Tags

Type your tag names separated by a space and hit enter

The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study.
Biochemistry. 1999 Aug 10; 38(32):10247-55.B

Abstract

Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA.

Authors+Show Affiliations

Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale 62901-4413, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, U.S. Gov't, P.H.S.

Language

eng

PubMed ID

10441118

Citation

Krueger, J K., et al. "The Solution Structure of the Sac7d/DNA Complex: a Small-angle X-ray Scattering Study." Biochemistry, vol. 38, no. 32, 1999, pp. 10247-55.
Krueger JK, McCrary BS, Wang AH, et al. The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study. Biochemistry. 1999;38(32):10247-55.
Krueger, J. K., McCrary, B. S., Wang, A. H., Shriver, J. W., Trewhella, J., & Edmondson, S. P. (1999). The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study. Biochemistry, 38(32), 10247-55.
Krueger JK, et al. The Solution Structure of the Sac7d/DNA Complex: a Small-angle X-ray Scattering Study. Biochemistry. 1999 Aug 10;38(32):10247-55. PubMed PMID: 10441118.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The solution structure of the Sac7d/DNA complex: a small-angle X-ray scattering study. AU - Krueger,J K, AU - McCrary,B S, AU - Wang,A H, AU - Shriver,J W, AU - Trewhella,J, AU - Edmondson,S P, PY - 1999/8/11/pubmed PY - 1999/8/11/medline PY - 1999/8/11/entrez SP - 10247 EP - 55 JF - Biochemistry JO - Biochemistry VL - 38 IS - 32 N2 - Small-angle X-ray scattering has been used to study the structure of the multimeric complexes that form between double-stranded DNA and the archaeal chromatin protein Sac7d from Sulfolobus acidocaldarius. Scattering data from complexes of Sac7d with a defined 32-mer oligonucleotide, with poly[d(GC)], and with E. coli DNA indicate that the protein binds along the surface of an extended DNA structure. Molecular models of fully saturated Sac7d/DNA complexes were constructed using constraints from crystal structure and solution binding data. Conformational space was searched systematically by varying the parameters of the models within the constrained set to find the best fits between the X-ray scattering data and simulated scattering curves. The best fits were obtained for models composed of repeating segments of B-DNA with sharp kinks at contiguous protein binding sites. The results are consistent with extrapolation of the X-ray crystal structure of a 1:1 Sac7d/octanucleotide complex [Robinson, H., et al. (1998) Nature 392, 202-205] to polymeric DNA. The DNA conformation in our multimeric Sac7d/DNA model has the base pairs tilted by about 35 degrees and displaced 3 A from the helix axis. There is a large roll between two base pairs at the protein-induced kink site, resulting in an overall bending angle of about 70 degrees for Sac7d binding. Regularly repeating bends in the fully saturated complex result in a zigzag structure with negligible compaction of DNA. The Sac7d molecules in the model form a unique structure with two left-handed helical ribbons winding around the outside of the right-handed duplex DNA. SN - 0006-2960 UR - https://www.unboundmedicine.com/medline/citation/10441118/The_solution_structure_of_the_Sac7d/DNA_complex:_a_small_angle_X_ray_scattering_study_ L2 - https://doi.org/10.1021/bi990782c DB - PRIME DP - Unbound Medicine ER -