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PDBsum entry 1tau
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Transferase/DNA
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PDB id
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1tau
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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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Nature
382:278-281
(1996)
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PubMed id:
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Structure of Taq polymerase with DNA at the polymerase active site.
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S.H.Eom,
J.Wang,
T.A.Steitz.
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ABSTRACT
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The DNA polymerase from Thermus aquaticus (Taq polymerase) is homologous to
Escherichia coli DNA polymerase I (Pol I) and likewise has domains responsible
for DNA polymerase and 5' nuclease activities. The structures to the polymerase
domains of Taq polymerase and of the Klenow fragment (KF) of Pol I are almost
identical, whereas the structure of a vestigial editing 3'-5' exonuclease domain
of Taq polymerase that lies between the other two domains is dramatically
altered, resulting in the absence of this activity in the thermostable enzyme.
The structures have been solved for editing complexes between KF and
single-stranded DNA and for duplex DNA with a 3' overhanging single strand, but
not for a complex containing duplex DNA at the polymerase active-site. Here we
present the co-crystal structure of Taq polymerase with a blunt-ended duplex DNA
bound to the polymerase active-site cleft; the DNA neither bends nor goes
through the large polymerase cleft, and the structural form of the bound DNA is
between the B and A forms. A wide minor groove allows access to protein side
chains that hydrogen-bond to the N3 of purines and the O2 of pyrimidines at the
blunt-end terminus. Part of the DNA bound to the polymerase site shares a common
binding site with DNA bound to the exonuclease site, but they are translated
relative to each other by several angstroms along their helix axes.
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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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A.H.Riepsamen,
T.Gibson,
J.Rowe,
D.J.Chitwood,
S.A.Subbotin,
and
M.Dowton
(2011).
Poly(T) variation in heteroderid nematode mitochondrial genomes is predominantly an artefact of amplification.
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J Mol Evol,
72,
182-192.
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C.Baar,
M.d'Abbadie,
A.Vaisman,
M.E.Arana,
M.Hofreiter,
R.Woodgate,
T.A.Kunkel,
and
P.Holliger
(2011).
Molecular breeding of polymerases for resistance to environmental inhibitors.
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Nucleic Acids Res,
39,
e51.
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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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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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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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Nucleic Acids Res,
37,
7194-7205.
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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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S.G.Sarafianos,
B.Marchand,
K.Das,
D.M.Himmel,
M.A.Parniak,
S.H.Hughes,
and
E.Arnold
(2009).
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
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J Mol Biol,
385,
693-713.
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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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D.Sutlovic,
S.Gamulin,
M.Definis-Gojanovic,
D.Gugic,
and
S.Andjelinovic
(2008).
Interaction of humic acids with human DNA: proposed mechanisms and kinetics.
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Electrophoresis,
29,
1467-1472.
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J.Wardle,
P.M.Burgers,
I.K.Cann,
K.Darley,
P.Heslop,
E.Johansson,
L.J.Lin,
P.McGlynn,
J.Sanvoisin,
C.M.Stith,
and
B.A.Connolly
(2008).
Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya.
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Nucleic Acids Res,
36,
705-711.
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A.Jacewicz,
K.Makiela,
A.Kierzek,
J.W.Drake,
and
A.Bebenek
(2007).
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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E.S.Baker,
and
M.T.Bowers
(2007).
B-DNA helix stability in a solvent-free environment.
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J Am Soc Mass Spectrom,
18,
1188-1195.
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H.S.Huang,
I.B.Chen,
K.F.Huang,
W.C.Lu,
F.Y.Shieh,
Y.Y.Huang,
F.C.Huang,
and
J.J.Lin
(2007).
Synthesis and human telomerase inhibition of a series of regioisomeric disubstituted amidoanthraquinones.
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Chem Pharm Bull (Tokyo),
55,
284-292.
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K.Singh,
A.Srivastava,
S.S.Patel,
and
M.J.Modak
(2007).
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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R.A.Perlow-Poehnelt,
I.Likhterov,
L.Wang,
D.A.Scicchitano,
N.E.Geacintov,
and
S.Broyde
(2007).
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,
1397-1408.
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E.Longás,
M.de Vega,
J.M.Lázaro,
and
M.Salas
(2006).
Functional characterization of highly processive protein-primed DNA polymerases from phages Nf and GA-1, endowed with a potent strand displacement capacity.
