 |
PDBsum entry 1sap
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
DNA binding protein
|
PDB id
|
|
|
|
1sap
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Solution structure of the DNA-Binding protein sac7d from the hyperthermophile sulfolobus acidocaldarius.
|
|
|
Authors
|
|
S.P.Edmondson,
L.Qiu,
J.W.Shriver.
|
|
|
Ref.
|
|
Biochemistry, 1995,
34,
13289-13304.
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
|
|
|
|
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.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Noe r-Factors and structural refinement using firm, An iterative relaxation matrix program
|
|
|
Author
|
|
S.P.Edmondson.
|
|
|
Ref.
|
|
j magn reson, 1992,
98,
283.
|
|
|
|
|
|
|
|
