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Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex.
Nat Struct Biol. 1998 Jul; 5(7):579-84.NS

Abstract

Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein-DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable affinity. The nonspecific binding requirement is in contrast to that imposed on, for example, transcription factors and implies a different structural basis for the biomolecular recognition process. To address this issue, and the mechanism for archaeal DNA packing, we determined the structure of the Sso7d protein from Sulfolobus solfataricus in complex with DNA. Sso7d binds DNA by placing a triple-stranded beta-sheet across the DNA minor groove. The protein is anchored in this position by the insertion of hydrogen bond-donating side chains into the groove and additionally stabilized by electrostatic and non-polar interactions with the DNA backbone. This structure explains how strong binding can be achieved independent of DNA sequence. Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling.

Authors+Show Affiliations

Center for Structural Biochemistry, Department of Biotechnology, The Royal Institute of Technology (KTH), Huddinge, Sweden.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

9665172

Citation

Agback, P, et al. "Architecture of Nonspecific protein-DNA Interactions in the Sso7d-DNA Complex." Nature Structural Biology, vol. 5, no. 7, 1998, pp. 579-84.
Agback P, Baumann H, Knapp S, et al. Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. Nat Struct Biol. 1998;5(7):579-84.
Agback, P., Baumann, H., Knapp, S., Ladenstein, R., & Härd, T. (1998). Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. Nature Structural Biology, 5(7), 579-84.
Agback P, et al. Architecture of Nonspecific protein-DNA Interactions in the Sso7d-DNA Complex. Nat Struct Biol. 1998;5(7):579-84. PubMed PMID: 9665172.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Architecture of nonspecific protein-DNA interactions in the Sso7d-DNA complex. AU - Agback,P, AU - Baumann,H, AU - Knapp,S, AU - Ladenstein,R, AU - Härd,T, PY - 1998/7/17/pubmed PY - 1998/7/17/medline PY - 1998/7/17/entrez SP - 579 EP - 84 JF - Nature structural biology JO - Nat Struct Biol VL - 5 IS - 7 N2 - Many biochemical processes, including DNA packing, maintenance and control, rely on non-sequence specific protein-DNA interactions. Nonspecific DNA-binding proteins have evolved to tolerate a wide range of DNA sequences, yet bind with a respectable affinity. The nonspecific binding requirement is in contrast to that imposed on, for example, transcription factors and implies a different structural basis for the biomolecular recognition process. To address this issue, and the mechanism for archaeal DNA packing, we determined the structure of the Sso7d protein from Sulfolobus solfataricus in complex with DNA. Sso7d binds DNA by placing a triple-stranded beta-sheet across the DNA minor groove. The protein is anchored in this position by the insertion of hydrogen bond-donating side chains into the groove and additionally stabilized by electrostatic and non-polar interactions with the DNA backbone. This structure explains how strong binding can be achieved independent of DNA sequence. Sso7d binding also distorts the DNA conformation and introduces significant unwinding of the helix. This effect suggests a mechanism for DNA packing in Sulfolobus based on negative DNA supercoiling. SN - 1072-8368 UR - https://www.unboundmedicine.com/medline/citation/9665172/Architecture_of_nonspecific_protein_DNA_interactions_in_the_Sso7d_DNA_complex_ L2 - https://www.lens.org/lens/search/patent/list?q=citation_id:9665172 DB - PRIME DP - Unbound Medicine ER -