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PDBsum entry 1bpy
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Transferase/DNA
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PDB id
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1bpy
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Contents |
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* Residue conservation analysis
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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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Biochemistry
36:11205-11215
(1997)
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PubMed id:
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Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
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M.R.Sawaya,
R.Prasad,
S.H.Wilson,
J.Kraut,
H.Pelletier.
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ABSTRACT
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DNA polymerase beta (pol beta) fills single nucleotide (nt) gaps in DNA produced
by the base excision repair pathway of mammalian cells. Crystal structures have
been determined representing intermediates in the 1 nt gap-filling reaction of
pol beta: the binary complex with a gapped DNA substrate (2.4 A resolution), the
ternary complex including ddCTP (2.2 A), and the binary product complex
containing only nicked DNA (2.6 A). Upon binding ddCTP to the binary gap
complex, the thumb subdomain rotates into the closed conformation to contact the
otherwise solvent-exposed ddCTP-template base pair. Thumb movement triggers
further conformational changes which poise catalytic residue Asp192, dNTP, and
template for nucleotidyl transfer, effectively assembling the active site. In
the product nicked DNA complex, the thumb returns to the open conformation as in
the gapped binary DNA complex, facilitating dissociation of the product. These
findings suggest that pol beta may enhance fidelity by an induced fit mechanism
in which correct base pairing between template and incoming dNTP induces
alignment of catalytic groups for catalysis (via thumb closure), but incorrect
base pairing will not. The structures also reveal that pol beta binds both
gapped and nicked DNA with a 90 degrees kink occurring precisely at the
5'-phosphodiester linkage of the templating residue. If the DNA were not kinked
in this way, contact between the thumb and dNTP-template base pair, presumably
important for the checking mechanism, would be impossible, especially when the
gap is but a single nucleotide. Such a 90 degrees kink may be a mechanistic
feature employed by any polymerase involved in filling gaps to completion.
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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.S.Jaiswal,
S.Banerjee,
R.Aneja,
F.H.Sarkar,
D.A.Ostrov,
and
S.Narayan
(2011).
DNA polymerase β as a novel target for chemotherapeutic intervention of colorectal cancer.
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PLoS One,
6,
e16691.
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C.L.An,
D.Chen,
and
N.M.Makridakis
(2011).
Systematic biochemical analysis of somatic missense mutations in DNA polymerase β found in prostate cancer reveal alteration of enzymatic function.
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Hum Mutat,
32,
415-423.
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M.Herrera-Marschitz,
P.Morales,
L.Leyton,
D.Bustamante,
V.Klawitter,
P.Espina-Marchant,
C.Allende,
F.Lisboa,
G.Cunich,
A.Jara-Cavieres,
T.Neira,
M.A.Gutierrez-Hernandez,
V.Gonzalez-Lira,
N.Simola,
A.Schmitt,
M.Morelli,
R.Andrew Tasker,
and
P.J.Gebicke-Haerter
(2011).
Perinatal asphyxia: current status and approaches towards neuroprotective strategies, with focus on sentinel proteins.
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Neurotox Res,
19,
603-627.
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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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A.K.Hinz,
Y.Wang,
and
M.J.Smerdon
(2010).
Base excision repair in a glucocorticoid response element: effect of glucocorticoid receptor binding.
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J Biol Chem,
285,
28683-28690.
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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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D.Sun,
G.Lee,
J.H.Lee,
H.Y.Kim,
H.W.Rhee,
S.Y.Park,
K.J.Kim,
Y.Kim,
B.Y.Kim,
J.I.Hong,
C.Park,
H.E.Choy,
J.H.Kim,
Y.H.Jeon,
and
J.Chung
(2010).
A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses.
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Nat Struct Mol Biol,
17,
1188-1194.
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PDB codes:
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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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G.M.Giambasu,
T.S.Lee,
C.P.Sosa,
M.P.Robertson,
W.G.Scott,
and
D.M.York
(2010).
Identification of dynamical hinge points of the L1 ligase molecular switch.
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RNA,
16,
769-780.
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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.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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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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U.Bren,
J.Lah,
M.Bren,
V.Martínek,
and
J.Florián
(2010).
DNA duplex stability: the role of preorganized electrostatics.
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J Phys Chem B,
114,
2876-2885.
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Y.Li,
and
T.Schlick
(2010).
Modeling DNA polymerase μ motions: subtle transitions before chemistry.
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Biophys J,
99,
3463-3472.
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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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A.S.Jaiswal,
S.Banerjee,
H.Panda,
C.D.Bulkin,
T.Izumi,
F.H.Sarkar,
D.A.Ostrov,
and
S.Narayan
(2009).
A novel inhibitor of DNA polymerase beta enhances the ability of temozolomide to impair the growth of colon cancer cells.
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Mol Cancer Res,
7,
1973-1983.
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B.G.Vértessy,
and
J.Tóth
(2009).
Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases.
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Acc Chem Res,
42,
97.
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C.Castro,
E.D.Smidansky,
J.J.Arnold,
K.R.Maksimchuk,
I.Moustafa,
A.Uchida,
M.Götte,
W.Konigsberg,
and
C.E.Cameron
(2009).
