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PDBsum entry 2bpf
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Transferase/DNA
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PDB id
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2bpf
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Transferase/DNA
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Title:
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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddctp
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Structure:
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DNA (5'-d( Gp Gp Gp Cp Gp Cp Cp G)-3'). Chain: t. Engineered: yes. DNA (5'-d( Cp Gp Gp Cp Gp Cp C)-3'). Chain: p. Engineered: yes. Protein (DNA polymerase beta . Chain: a. Engineered: yes
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Source:
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Synthetic: yes. Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Trimer (from
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Resolution:
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Authors:
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H.Pelletier,M.R.Sawaya,A.Kumar,S.H.Wilson,J.Kraut
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Key ref:
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H.Pelletier
et al.
(1994).
Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
Science,
264,
1891-1903.
PubMed id:
DOI:
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Date:
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19-May-94
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Release date:
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14-Dec-94
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PROCHECK
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Headers
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References
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P06766
(DPOLB_RAT) -
DNA polymerase beta from Rattus norvegicus
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Seq:
Struc:
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335 a.a.
324 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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G-G-G-C-G-C-C-G
8 bases
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C-G-G-C-G-C-C
7 bases
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Enzyme class 1:
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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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Enzyme class 2:
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E.C.4.2.99.-
- ?????
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Enzyme class 3:
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E.C.4.2.99.18
- DNA-(apurinic or apyrimidinic site) lyase.
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Reaction:
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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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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Science
264:1891-1903
(1994)
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PubMed id:
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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
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H.Pelletier,
M.R.Sawaya,
A.Kumar,
S.H.Wilson,
J.Kraut.
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ABSTRACT
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Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA
template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined
at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of
dideoxycytidine (ddC), a nucleoside analog that targets the reverse
transcriptase of human immunodeficiency virus (HIV) and is at present used to
treat AIDS. Although crystals of the two complexes belong to different space
groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP
interactions are not affected by crystal packing forces. In the pol beta active
site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and
two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these
residues, Asp190 and Asp256, are present in the amino acid sequences of all
polymerases so far studied and are also spatially similar in the four
polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1
reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal
structures are now known. A two-metal ion mechanism is described for the
nucleotidyl transfer reaction and may apply to all polymerases. In the ternary
complex structures analyzed, pol beta binds to the DNA template-primer in a
different manner from that recently proposed for other polymerase-DNA models.
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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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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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B.Knobloch,
A.Mucha,
B.P.Operschall,
H.Sigel,
M.Jeżowska-Bojczuk,
H.Kozłowski,
and
R.K.Sigel
(2011).
Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria.
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Chemistry,
17,
5393-5403.
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D.C.Knapp,
S.Serva,
J.D'Onofrio,
A.Keller,
A.Lubys,
A.Kurg,
M.Remm,
and
J.W.Engels
(2011).
Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension.
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Chemistry,
17,
2903-2915.
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J.Orans,
E.A.McSweeney,
R.R.Iyer,
M.A.Hast,
H.W.Hellinga,
P.Modrich,
and
L.S.Beese
(2011).
Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family.
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Cell,
145,
212-223.
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PDB codes:
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P.Xie
(2011).
A model for the dynamics of mammalian family X DNA polymerases.
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J Theor Biol,
277,
111-122.
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|
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S.E.Tsutakawa,
S.Classen,
B.R.Chapados,
A.S.Arvai,
L.D.Finger,
G.Guenther,
C.G.Tomlinson,
P.Thompson,
A.H.Sarker,
B.Shen,
P.K.Cooper,
J.A.Grasby,
and
J.A.Tainer
(2011).
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily.
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Cell,
145,
198-211.
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PDB codes:
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A.Fernández-Botello,
B.P.Operschall,
A.Holy,
V.Moreno,
and
H.Sigel
(2010).
Metal ion-binding properties of 9-[(2-phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antiviral nucleotide analogue 9-[(2-phosphonomethoxy)ethyl]adenine (PMEA). Steric guiding of metal ion-coordination by the purine-amino group.
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Dalton Trans,
39,
6344-6354.
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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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J.A.Brown,
K.A.Fiala,
J.D.Fowler,
S.M.Sherrer,
S.A.Newmister,
W.W.Duym,
and
Z.Suo
(2010).
A novel mechanism of sugar selection utilized by a human X-family DNA polymerase.
