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PDBsum entry 2bdp
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Transferase/DNA
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PDB id
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2bdp
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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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DOI no:
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Nature
391:304-307
(1998)
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PubMed id:
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Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.
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J.R.Kiefer,
C.Mao,
J.C.Braman,
L.S.Beese.
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ABSTRACT
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DNA polymerases copy DNA templates with remarkably high fidelity, checking for
correct base-pair formation both at nucleotide insertion and at subsequent DNA
extension steps. Despite extensive biochemical, genetic and structural studies,
the mechanism by which nucleotides are correctly incorporated is not known. Here
we present high-resolution crystal structures of a thermostable bacterial
(Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer
templates bound productively at the polymerase active site. The active site
retains catalytic activity, allowing direct observation of the products of
several rounds of nucleotide incorporation. The polymerase also retains its
ability to discriminate between correct and incorrectly paired nucleotides in
the crystal. Comparison of the structures of successively translocated complexes
allows the structural features for the sequence-independent molecular
recognition of correctly formed base pairs to be deduced unambiguously. These
include extensive interactions with the first four to five base pairs in the
minor groove, location of the terminal base pair in a pocket of excellent steric
complementarity favouring correct base-pair formation, and a conformational
switch from B-form to underwound A-form DNA at the polymerase active site.
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Selected figure(s)
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Figure 1.
Figure 1 Structure of the Bacillus fragment with duplex DNA
bound at the polymerase active site. The Bacillus fragment
molecular surface is coloured according to its proximity to the
DNA, with all points less than 3.5 ? coloured magenta, between
3.5 and 5.0 ? yellow, and greater than 5 ? blue. Bound water
molecules were not included in this calculation.
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Figure 4.
Figure 4 Polymerase active site with observed DNA and
modelled dTTP. The position of dTTP (violet) was based on the
 -polymerase
complex18, adjusted such that the base ring stacks with the
primer and one oxygen from each phosphate group was within 3 ?
of the observed metal ion (gold). The sugar pucker of the primer
terminus was made C3'-endo, which shifted its 3'-OH to within
1.7 ? of the modelled  -phosphate
of the dTTP. A second metal ion (violet) was modelled to be
within 3 ? of the 3'-OH of the primer, the -phosphate
group, and residues Asp 830 and Glu 831. The observed 5'
template overhang cannot accept an incoming dNTP without a
conformational change of the O helix.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(1998,
391,
304-307)
copyright 1998.
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Figures were
selected
by an automated process.
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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.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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E.A.Motea,
and
A.J.Berdis
(2010).
Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase.
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Biochim Biophys Acta,
1804,
1151-1166.
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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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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.Venkatramani,
and
R.Radhakrishnan
(2010).
Computational delineation of the catalytic step of a high-fidelity DNA polymerase.
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Protein Sci,
19,
815-825.
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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.Kimoto,
R.Kawai,
T.Mitsui,
S.Yokoyama,
and
I.Hirao
(2009).
An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules.
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Nucleic Acids Res,
37,
e14.
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M.Renders,
M.Abramov,
M.Froeyen,
and
P.Herdewijn
(2009).
Polymerase-catalysed incorporation of glucose nucleotides into a DNA duplex.
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Chemistry,
15,
5463-5470.
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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.
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Biochemistry,
48,
4633-4641.
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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.
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Biochemistry,
48,
4677-4690.
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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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G.T.Hwang,
and
F.E.Romesberg
(2008).
Unnatural substrate repertoire of A, B, and X family DNA polymerases.
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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.
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Chembiochem,
9,
1243-1250.
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M.Renders,
R.Lievrouw,
M.Krecmerová,
A.Holý,
and
P.Herdewijn
(2008).
Enzymatic polymerization of phosphonate nucleosides.
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Chembiochem,
9,
2883-2888.
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N.Minakawa,
Y.Kawano,
S.Murata,
N.Inoue,
and
A.Matsuda
(2008).
Oligodeoxynucleotides containing 3-bromo-3-deazaadenine and 7-bromo-7-deazaadenine 2'-deoxynucleosides as chemical probes to investigate DNA-protein interactions.
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Chembiochem,
9,
464-470.
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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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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.
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Proteins,
71,
1360-1372.
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S.Broyde,
L.Wang,
O.Rechkoblit,
N.E.Geacintov,
and
D.J.Patel
(2008).
Lesion processing: high-fidelity versus lesion-bypass DNA polymerases.
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Trends Biochem Sci,
33,
209-219.
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S.E.Hile,
and
K.A.Eckert
(2008).
DNA polymerase kappa produces interrupted mutations and displays polar pausing within mononucleotide microsatellite sequences.
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Nucleic Acids Res,
36,
688-696.
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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:
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W.Rutvisuttinunt,
P.R.Meyer,
and
W.A.Scott
(2008).
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
(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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C.Castro,
E.Smidansky,
K.R.Maksimchuk,
J.J.Arnold,
V.S.Korneeva,
M.Götte,
W.Konigsberg,
and
C.E.Cameron
(2007).
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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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.
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Proc Natl Acad Sci U S A,
104,
14598-14603.
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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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M.E.Arana,
K.Takata,
M.Garcia-Diaz,
R.D.Wood,
and
T.A.Kunkel
(2007).
A unique error signature for human DNA polymerase nu.
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DNA Repair (Amst),
6,
213-223.
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N.Z.Rudinger,
R.Kranaster,
and
A.Marx
(2007).
Hydrophobic amino acid and single-atom substitutions increase DNA polymerase selectivity.
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Chem Biol,
14,
185-194.
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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.Amir,
and
S.Rozen
(2006).
Easy access to the family of thiazole N-oxides using HOF x CH3CN.
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Chem Commun (Camb),
(),
2262-2264.