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Nucleic Acids Res,
34,
6051-6063.
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H.D.Cho,
Y.Chen,
G.Varani,
and
A.M.Weiner
(2006).
A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation.
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J Biol Chem,
281,
9801-9811.
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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.
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Biophys J,
90,
1739-1751.
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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.
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Cell,
126,
881-892.
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PDB codes:
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M.Kuwahara,
J.Nagashima,
M.Hasegawa,
T.Tamura,
R.Kitagata,
K.Hanawa,
S.Hososhima,
T.Kasamatsu,
H.Ozaki,
and
H.Sawai
(2006).
Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA.
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Nucleic Acids Res,
34,
5383-5394.
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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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P.Pérez-Arnaiz,
J.M.Lázaro,
M.Salas,
and
M.de Vega
(2006).
Involvement of phi29 DNA polymerase thumb subdomain in the proper coordination of synthesis and degradation during DNA replication.
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Nucleic Acids Res,
34,
3107-3115.
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B.Borstnik,
and
D.Pumpernik
(2005).
Evidence on DNA slippage step-length distribution.
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Phys Rev E Stat Nonlin Soft Matter Phys,
71,
031913.
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H.D.Cho,
C.L.Verlinde,
and
A.M.Weiner
(2005).
Archaeal CCA-adding enzymes: central role of a highly conserved beta-turn motif in RNA polymerization without translocation.
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J Biol Chem,
280,
9555-9566.
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J.Wang
(2005).
DNA polymerases: Hoogsteen base-pairing in DNA replication?
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Nature,
437,
E6.
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PDB code:
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K.Nejedlý,
J.Chládková,
M.Vorlíckov,
I.Hrabcová,
and
J.Kypr
(2005).
Mapping the B-A conformational transition along plasmid DNA.
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Nucleic Acids Res,
33,
e5.
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N.Luo,
and
L.S.Kaguni
(2005).
Mutations in the spacer region of Drosophila mitochondrial DNA polymerase affect DNA binding, processivity, and the balance between Pol and Exo function.
|
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J Biol Chem,
280,
2491-2497.
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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,
19,
345-355.
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V.Kempeneers,
M.Renders,
M.Froeyen,
and
P.Herdewijn
(2005).
Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization.
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Nucleic Acids Res,
33,
3828-3836.
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A.J.Schoeffler,
A.M.Joubert,
F.Peng,
F.Khan,
C.C.Liu,
and
V.J.LiCata
(2004).
Extreme free energy of stabilization of Taq DNA polymerase.
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Proteins,
54,
616-621.
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C.L.Hendrickson,
K.G.Devine,
and
S.A.Benner
(2004).
Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2'-deoxyadenosine.
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Nucleic Acids Res,
32,
2241-2250.
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D.Das,
and
M.M.Georgiadis
(2004).
The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus.
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Structure,
12,
819-829.
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PDB codes:
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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.
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Biophys J,
87,
1478-1497.
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J.H.Eastberg,
J.Pelletier,
and
B.L.Stoddard
(2004).
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
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Nucleic Acids Res,
32,
653-660.
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PDB codes:
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J.K.Kumar,
E.T.Chiu,
S.Tabor,
and
C.C.Richardson
(2004).
A unique region in bacteriophage t7 DNA polymerase important for exonucleolytic hydrolysis of DNA.
|
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J Biol Chem,
279,
42018-42025.
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R.A.Perlow-Poehnelt,
I.Likhterov,
D.A.Scicchitano,
N.E.Geacintov,
and
S.Broyde
(2004).
The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches.
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J Biol Chem,
279,
36951-36961.
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V.L.Arcus,
K.Bäckbro,
A.Roos,
E.L.Daniel,
and
E.N.Baker
(2004).
Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.
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J Biol Chem,
279,
16471-16478.
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PDB codes:
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V.Truniger,
J.M.Lázaro,
and
M.Salas
(2004).
Function of the C-terminus of phi29 DNA polymerase in DNA and terminal protein binding.
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Nucleic Acids Res,
32,
361-370.
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W.A.Beard,
D.D.Shock,
and
S.H.Wilson
(2004).
Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates.
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J Biol Chem,
279,
31921-31929.
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A.M.Joubert,
A.S.Byrd,
and
V.J.LiCata
(2003).