Nucleic acid polymerases use a general acid for nucleotidyl transfer.
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Nat Struct Mol Biol,
16,
212-218.
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E.Arehart,
S.Gleim,
B.White,
J.Hwa,
and
J.H.Moore
(2009).
Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms.
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BioData Min,
2,
2.
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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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J.F.Sydow,
F.Brueckner,
A.C.Cheung,
G.E.Damsma,
S.Dengl,
E.Lehmann,
D.Vassylyev,
and
P.Cramer
(2009).
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
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Mol Cell,
34,
710-721.
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PDB codes:
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K.A.Donigan,
and
J.B.Sweasy
(2009).
Sequence context-specific mutagenesis and base excision repair.
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Mol Carcinog,
48,
362-368.
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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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M.C.Foley,
and
T.Schlick
(2009).
Relationship between conformational changes in pol lambda's active site upon binding incorrect nucleotides and mismatch incorporation rates.
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J Phys Chem B,
113,
13035-13047.
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M.Garcia-Diaz,
K.Bebenek,
A.A.Larrea,
J.M.Havener,
L.Perera,
J.M.Krahn,
L.C.Pedersen,
D.A.Ramsden,
and
T.A.Kunkel
(2009).
Template strand scrunching during DNA gap repair synthesis by human polymerase lambda.
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Nat Struct Mol Biol,
16,
967-972.
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N.Leulliot,
L.Cladière,
F.Lecointe,
D.Durand,
U.Hübscher,
and
H.van Tilbeurgh
(2009).
The Family X DNA Polymerase from Deinococcus radiodurans Adopts a Non-standard Extended Conformation.
|
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J Biol Chem,
284,
11992-11999.
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PDB code:
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N.M.Makridakis,
L.F.Caldas Ferraz,
and
J.K.Reichardt
(2009).
Genomic analysis of cancer tissue reveals that somatic mutations commonly occur in a specific motif.
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Hum Mutat,
30,
39-48.
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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.Biswas,
M.Guharoy,
and
P.Chakrabarti
(2009).
Dissection, residue conservation, and structural classification of protein-DNA interfaces.
|
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Proteins,
74,
643-654.
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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.
|
| |
Anal Biochem,
384,
136-144.
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A.Abyzov,
A.Uzun,
P.R.Strauss,
and
V.A.Ilyin
(2008).
An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.
|
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PLoS Comput Biol,
4,
e1000066.
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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.
|
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J Mol Biol,
384,
1086-1097.
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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.
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Nucleic Acids Res,
36,
5736-5749.
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D.L.Murphy,
J.Kosa,
J.Jaeger,
and
J.B.Sweasy
(2008).
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding.
|
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Biochemistry,
47,
8048-8057.
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G.Martin,
S.Doublié,
and
W.Keller
(2008).
Determinants of substrate specificity in RNA-dependent nucleotidyl transferases.
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Biochim Biophys Acta,
1779,
206-216.
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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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G.Yang,
J.Wang,
Y.Cheng,
G.E.Dutschman,
H.Tanaka,
M.Baba,
and
Y.C.Cheng
(2008).
Mechanism of inhibition of human immunodeficiency virus type 1 reverse transcriptase by a stavudine analogue, 4'-ethynyl stavudine triphosphate.
|
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Antimicrob Agents Chemother,
52,
2035-2042.
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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.
|
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J Biol Chem,
283,
36711-36723.
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|
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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.H.Tang,
M.Niebuhr,
A.Aulabaugh,
and
M.D.Tsai
(2008).
Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering.
|
| |
Nucleic Acids Res,
36,
849-860.
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K.H.Tang,
M.Niebuhr,
C.S.Tung,
H.C.Chan,
C.C.Chou,
and
M.D.Tsai
(2008).
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.
|
| |
Nucleic Acids Res,
36,
2948-2957.
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PDB code:
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|
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K.K.Ng,
J.J.Arnold,
and
C.E.Cameron
(2008).
Structure-function relationships among RNA-dependent RNA polymerases.
|
| |
Curr Top Microbiol Immunol,
320,
137-156.
|
|
|
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|
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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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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.
|
| |
Mol Cell,
30,
315-324.
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PDB codes:
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V.N.Vyjayanti,
N.S.Chary,
and
K.S.Rao
(2008).
On the inhibitory affect of some dementia drugs on DNA polymerase Beta activity.
|
| |
Neurochem Res,
33,
2187-2196.
|
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Y.Xiang,
M.F.Goodman,
W.A.Beard,
S.H.Wilson,
and
A.Warshel
(2008).
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.
|
| |
Proteins,
70,
231-247.
|
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A.F.Moon,
M.Garcia-Diaz,
K.Bebenek,
B.J.Davis,
X.Zhong,
D.A.Ramsden,
T.A.Kunkel,
and
L.C.Pedersen
(2007).
Structural insight into the substrate specificity of DNA Polymerase mu.
|
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Nat Struct Mol Biol,
14,
45-53.