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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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E.Pienaar,
M.Theron,
M.Nelson,
and
H.J.Viljoen
(2006).
A quantitative model of error accumulation during PCR amplification.
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Comput Biol Chem,
30,
102-111.
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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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I.Hirao,
M.Kimoto,
T.Mitsui,
T.Fujiwara,
R.Kawai,
A.Sato,
Y.Harada,
and
S.Yokoyama
(2006).
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA.
|
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Nat Methods,
3,
729-735.
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J.Chiu,
D.Tillett,
and
P.E.March
(2006).
Mutation of Phe102 to Ser in the carboxyl terminal helix of Escherichia coli thioredoxin affects the stability and processivity of T7 DNA polymerase.
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Proteins,
64,
477-485.
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J.J.Warren,
L.J.Forsberg,
and
L.S.Beese
(2006).
The structural basis for the mutagenicity of O(6)-methyl-guanine lesions.
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Proc Natl Acad Sci U S A,
103,
19701-19706.
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PDB codes:
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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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R.Radhakrishnan,
K.Arora,
Y.Wang,
W.A.Beard,
S.H.Wilson,
and
T.Schlick
(2006).
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.
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Biochemistry,
45,
15142-15156.
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R.Radhakrishnan,
and
T.Schlick
(2006).
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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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.
|
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Mol Cell,
24,
245-255.
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T.A.Steitz
(2006).
Visualizing polynucleotide polymerase machines at work.
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EMBO J,
25,
3458-3468.
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D.Summerer,
N.Z.Rudinger,
I.Detmer,
and
A.Marx
(2005).
Enhanced fidelity in mismatch extension by DNA polymerase through directed combinatorial enzyme design.
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Angew Chem Int Ed Engl,
44,
4712-4715.
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G.W.Hsu,
X.Huang,
N.P.Luneva,
N.E.Geacintov,
and
L.S.Beese
(2005).
Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication.
|
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J Biol Chem,
280,
3764-3770.
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PDB code:
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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.D.Ahle,
S.Barr,
A.M.Chin,
and
T.R.Battersby
(2005).
Sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases.
|
| |
Nucleic Acids Res,
33,
3176-3184.
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J.K.Ichida,
A.Horhota,
K.Zou,
L.W.McLaughlin,
and
J.W.Szostak
(2005).
High fidelity TNA synthesis by Therminator polymerase.
|
| |
Nucleic Acids Res,
33,
5219-5225.
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M.F.Langelier,
D.Baali,
V.Trinh,
J.Greenblatt,
J.Archambault,
and
B.Coulombe
(2005).
The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II.
|
| |
Nucleic Acids Res,
33,
2629-2639.
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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.
|
| |
J Biol Chem,
280,
2491-2497.
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R.E.Johnson,
L.Prakash,
and
S.Prakash
(2005).
Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase eta.
|
| |
Proc Natl Acad Sci U S A,
102,
12359-12364.
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S.Duigou,
S.D.Ehrlich,
P.Noirot,
and
M.F.Noirot-Gros
(2005).
DNA polymerase I acts in translesion synthesis mediated by the Y-polymerases in Bacillus subtilis.
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| |
Mol Microbiol,
57,
678-690.
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S.Prakash,
R.E.Johnson,
and
L.Prakash
(2005).
Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function.
|
| |
Annu Rev Biochem,
74,
317-353.
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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.
|
| |
Structure,
13,
1225-1233.
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PDB codes:
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A.M.Sismour,
S.Lutz,
J.H.Park,
M.J.Lutz,
P.L.Boyer,
S.H.Hughes,
and
S.A.Benner
(2004).
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1.
|
| |
Nucleic Acids Res,
32,
728-735.
|
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A.S.Meyer,
M.Blandino,
and
T.E.Spratt
(2004).
Escherichia coli DNA polymerase I (Klenow fragment) uses a hydrogen-bonding fork from Arg668 to the primer terminus and incoming deoxynucleotide triphosphate to catalyze DNA replication.
|
| |
J Biol Chem,
279,
33043-33046.
|
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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.
|
| |
Nucleic Acids Res,
32,
2241-2250.
|
|
|
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Nature,
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PDB codes:
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PDB code:
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Cell,
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PDB codes:
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T.A.Steitz,
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Cell,
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PDB codes:
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D.Shinde,
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Proc Natl Acad Sci U S A,
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PDB codes:
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S.Limsirichaikul,
M.Ogawa,
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Effects of vinylphosphonate internucleotide linkages on the cleavage specificity of exonuclease III and on the activity of DNA polymerase I.
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Biochemistry,
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Eur J Biochem,
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Bioessays,
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In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity.
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Nature,
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Low fidelity DNA synthesis by a y family DNA polymerase due to misalignment in the active site.
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J Biol Chem,
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Using 2-aminopurine fluorescence to detect base unstacking in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase.
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Biochemistry,
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Nucleic Acids Res,
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Science,
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PDB code:
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A.Goel,
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Nucleic Acids Res,
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Cell,
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PDB codes:
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J.M.Ogle,
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Recognition of cognate transfer RNA by the 30S ribosomal subunit.
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Science,
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PDB codes:
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J.W.Arndt,
W.Gong,
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Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes.
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Biochemistry,
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PDB codes:
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Nucleic Acids Res,
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PDB code:
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Biochemistry,
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Proc Natl Acad Sci U S A,
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Cold Spring Harb Symp Quant Biol,
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Site-specific incorporation of nucleoside analogs by HIV-1 reverse transcriptase and the template grip mutant P157S. Template interactions influence substrate recognition at the polymerase active site.
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PDB code:
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Identification of conserved residues contributing to the activities of adenovirus DNA polymerase.
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Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases.
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PDB codes:
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Where a reference describes a PDB structure, the PDB
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