Three-dimensional solution structure of the N-terminal domain of DNA polymerase beta and mapping of the ssDNA interaction interface

被引:51
作者
Liu, DJ
Prasad, R
Wilson, SH
DeRose, EF
Mullen, GP
机构
[1] UNIV CONNECTICUT, CTR HLTH, DEPT BIOCHEM, FARMINGTON, CT 06032 USA
[2] UNIV TEXAS, MED BRANCH, SEALY CTR MOL SCI, GALVESTON, TX 77555 USA
[3] UNIV WISCONSIN, DEPT CHEM, MILWAUKEE, WI 53201 USA
关键词
D O I
10.1021/bi952656o
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 J(NH alpha) couplings indicative of well-structured helices, and by C-13(alpha) chemical shifts characteristic of helices. The root mean square deviation for heavy backbone atoms within the helices was 0.64 Angstrom 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 (K-D = 10 mu M). 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 H-1 and N-15 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.
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收藏
页码:6188 / 6200
页数:13
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