucleic Acids Res,
33,
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I.Rodríguez,
J.M.Lázaro,
L.Blanco,
S.Kamtekar,
A.J.Berman,
J.Wang,
T.A.Steitz,
M.Salas,
and
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(2005).
A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity.
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Proc Natl Acad Sci U S A,
102,
6407-6412.
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J.D.Ahle,
S.Barr,
A.M.Chin,
and
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Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases.
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Nucleic Acids Res,
33,
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J.Deval,
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J.Boretto,
C.Guerreiro,
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Mechanistic insights into the suppression of drug resistance by human immunodeficiency virus type 1 reverse transcriptase using alpha-boranophosphate nucleoside analogs.
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J Biol Chem,
280,
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J.Florián,
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Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases.
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Proc Natl Acad Sci U S A,
102,
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J.K.Ichida,
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K.Zou,
L.W.McLaughlin,
and
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High fidelity TNA synthesis by Therminator polymerase.
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Nucleic Acids Res,
33,
5219-5225.
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M.Garcia-Diaz,
K.Bebenek,
J.M.Krahn,
T.A.Kunkel,
and
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A closed conformation for the Pol lambda catalytic cycle.
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Nat Struct Mol Biol,
12,
97-98.
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PDB codes:
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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.
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Mol Cell,
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345-355.
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R.E.Johnson,
L.Prakash,
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Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota.
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Proc Natl Acad Sci U S A,
102,
10466-10471.
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R.E.Johnson,
L.Prakash,
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Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase eta.
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Proc Natl Acad Sci U S A,
102,
12359-12364.
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S.Prakash,
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Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
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Annu Rev Biochem,
74,
317-353.
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T.Nishino,
K.Komori,
D.Tsuchiya,
Y.Ishino,
and
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Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.
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Structure,
13,
143-153.
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PDB code:
|
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|
|
|
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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.
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Structure,
13,
1225-1233.
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PDB codes:
|
|
|
|
|
|
|
|
V.Sosunov,
S.Zorov,
E.Sosunova,
A.Nikolaev,
I.Zakeyeva,
I.Bass,
A.Goldfarb,
V.Nikiforov,
K.Severinov,
and
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The involvement of the aspartate triad of the active center in all catalytic activities of multisubunit RNA polymerase.
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Nucleic Acids Res,
33,
4202-4211.
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W.T.Wolfle,
M.T.Washington,
E.T.Kool,
T.E.Spratt,
S.A.Helquist,
L.Prakash,
and
S.Prakash
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Evidence for a Watson-Crick hydrogen bonding requirement in DNA synthesis by human DNA polymerase kappa.
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Mol Cell Biol,
25,
7137-7143.
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W.Zheng,
B.R.Brooks,
S.Doniach,
and
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Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.
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| |
Structure,
13,
565-577.
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Z.Bu,
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D.T.Nair,
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Nature,
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PDB code:
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D.Temiakov,
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Cell,
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PDB code:
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D.W.Gohara,
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Cell,
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S.Tuske,
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Nat Struct Mol Biol,
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PDB codes:
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Nat Struct Mol Biol,
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PDB codes:
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D.Shinde,
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PDB codes:
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Proc Natl Acad Sci U S A,
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PDB codes:
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PDB codes:
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PDB codes:
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Biochemistry,
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EMBO J,
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PDB code:
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Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases.
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Biochemistry,
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Varied Molecular Interactions at the Active Sites of Several DNA Polymerases: Nonpolar Nucleoside Isosteres as Probes.
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J Am Chem Soc,
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Misincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation.
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Biochemistry,
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Poliovirus RNA-dependent RNA polymerase (3D(pol)). Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub).
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Proc Natl Acad Sci U S A,
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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.
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Biochemistry,
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Biochemistry,
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PDB code:
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G.Martin,
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PDB code:
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Two-metal-Ion catalysis in adenylyl cyclase.
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PDB codes:
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M.A.Walsh,
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MAD data collection - current trends.
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Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove.
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Proc Natl Acad Sci U S A,
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PDB codes:
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Y.Zhao,
D.Jeruzalmi,
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Crystal structure of an archaebacterial DNA polymerase.
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Structure,
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PDB codes:
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|
|
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|
|
|
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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|
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