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PDBsum entry 1dk2
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Backbone dynamics and refined solution structure of the n-Terminal domain of DNA polymerase beta. Correlation with DNA binding and drp lyase activity.
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Authors
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M.W.Maciejewski,
D.Liu,
R.Prasad,
S.H.Wilson,
G.P.Mullen.
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Ref.
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J Mol Biol, 2000,
296,
229-253.
[DOI no: ]
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PubMed id
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Abstract
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Mammalian DNA polymerase beta functions in the base excision DNA repair pathway
filling in short patches (1-5 nt) in damaged DNA and removing deoxyribose
5'-phosphate from the 5'-side of damaged DNA. The backbone dynamics and the
refined solution structure of the N-terminal domain of beta-Pol have been
characterized in order to establish the potential contribution(s) of backbone
motion to the DNA binding and deoxyribose 5'-phosphate lyase function of this
domain. The N-terminal domain is formed from four helices packed as two
antiparallel pairs with a 60 degrees crossing between the pairs. The RMSD of the
NMR conformers (residues 13-80) is 0.37 A for the backbone heavy atoms and 0.78
A for all heavy atoms. NMR characterization of the binding site(s) for a
ssDNA-5mer, ssDNA-8mer, ssDNA-9mer, and dsDNA-12mer shows a consensus surface
for the binding of these various DNA oligomers, that surrounds and includes the
deoxyribose 5'-phosphate lyase active site region. Connection segments between
helices 1 and 2 and between helices 3 and 4 each contribute to DNA binding.
Helix-3-turn-helix-4 forms a helix-hairpin-helix motif. The highly conserved
hairpin sequence (LPGVG) displays a significant degree of picosecond time-scale
motion within the backbone, that is possibly important for DNA binding at the
phosphodiester backbone. An Omega-loop connecting helices 1 and 2 and helix-2
itself display significant exchange contributions (R(ex)) at the backbone amides
due to apparent conformational type motion on a millisecond time-scale. This
motion is likely important in allowing the Omega-loop and helix-2 to shift
toward, and productively interact with, gapped DNA. The deoxyribose 5'-phosphate
lyase catalytic residues that include K72 which forms the Schiff's base, Y39
which is postulated to promote proton transfer to the aldehyde, and K35 which
assists in phosphate elimination, show highly restricted backbone motion. H34,
which apparently participates in detection of the abasic site hole and assists
in the opening of the hemiacetal, shows conformational exchange.
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Figure 10.
Figure 10. The hairpin turn of b-Pol and the
helix-hairpin-helix (HhH) motifs of b-Pol, AlkA and endonuclease
III. (a) An overlay of 25 superimposed structural conformers
(residues 61-66) illustrating the hydrogen bond between the
amide proton of V65 and the carbonyl oxygen atom of L62. The
distance between the amide proton and carbonyl oxygen atom
ranges from 2.64 to 2.68 Å. (b) A superimposition of the
HhH motifs of the refined N-terminal domain of DNA polymerase b
(residues 59-76), AlkA (residues 209-226) and endonuclease III
(residues 111-128). The labeled side-chains K60, K68 and K72 are
for DNA polymerase b and correspond to Q210, W218, and Y222 in
AlkA and E112, K120, and V124 in endonuclease III.
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Figure 11.
Figure 11. Comparison of refined NMR solution structure of
b-Pol to the gapped DNA b-Pol crystal structure. Ribbon overlay
for residues 13-80 of a representative structure (#1) and the
gapped DNA crystal structure of DNA polymerase b. The ribbon for
the NMR solution structure is shown in red while the crystal
structure is shown in green. Side-chains for residues H34, K35,
Y39, K60, K68 and K72 which have been shown to be important for
DNA binding and/or catalysis are shown in magenta for the NMR
structure and light green in the crystal structure. Gapped DNA
from the crystal structure is shown in blue.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
296,
229-253)
copyright 2000.
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Secondary reference #1
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Title
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Three-Dimensional solution structure of the n-Terminal domain of DNA polymerase beta and mapping of the ssdna interaction interface.
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Authors
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D.Liu,
R.Prasad,
S.H.Wilson,
E.F.Derose,
G.P.Mullen.
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Ref.
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Biochemistry, 1996,
35,
6188-6200.
[DOI no: ]
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PubMed id
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Secondary reference #2
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Title
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Assignments of 1h, 15n, And 13c resonances for the backbone and side chains of the n-Terminal domain of DNA polymerase beta. Determination of the secondary structure and tertiary contacts.
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Authors
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D.Liu,
E.F.Derose,
R.Prasad,
S.H.Wilson,
G.P.Mullen.
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Ref.
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Biochemistry, 1994,
33,
9537-9545.
[DOI no: ]
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PubMed id
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