1SAP

HYPERTHERMOPHILE PROTEIN, RELAXATION MATRIX REFINEMENT STRUCTURE

Summary for 1SAP

• Entry DOI: 10.2210/pdb1sap/pdb
• NMR Information: BMRB: 5905,5908
• Descriptor: SAC7D (1 entity in total)
• Functional Keywords: dna-binding protein, dna binding protein
• Biological source: Sulfolobus acidocaldarius
• Cellular location: Cytoplasm : P13123
• Total number of polymer chains: 1
• Total formula weight: 7626.91

Authors

Edmondson, S.P.,Shriver, J.W. (deposition date: 1995-04-25, release date: 1995-09-15, Last modification date: 2024-05-01)

Primary citation

Edmondson, S.P.,Qiu, L.,Shriver, J.W.
Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius.
Biochemistry, 34:13289-13304, 1995

PubMed Abstract: The Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius are a heterogeneous mixture of small, thermostable, nonspecific DNA-binding proteins. One of these proteins, Sac7d, has been overexpressed in Escherichia coli to provide a homogeneous preparation for structure, stability, and function studies. We present here essentially complete sequence-specific 1H NMR assignments for Sac7d, a delineation of secondary structural elements, and the high-resolution solution structure obtained from a full relaxation matrix refinement. The final structure provides an excellent fit to the NMR data with an NOE R-factor of 0.27 for backbone NOEs. The structure has a compact globular fold with 82% of the sequence involved in regular secondary structure: an antiparallel two-stranded beta-ribbon with a tight turn, followed by a short 3(10) helix, an antiparallel three-stranded beta-sheet, another short 3(10) helix, and finally four turns of alpha-helix. The amphipathic alpha-helix packs across the hydrophobic face of the three-stranded beta-sheet in an open-faced sandwich arrangement with at least one turn of the helix exposed beyond the sheet. The hydrophobic face of the beta-ribbon packs against a corner of the twisted beta-sheet. The single tryptophan responsible for the 88% fluorescence quenching upon DNA binding is exposed on the surface of the three-stranded beta-sheet. Lysines 5 and 7, whose monomethylation may be associated with enhanced thermostability, are highly solvent exposed along the inner edge of the two-stranded ribbon. The structure of Sac7d differs in many respects from that reported for the homologous native Sso7d [Baumann et al. (1994) Nature Struct. Biol. 1, 808] with a backbone RMSD greater than 3.0 A, largely due to the packing and length of the C-terminal alpha-helix which may be important in Sac7d DNA binding.

PubMed: 7577913
DOI: 10.1021/bi00041a004

Experimental method

SOLUTION NMR