1bno
NMR SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF DNA POLYMERASE BETA, MINIMIZED AVERAGE STRUCTURE
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OverviewOverview
DNA polymerase beta (beta-Pol) consists of an N-terminal ssDNA binding, domain with deoxyribose phosphodiesterase activity and a C-terminal domain, with nucleotidyltransferase activity. The solution structure of the cloned, N-terminal domain of beta-Pol has been determined by multidimensional, heteronuclear NMR using experimental restraints that included 1030, distances based on analysis of NOE connectivities, 68 phi, chi 1, and chi, 2 torsion angles based on analysis of couplings, and 22 hydrogen bonds., Hydrogen bonds were assessed only within helices by the absence of, saturation transfer from water at pH 6.7, by NOEs and JNH alpha couplings, indicative of well-structured helices, and by 13C alpha chemical shifts, characteristic of helices. The root mean square deviation for heavy, backbone atoms within the helices was 0.64 A in 55 structures. The, solution structure of the N-terminal domain is formed from four helices, packed as two antiparallel pairs crossing at 50 degrees in a V-like shape., The domain binds p(dT)8, a template analogue, as a 1:1 complex in 100 mM, NaCl (KD = 10 microM). Analysis of the binding equilibria at increasing, NaCl concentrations indicated that ionic contacts contribute to the, complex. The binding interaction was mapped to one face of the domain by, characterizing backbone 1H and 15N chemical shift changes. Assigned, intermolecular NOEs from 2D NOESY support the assessment of the binding, interface. The structure that forms the interaction surface includes an, antiparallel helix-3-turn-helix-4 motif and residues adjacent to an, omega-type loop connecting helix-1 and helix-2. Sites appropriate for, nucleotide contact on the structure are described. The mapped interaction, interface for a ssDNA template is the first described for a DNA, polymerase.
About this StructureAbout this Structure
1BNO 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
Three-dimensional solution structure of the N-terminal domain of DNA polymerase beta and mapping of the ssDNA interaction interface., Liu D, Prasad R, Wilson SH, DeRose EF, Mullen GP, Biochemistry. 1996 May 21;35(20):6188-200. PMID:8639559
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