Global conformations, hydrodynamics, and X-ray scattering properties of Taq and Escherichia coli DNA polymerases in solution.
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J Biol Chem,
278,
25341-25347.
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C.L.Li,
L.I.Hor,
Z.F.Chang,
L.C.Tsai,
W.Z.Yang,
and
H.S.Yuan
(2003).
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
|
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EMBO J,
22,
4014-4025.
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PDB codes:
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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.
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Nucleic Acids Res,
31,
974-980.
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H.D.Cho,
A.K.Oyelere,
S.A.Strobel,
and
A.M.Weiner
(2003).
Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): deciphering the basis for nucleotide selection.
|
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RNA,
9,
970-981.
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K.Datta,
and
V.J.LiCata
(2003).
Salt dependence of DNA binding by Thermus aquaticus and Escherichia coli DNA polymerases.
|
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J Biol Chem,
278,
5694-5701.
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K.Datta,
and
V.J.LiCata
(2003).
Thermodynamics of the binding of Thermus aquaticus DNA polymerase to primed-template DNA.
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Nucleic Acids Res,
31,
5590-5597.
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K.E.McGinness,
and
G.F.Joyce
(2003).
In search of an RNA replicase ribozyme.
|
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Chem Biol,
10,
5.
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K.Singh,
and
M.J.Modak
(2003).
Presence of 18-A long hydrogen bond track in the active site of Escherichia coli DNA polymerase I (Klenow fragment). Its requirement in the stabilization of enzyme-template-primer complex.
|
| |
J Biol Chem,
278,
11289-11302.
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M.T.Washington,
S.A.Helquist,
E.T.Kool,
L.Prakash,
and
S.Prakash
(2003).
Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta.
|
| |
Mol Cell Biol,
23,
5107-5112.
|
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N.Kojima,
K.Inoue,
R.Nakajima-Shibata,
S.Kawahara,
and
E.Ohtsuka
(2003).
A new, but old, nucleoside analog: the first synthesis of 1-deaza-2'-deoxyguanosine and its properties as a nucleoside and as oligodeoxynucleotides.
|
| |
Nucleic Acids Res,
31,
7175-7188.
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P.Jałoszyński,
C.Masutani,
F.Hanaoka,
A.B.Perez,
and
S.Nishimura
(2003).
8-Hydroxyguanine in a mutational hotspot of the c-Ha-ras gene causes misreplication, 'action-at-a-distance' mutagenesis and inhibition of replication.
|
| |
Nucleic Acids Res,
31,
6085-6095.
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S.J.Johnson,
J.S.Taylor,
and
L.S.Beese
(2003).
Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
|
| |
Proc Natl Acad Sci U S A,
100,
3895-3900.
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PDB codes:
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S.Jones,
H.P.Shanahan,
H.M.Berman,
and
J.M.Thornton
(2003).
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
|
| |
Nucleic Acids Res,
31,
7189-7198.
|
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S.Jones,
J.A.Barker,
I.Nobeli,
and
J.M.Thornton
(2003).
Using structural motif templates to identify proteins with DNA binding function.
|
| |
Nucleic Acids Res,
31,
2811-2823.
|
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A.Dussy,
C.Meyer,
E.Quennet,
T.A.Bickle,
B.Giese,
and
A.Marx
(2002).
New light-sensitive nucleosides for caged DNA strand breaks.
|
| |
Chembiochem,
3,
54-60.
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C.L.Fata,
S.G.Sawicki,
and
D.L.Sawicki
(2002).
Alphavirus minus-strand RNA synthesis: identification of a role for Arg183 of the nsP4 polymerase.
|
| |
J Virol,
76,
8632-8640.
|
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E.T.Kool
(2002).
Active site tightness and substrate fit in DNA replication.
|
| |
Annu Rev Biochem,
71,
191-219.
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K.M.Kazmierczak,
E.K.Davydova,
A.A.Mustaev,
and
L.B.Rothman-Denes
(2002).
The phage N4 virion RNA polymerase catalytic domain is related to single-subunit RNA polymerases.
|
| |
EMBO J,
21,
5815-5823.
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|
|
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Biochemistry,
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Cell,
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PDB codes:
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T.Ohtsuki,
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A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from bacillus subtilis.
