1dk2: Difference between revisions

Revision as of 13:17, 21 February 2008

REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA

OverviewOverview

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.

About this StructureAbout this Structure

1DK2 is a Single protein structure of sequence from Rattus norvegicus. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.

ReferenceReference

Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity., Maciejewski MW, Liu D, Prasad R, Wilson SH, Mullen GP, J Mol Biol. 2000 Feb 11;296(1):229-53. PMID:10656829

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OCA

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-[[Image:1dk2.jpg|left|200px]]<br /><applet load="1dk2" size="450" color="white" frame="true" align="right" spinBox="true"
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 caption="1dk2" />
 '''REFINED SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-DK2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DK2 OCA].
+DK2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DK2 OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Liu, D-J.]]
-[[Category: Maciejewski, M.W.]]
+[[Category: Maciejewski, M W.]]
-[[Category: Mullen, G.P.]]
+[[Category: Mullen, G P.]]
 [[Category: Prasad, R.]]
-[[Category: Wilson, S.H.]]
+[[Category: Wilson, S H.]]
 [[Category: deoxyribose 5'-phosphate lyase]]
 [[Category: dna-binding]]
 [[Category: nucleotidyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:20:56 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:17:24 2008''