PDBsum entry 1dk2

Transferase

PDB id: 1dk2

Contents

Protein chain

86 a.a. *

* Residue conservation analysis

PDB id:

1dk2

Name:

Transferase

Title:

Refined solution structure of the n-terminal domain of DNA polymerase beta

Structure:

DNA polymerase beta. Chain: a. Fragment: n-terminal domain, residues 1-87. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

25 models

Authors:

M.W.Maciejewski,R.Prasad,D.-J.Liu,S.H.Wilson,G.P.Mullen

Key ref:

M.W.Maciejewski et al. (2000). Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity. J Mol Biol, 296, 229-253. PubMed id: 10656829 DOI: 10.1006/jmbi.1999.3455

Date:

06-Dec-99 Release date: 14-Feb-00

Protein chain

P06766  (DPOLB_RAT) -  DNA polymerase beta from Rattus norvegicus

Seq: 335 a.a.

Struc: 86 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.4.2.99.- - ?????
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 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⁺

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.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1006/jmbi.1999.3455

J Mol Biol 296:229-253 (2000)

PubMed id: 10656829

Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity.

M.W.Maciejewski, D.Liu, R.Prasad, S.H.Wilson, G.P.Mullen.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 296, 229-253) copyright 2000.

Figures were selected by an automated process.