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Structure,
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PDB code:
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D.T.Minnick,
K.Bebenek,
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J Biol Chem,
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Science,
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PDB code:
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Cell,
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Biochemistry,
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Interaction of Escherichia coli DNA polymerase I (Klenow fragment) with primer-templates containing N-acetyl-2-aminofluorene or N-2-aminofluorene adducts in the active site.
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J Biol Chem,
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3-methyladenine DNA glycosylases: structure, function, and biological importance.
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Bioessays,
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Structure,
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Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site.
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Chem Biol,
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Base substitution specificity of DNA polymerase beta depends on interactions in the DNA minor groove.
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J Biol Chem,
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Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
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Cell,
99,
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PDB codes:
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B.P.Engelward,
J.M.Allan,
A.J.Dreslin,
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A chemical and genetic approach together define the biological consequences of 3-methyladenine lesions in the mammalian genome.
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Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
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EMBO J,
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PDB code:
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D.Yue,
A.M.Weiner,
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J Biol Chem,
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Biopolymers,
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Transcription regulation, initiation, and "DNA scrunching" by T7 RNA polymerase.
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Cold Spring Harb Symp Quant Biol,
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Nat Struct Biol,
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Contacts between reverse transcriptase and the primer strand govern the transition from initiation to elongation of HIV-1 reverse transcription.
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J Biol Chem,
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Trends Biochem Sci,
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A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides.
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Proc Natl Acad Sci U S A,
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Inhibition of DNA polymerase reactions by pyrimidine nucleotide analogues lacking the 2-keto group.
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Nucleic Acids Res,
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phi29 DNA polymerase residue Ser122, a single-stranded DNA ligand for 3'-5' exonucleolysis, is required to interact with the terminal protein.
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J Biol Chem,
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CCA addition by tRNA nucleotidyltransferase: polymerization without translocation?
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EMBO J,
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Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.
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Proc Natl Acad Sci U S A,
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PDB code:
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R.Strick,
and
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DNA binding properties and processive proofreading of herpes simplex virus type 1 DNA polymerase.
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Biochim Biophys Acta,
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T.A.Kunkel,
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Nat Struct Biol,
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T.E.Carver,
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Recognition of sequence-directed DNA structure by the Klenow fragment of DNA polymerase I.
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Biochemistry,
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W.A.Beard,
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Vertical-scanning mutagenesis of a critical tryptophan in the minor groove binding track of HIV-1 reverse transcriptase. Molecular nature of polymerase-nucleic acid interactions.
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J Biol Chem,
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Effects of mutations on the partitioning of DNA substrates between the polymerase and 3'-5' exonuclease sites of DNA polymerase I (Klenow fragment).
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Biochemistry,
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W.S.Furey,
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Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment.
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Biochemistry,
37,
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A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
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Nat Struct Biol,
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PDB code:
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Y.Li,
S.Korolev,
and
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(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.
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EMBO J,
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7514-7525.
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PDB codes:
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Y.Li,
Y.Kong,
S.Korolev,
and
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(1998).
Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.
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Protein Sci,
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PDB code:
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A.J.King,
W.R.Teertstra,
and
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Dissociation of the protein primer and DNA polymerase after initiation of adenovirus DNA replication.
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J Biol Chem,
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C.M.Joyce
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Choosing the right sugar: how polymerases select a nucleotide substrate.
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Proc Natl Acad Sci U S A,
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DNA polymerase beta in abasic site repair: a structurally conserved helix-hairpin-helix motif in lesion detection by base excision repair enzymes.
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Biochemistry,
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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.
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Biopolymers,
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Structure,
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PDB code:
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J.Wang,
A.K.Sattar,
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W.H.Konigsberg,
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(1997).
Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69.
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Cell,
89,
1087-1099.
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PDB codes:
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|
K.Bebenek,
W.A.Beard,
T.A.Darden,
L.Li,
R.Prasad,
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A minor groove binding track in reverse transcriptase.
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Nat Struct Biol,
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Structure of the hydrogen bonding complex of O6-methylguanine with cytosine and thymine during DNA replication.
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A thumb subdomain mutant of the large fragment of Escherichia coli DNA polymerase I with reduced DNA binding affinity, processivity, and frameshift fidelity.
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J Biol Chem,
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Peptide rescue of an N-terminal truncation of the Stoffel fragment of taq DNA polymerase.
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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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