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J Mol Biol,
395,
282-290.
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J.Guo,
L.Yu,
N.J.Turro,
and
J.Ju
(2010).
An integrated system for DNA sequencing by synthesis using novel nucleotide analogues.
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Acc Chem Res,
43,
551-563.
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J.Yamtich,
D.Starcevic,
J.Lauper,
E.Smith,
I.Shi,
S.Rangarajan,
J.Jaeger,
and
J.B.Sweasy
(2010).
Hinge residue I174 is critical for proper dNTP selection by DNA polymerase beta.
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Biochemistry,
49,
2326-2334.
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J.Yamtich,
and
J.B.Sweasy
(2010).
DNA polymerase family X: function, structure, and cellular roles.
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Biochim Biophys Acta,
1804,
1136-1150.
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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.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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M.de Vega,
J.M.Lázaro,
M.Mencía,
L.Blanco,
and
M.Salas
(2010).
Improvement of φ29 DNA polymerase amplification performance by fusion of DNA binding motifs.
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Proc Natl Acad Sci U S A,
107,
16506-16511.
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N.Staiger,
and
A.Marx
(2010).
A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides.
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Chembiochem,
11,
1963-1966.
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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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S.H.Wilson,
W.A.Beard,
D.D.Shock,
V.K.Batra,
N.A.Cavanaugh,
R.Prasad,
E.W.Hou,
Y.Liu,
K.Asagoshi,
J.K.Horton,
D.F.Stefanick,
P.S.Kedar,
M.J.Carrozza,
A.Masaoka,
and
M.L.Heacock
(2010).
Base excision repair and design of small molecule inhibitors of human DNA polymerase β.
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Cell Mol Life Sci,
67,
3633-3647.
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S.J.Hyde,
B.E.Eckenroth,
B.A.Smith,
W.A.Eberley,
N.H.Heintz,
J.E.Jackman,
and
S.Doublié
(2010).
tRNA(His) guanylyltransferase (THG1), a unique 3'-5' nucleotidyl transferase, shares unexpected structural homology with canonical 5'-3' DNA polymerases.
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Proc Natl Acad Sci U S A,
107,
20305-20310.
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PDB codes:
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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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Y.Zhang,
E.L.Pohlmann,
J.Serate,
M.C.Conrad,
and
G.P.Roberts
(2010).
Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein.
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J Bacteriol,
192,
2711-2721.
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F.Romain,
I.Barbosa,
J.Gouge,
F.Rougeon,
and
M.Delarue
(2009).
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region.
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Nucleic Acids Res,
37,
4642-4656.
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J.D.Fowler,
J.A.Brown,
M.Kvaratskhelia,
and
Z.Suo
(2009).
Probing conformational changes of human DNA polymerase lambda using mass spectrometry-based protein footprinting.
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J Mol Biol,
390,
368-379.
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K.S.Keating,
S.C.Flores,
M.B.Gerstein,
and
L.A.Kuhn
(2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
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Protein Sci,
18,
359-371.
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M.A.van Bochove,
M.Swart,
and
F.M.Bickelhaupt
(2009).
Stepwise walden inversion in nucleophilic substitution at phosphorus.
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Phys Chem Chem Phys,
11,
259-267.
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P.B.Balbo,
and
A.Bohm
(2009).
Proton transfer in the mechanism of polyadenylate polymerase.
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Biochem J,
420,
229-238.
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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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T.G.Upton,
B.A.Kashemirov,
C.E.McKenna,
M.F.Goodman,
G.K.Prakash,
R.Kultyshev,
V.K.Batra,
D.D.Shock,
L.C.Pedersen,
W.A.Beard,
and
S.H.Wilson
(2009).
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.
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Org Lett,
11,
1883-1886.
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PDB code:
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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.Toh,
D.Takeshita,
T.Numata,
S.Fukai,
O.Nureki,
and
K.Tomita
(2009).
Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme.
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EMBO J,
28,
3353-3365.
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PDB codes:
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Z.Song,
K.J.Parker,
I.Enoh,
H.Zhao,
and
O.Olubajo
(2009).
Myosin-catalyzed ATP hydrolysis elucidated by 31P NMR kinetic studies and 1H PFG-diffusion measurements.
|
| |
Anal Bioanal Chem,
395,
1453-1459.
|
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B.Baños,
J.M.Lázaro,
L.Villar,
M.Salas,
and
M.de Vega
(2008).
Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase.
|
| |
Nucleic Acids Res,
36,
5736-5749.
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D.L.Croteau,
Y.Peng,
and
B.Van Houten
(2008).
DNA repair gets physical: mapping an XPA-binding site on ERCC1.
|
| |
DNA Repair (Amst),
7,
819-826.
|
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F.Liang,
N.Jain,
T.Hutchens,
D.D.Shock,
W.A.Beard,
S.H.Wilson,
M.P.Chiarelli,
and
B.P.Cho
(2008).
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT.
|
| |
J Med Chem,
51,
6460-6470.
|
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G.Lahoud,
V.Timoshchuk,
A.Lebedev,
M.de Vega,
M.Salas,
K.Arar,
Y.M.Hou,
and
H.Gamper
(2008).
Enzymatic synthesis of structure-free DNA with pseudo-complementary properties.
|
| |
Nucleic Acids Res,
36,
3409-3419.
|
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|
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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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M.H.Lamers,
and
M.O'Donnell
(2008).
A consensus view of DNA binding by the C family of replicative DNA polymerases.
|
| |
Proc Natl Acad Sci U S A,
105,
20565-20566.
|
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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:
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S.Dalal,
D.Starcevic,
J.Jaeger,
and
J.B.Sweasy
(2008).
The I260Q variant of DNA polymerase beta extends mispaired primer termini due to its increased affinity for deoxynucleotide triphosphate substrates.
|
| |
Biochemistry,
47,
12118-12125.
|
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S.J.Garforth,
M.A.Parniak,
and
V.R.Prasad
(2008).
Utilization of a deoxynucleoside diphosphate substrate by HIV reverse transcriptase.
|
| |
PLoS ONE,
3,
e2074.
|
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|
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|
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S.Kumar,
M.Bakhtina,
and
M.D.Tsai
(2008).
Altered order of substrate binding by DNA polymerase X from African Swine Fever virus.
|
| |
Biochemistry,
47,
7875-7887.
|
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S.O.Yesylevskyy,
V.N.Kharkyanen,
and
A.P.Demchenko
(2008).
The blind search for the closed states of hinge-bending proteins.
|
| |
Proteins,
71,
831-843.
|
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W.J.Allen,
P.J.Rothwell,
and
G.Waksman
(2008).
An intramolecular FRET system monitors fingers subdomain opening in Klentaq1.
|
| |
Protein Sci,
17,
401-408.
|
|
|
|
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|
|
W.Yang
(2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
|
| |
Nat Struct Mol Biol,
15,
1228-1231.
|
|
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|
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A.F.Moon,
M.Garcia-Diaz,
V.K.Batra,
W.A.Beard,
K.Bebenek,
T.A.Kunkel,
S.H.Wilson,
and
L.C.Pedersen
(2007).
The X family portrait: structural insights into biological functions of X family polymerases.
|
| |
DNA Repair (Amst),
6,
1709-1725.
|
|
|
|
|
|
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A.J.Berman,
S.Kamtekar,
J.L.Goodman,
J.M.Lázaro,
M.de Vega,
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Structure,
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Nat Struct Mol Biol,
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PDB code:
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Nature,
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PDB code:
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L.Yang,
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A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.
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Mol Cell,
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PDB code:
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R.B.Gómez-Coca,
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Structural and energetic characterization of nucleic acid-binding to the fingers domain of Moloney murine leukemia virus reverse transcriptase.
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Proteins,
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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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Nature,
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PDB codes:
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D.Shah,
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Biochemistry,
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Structure,
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PDB codes:
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K.E.McGinness,
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Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
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Biochemistry,
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Genes Cells,
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PDB codes:
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Proteins,
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Mol Cell,
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB codes:
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Mol Cell,
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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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G.Martin,
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J Bacteriol,
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Nucleic Acids Res,
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Specific inhibition of DNA polymerase beta by its 14 kDa domain: role of single- and double-stranded DNA binding and 5'-phosphate recognition.
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Nucleic Acids Res,
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Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns.
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DNA polymerase beta bypasses in vitro a single d(GpG)-cisplatin adduct placed on codon 13 of the HRAS gene.
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Mechanistic implications from the structure of a catalytic fragment of Moloney murine leukemia virus reverse transcriptase.
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PDB code:
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Proc Natl Acad Sci U S A,
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PDB code:
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U.K.Urs,
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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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