A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core.


Abstract

Sso7d is a basic 7-kDa DNA-binding protein from Sulfolobus solfataricus, also endowed with ribonuclease activity. The protein consists of a double-stranded antiparallel beta-sheet, onto which an orthogonal triple-stranded antiparallel beta-sheet is packed, and of a small helical stretch at the C-terminus. Furthermore, the two beta-sheets enclose an aromatic cluster displaying a fishbone geometry. We previously cloned the Sso7d-encoding gene, expressed it in Escherichia coli, and produced several single-point mutants, either of residues located in the hydrophobic core or of Trp23, which is exposed to the solvent and plays a major role in DNA binding. The mutation F31A was dramatically destabilizing, with a loss in thermo- and piezostabilities by at least 27 K and 10 kbar, respectively. Here, we report the solution structure of the F31A mutant, which was determined by NMR spectroscopy using 744 distance constraints obtained from analysis of multidimensional spectra in conjunction with simulated annealing protocols. The most remarkable finding is the change in orientation of the Trp23 side chain, which in the wild type is completely exposed to the solvent, whereas in the mutant is largely buried in the aromatic cluster. This prevents the formation of a cavity in the hydrophobic core of the mutant, which would arise in the absence of structural rearrangements. We found additional changes produced by the mutation, notably a strong distortion in the beta-sheets with loss in several hydrogen bonds, increased flexibility of some stretches of the backbone, and some local strains. On one hand, these features may justify the dramatic destabilization provoked by the mutation; on the other hand, they highlight the crucial role of the hydrophobic core in protein stability. To the best of our knowledge, no similar rearrangement has been so far described as a result of a single-point mutation. Study holds ProTherm entries: 5897, 5898 Extra Details: 90% H2O and 10% D2O were added in the experiment DNA-binding protein; aromatic cluster; hydrophobic core;,structural rearrangement; hydrogen bond; protein stability

Submission Details

ID: m6ueuZs34

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:31 p.m.

Version: 1

Publication Details
Consonni R;Santomo L;Fusi P;Tortora P;Zetta L,Biochemistry (1999) A single-point mutation in the extreme heat- and pressure-resistant sso7d protein from sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core. PMID:10504241
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
1BBX 1998-10-14 NON-SPECIFIC PROTEIN-DNA INTERACTIONS IN THE SSO7D-DNA COMPLEX, NMR, 1 STRUCTURE
1B4O 2000-01-05 NMR STUDY OF SSO7D MUTANT (F31A) MINIMIZED AVERAGE STRUCTURE
1JIC 1998-10-14 SOLUTION NMR STRUCTURE OF RECOMBINANT SSO7D WITH RNASE ACTIVITY, MINIMIZED AVERAGE STRUCTURE
1SSO 1995-05-08 SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF A THERMOSTABLE PROTEIN FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS
2CVR 2006-08-29 NMR solution structure of sso7d mutant, K12L, 12 conformers
1C8C 2001-05-04 1.45 CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS
1BNZ 1998-11-11 2.0 SSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX
5B02 2016-03-23 2.21 Structure of the prenyltransferase MoeN5 with a fusion protein tag of Sso7d
6J8V 2019-04-17 2.23 Structure of MOEN5-SSO7D fusion protein in complex with ligand 2
5B0I 2016-03-23 2.26 Structure of MoeN5-Sso7d fusion protein in complex with beta-octyl glucoside
5GWW 2017-09-20 2.3 Structure of MoeN5-Sso7d fusion protein in complex with a permethylated substrate analogue
6J8W 2019-04-17 2.35 Structure of MOEN5-SSO7D fusion protein in complex with lig 1
5GWV 2017-09-20 2.4 Structure of MoeN5-Sso7d fusion protein in complex with a substrate analogue
5B0J 2016-03-23 2.5 Structure of MoeN5-Sso7d fusion protein in complex with beta-undecyl maltoside
5B03 2016-03-23 2.6 Structure of MoeN5-Sso7d fusion protein in complex with geranyl pyrophosphate
5B0K 2016-03-23 2.75 Structure of MoeN5-Sso7d fusion protein in complex with beta-decyl maltoside
5B0L 2016-03-23 2.8 Structure of MoeN5-Sso7d fusion protein in complex with beta-nonyl glucoside
5B0M 2016-03-23 3.05 Structure of MoeN5-Sso7d fusion protein in complex with beta-dodecyl maltoside
5U1C 2017-01-11 3.9 Structure of tetrameric HIV-1 Strand Transfer Complex Intasome

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
93.2 DNA-binding protein 7a Q96X56 DN7_SULTO
96.9 DNA-binding protein 7d O59632 DN7B_SACSH
98.4 DNA-binding protein 7a F0NJT3 DN7B_SULIH
100.0 DNA-binding protein 7a D2PHL8 DN7A_SULID
100.0 DNA-binding protein 7d P39476 DN7D_SACS2
100.0 DNA-binding protein 7a P61990 DN7A_SACSH
100.0 DNA-binding protein 7a P61991 DN7A_SACS2