Stability and flexibility in the structure of the hyperthermophile DNA-binding protein Sac7d.


Abstract

Sac7d is a chromatin protein from the hyperthermophile Sulfolobus acidocaldarius that severely kinks duplex DNA with negligible change in protein structure. In previous work, the overall stability of Sac7d has been well-characterized with a global analysis of the linkage of folding, protonation, and anion binding. We extend that work here with NMR measurements of global stability as well as the distribution of stability and flexibility in the solution structure. Native state amide hydrogen exchange has been used to identify the most-protected core amide protons which exchange through global unfolding. The pH and temperature dependence of stability defined by native state exchange is in excellent agreement with the free energy surface determined by a linkage analysis of the dependence of folding on pH, salt, and temperature. These results confirm that the deltaC(P) obtained from a Kirchhoff analysis of DSC data (i.e., deltaH vs Tm) is incorrect, and an accurate description of the protein stability curve for Sac7d requires a measure of the thermodynamic contributions of protonation and anion binding. Amide hydrogen exchange, along with generalized order parameters determined by 15N relaxation data, demonstrates considerable variation in stability throughout the structure with some of the least stable regions occurring at the N- and C-termini. The most stable and inflexible region of the backbone occurs primarily in the DNA-binding beta-sheet which is responsible for bending DNA. Study holds ProTherm entries: 19584, 19585, 19586, 19587, 19588, 19589, 19590, 19591, 19592 Extra Details: Experiments were carried out on the amide group of W24 hyperthermophile; flexibility; anion binding; DNA-binding

Submission Details

ID: zgSPcu6a3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:51 p.m.

Version: 1

Publication Details
Kahsai MA;Martin E;Edmondson SP;Shriver JW,Biochemistry (2005) Stability and flexibility in the structure of the hyperthermophile DNA-binding protein Sac7d. PMID:16216073
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1XX8 2005-02-08 NMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein
1SAP 1995-09-15 HYPERTHERMOPHILE PROTEIN, RELAXATION MATRIX REFINEMENT STRUCTURE
1XYI 2005-02-08 1.45 Hyperthermophile chromosomal protein Sac7d double mutant Val26Ala/Met29Ala in complex with DNA GCGATCGC
4CJ2 2014-05-21 1.5 Crystal structure of HEWL in complex with affitin H4
2XIW 2011-07-13 1.5 Crystal structure of the Sac7d-derived IgG1-binder C3-C24S
1WTO 2005-02-22 1.5 Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC
1BF4 1999-11-10 1.6 CHROMOSOMAL DNA-BINDING PROTEIN SSO7D/D(GCGAACGC) COMPLEX
1WTV 2005-02-22 1.6 Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GTAATTAC
1AZP 1999-01-13 1.6 HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
4CJ1 2014-05-21 1.63 Crystal structure of CelD in complex with affitin H3
1WTQ 2005-02-22 1.7 Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GTAATTAC
1WTR 2005-02-22 1.8 Hyperthermophile chromosomal protein SAC7D single mutant M29A in complex with DNA GCGATCGC
1WTP 2005-02-22 1.9 Hyperthermophile chromosomal protein SAC7D single mutant M29F in complex with DNA GCGA(UBr)CGC
1WD0 2004-08-03 1.9 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
1AZQ 1999-01-13 1.94 HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX
1WTX 2005-02-22 2.2 Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GTAATTAC
1CA6 2000-02-23 2.2 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
1WD1 2004-08-03 2.2 Crystal structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
1CA5 2000-02-23 2.2 INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA
1WTW 2005-02-22 2.2 Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GCGATCGC
1WVL 2005-08-02 2.6 Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
92.9 DNA-binding protein 7d F4B8X5 DN7C_ACIHW
91.4 DNA-binding protein 7d F4B9I5 DN7B_ACIHW
92.3 DNA-binding protein 7d P13125 DN7E_SULAC
100.0 DNA-binding protein 7d P13123 DN7D_SULAC