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PDB code:
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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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D.R.Langley,
A.W.Walsh,
C.J.Baldick,
B.J.Eggers,
R.E.Rose,
S.M.Levine,
A.J.Kapur,
R.J.Colonno,
and
D.J.Tenney
(2007).
Inhibition of hepatitis B virus polymerase by entecavir.
|
| |
J Virol,
81,
3992-4001.
|
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|
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G.C.Lin,
J.Jaeger,
and
J.B.Sweasy
(2007).
Loop II of DNA polymerase beta is important for polymerization activity and fidelity.
|
| |
Nucleic Acids Res,
35,
2924-2935.
|
|
|
|
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|
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G.Martin,
and
W.Keller
(2007).
RNA-specific ribonucleotidyl transferases.
|
| |
RNA,
13,
1834-1849.
|
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|
|
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PDB code:
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P.B.Balbo,
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P.Oelschlaeger,
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J Mol Biol,
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P.R.Meyer,
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PLoS ONE,
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Biochemistry,
46,
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PDB codes:
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A.M.DeLucia,
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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,
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B.A.Sampoli Benítez,
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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,
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Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D.
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Proc Natl Acad Sci U S A,
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PDB codes:
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I.Jagannathan,
H.A.Cole,
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J Biol Chem,
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L.V.Gening,
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RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa.
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Nucleic Acids Res,
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Biophys J,
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M.H.Lamers,
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Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.
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Cell,
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PDB codes:
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N.Pourmand,
M.Karhanek,
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Direct electrical detection of DNA synthesis.
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Proc Natl Acad Sci U S A,
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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,
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O.Rechkoblit,
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Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion.
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PLoS Biol,
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PDB codes:
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P.Lin,
L.C.Pedersen,
V.K.Batra,
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Energy analysis of chemistry for correct insertion by DNA polymerase beta.
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Proc Natl Acad Sci U S A,
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A specific loop in human DNA polymerase mu allows switching between creative and DNA-instructed synthesis.
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Nucleic Acids Res,
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Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.
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Biochemistry,
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Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta.
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Biochem Biophys Res Commun,
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The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
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Cell,
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PDB codes:
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V.K.Batra,
D.D.Shock,
R.Prasad,
W.A.Beard,
E.W.Hou,
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Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features.
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Proc Natl Acad Sci U S A,
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PDB code:
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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,
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757-766.
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PDB codes:
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W.W.Duym,
K.A.Fiala,
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Kinetic effect of a downstream strand and its 5'-terminal moieties on single nucleotide gap-filling synthesis catalyzed by human DNA polymerase lambda.
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J Biol Chem,
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Protein Sci,
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C.Lehmann,
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Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase.
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Proteins,
60,
807-811.
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PDB code:
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J.Deng,
N.L.Ernst,
S.Turley,
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Structural basis for UTP specificity of RNA editing TUTases from Trypanosoma brucei.
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EMBO J,
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PDB codes:
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M.Garcia-Diaz,
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J.M.Krahn,
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A closed conformation for the Pol lambda catalytic cycle.
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Nat Struct Mol Biol,
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PDB codes:
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N.Kasai,
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Sulfoquinovosylmonoacylglycerol inhibitory mode analysis of rat DNA polymerase beta.
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FEBS J,
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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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R.C.Holmberg,
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Biomol Eng,
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J Am Chem Soc,
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Recognition and processing of cisplatin- and oxaliplatin-DNA adducts.
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Crit Rev Oncol Hematol,
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Annu Rev Biochem,
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Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
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Structure,
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1225-1233.
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PDB codes:
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B.Tippin,
S.Kobayashi,
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To slip or skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases.
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J Biol Chem,
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Aromatic residues located close to the active center are essential for the catalytic reaction of flap endonuclease-1 from hyperthermophilic archaeon Pyrococcus horikoshii.
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J Biol Chem,
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Structure of a bifunctional DNA primase-polymerase.
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Nat Struct Mol Biol,
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PDB codes:
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G.Martin,
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Sequence motifs that distinguish ATP(CTP):tRNA nucleotidyl transferases from eubacterial poly(A) polymerases.
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RNA,
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Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
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Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping.
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J Biol Chem,
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Biophys J,
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Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
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EMBO J,
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PDB codes:
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L.Yang,
W.A.Beard,
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Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.
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Biophys J,
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Repair of U/G and U/A in DNA by UNG2-associated repair complexes takes place predominantly by short-patch repair both in proliferating and growth-arrested cells.
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Nucleic Acids Res,
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J Biol Chem,
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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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M.Hogg,
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Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site.
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PDB codes:
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M.Pandey,
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Insights into the role of an active site aspartate in Ty1 reverse transcriptase polymerization.
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J Biol Chem,
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Q.Guo,
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Structural and kinetic analyses of the interaction of anthrax adenylyl cyclase toxin with reaction products cAMP and pyrophosphate.
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J Biol Chem,
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29427-29435.
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PDB code:
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R.A.Perlow-Poehnelt,
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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,
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Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing.
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Proc Natl Acad Sci U S A,
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PDB code:
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J.F.Ruiz,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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