PDBsum entry 1sap

DNA binding protein

PDB id: 1sap

Contents

Protein chain

66 a.a.

PDB id:

1sap

Name:

DNA binding protein

Title:

Hyperthermophile protein, relaxation matrix refinement structure

Structure:

Sac7d. Chain: a. Synonym: 7 kd hyperthermophile DNA-binding protein. Engineered: yes

Source:

Sulfolobus acidocaldarius. Organism_taxid: 2285. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

1 models

Authors:

S.P.Edmondson,J.W.Shriver

Key ref:

S.P.Edmondson et al. (1995). Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius. Biochemistry, 34, 13289-13304. PubMed id: 7577913

Date:

25-Apr-95 Release date: 15-Sep-95

Protein chain

P13123  (DN7D_SULAC) -  DNA-binding protein 7d from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)

Seq: 66 a.a.

Struc: 66 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Biochemistry 34:13289-13304 (1995)

PubMed id: 7577913

Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius.

S.P.Edmondson, L.Qiu, J.W.Shriver.

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.