Solution structure, stability, and nucleic acid binding of the hyperthermophile protein Sso10b2.


Abstract

The Sso10b (or Alba) family of proteins is a conserved group of archaeal and eukaryotic proteins which are thought to play a role in both chromatin organization and RNA metabolism. We describe here the solution structure and properties of Sso10b2 from Sulfolobus solfataricus. NMR data including residual dipolar couplings and (15)N relaxation data demonstrated that the protein adopts a beta(1)alpha(1)beta(2)alpha(2)beta(3)beta(4) topology with an IF-3-like fold. The protein dimerizes in solution at 30 degrees C via a hydrophobic surface defined by the C-terminal alpha(2)beta(3)beta(4) elements with a structure similar to one of the putative dimers indicated by previous crystal structures. DSC and circular dichroism data demonstrated an unusual two-state structural transition near the growth temperature which led to an increase in beta-sheet content without dissociation of the dimer. The cooperativity of the transition exceeded that of a dimer at pH 7, demonstrating the presence of higher order oligomers near the growth temperature at pH 7. Reverse titrations of Sso10b2 with nucleic acid showed that the protein binds single-stranded DNA (K(d) of 3 x 10(-)(7) M) with higher affinity than RNA (1.3 x 10(-)(6) M) or double-stranded DNA (1.5 x 10(-)(5) M) in 10 mM KH(2)PO(4) (pH 7.0, 20 degrees C). NMR chemical shift perturbation data indicated that single-stranded DNA and RNA binding occurred across the same dimer interface and encompassed a surface defined by the C-terminal ends of the beta(1), beta(2), and beta(3) strands of each monomer. Study holds ProTherm entries: 19546, 19547, 19548, 19549, 19550, 19551, 19552, 19553, 19554, 19555, 19556, 19557, 19558, 19559, 19560, 19561, 19562, 19563, 19564, 19565 Extra Details: Transition 1 residual dipolar couplings; hydrophobic surface; cooperativity; affinity

Submission Details

ID: GwV5yVyz

Submitter: Connie Wang

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

Version: 1

Publication Details
Biyani K;Kahsai MA;Clark AT;Armstrong TL;Edmondson SP;Shriver JW,Biochemistry (2005) Solution structure, stability, and nucleic acid binding of the hyperthermophile protein Sso10b2. PMID:16245938
Additional Information

Study Summary

Number of data points 60
Proteins DNA/RNA-binding protein Alba 2 ; DNA/RNA-binding protein Alba 2
Unique complexes 1
Assays/Quantities/Protocols Experimental Assay: dHcal pH:7.1 ; Experimental Assay: Tm pH:7.1 ; Experimental Assay: dHvH pH:7.1 ; Experimental Assay: dHcal pH:6.0, prot_conc:2.6 mg/mL ; Experimental Assay: Tm pH:6.0, prot_conc:2.6 mg/mL ; Experimental Assay: dHvH pH:6.0, prot_conc:2.6 mg/mL ; Experimental Assay: dHcal pH:6.0, prot_conc:2.0 mg/mL ; Experimental Assay: Tm pH:6.0, prot_conc:2.0 mg/mL ; Experimental Assay: dHvH pH:6.0, prot_conc:2.0 mg/mL ; Experimental Assay: dHcal pH:6.0, prot_conc:1.4 mg/mL ; Experimental Assay: Tm pH:6.0, prot_conc:1.4 mg/mL ; Experimental Assay: dHvH pH:6.0, prot_conc:1.4 mg/mL ; Experimental Assay: dHcal pH:6.0 ; Experimental Assay: Tm pH:6.0 ; Experimental Assay: dHvH pH:6.0 ; Experimental Assay: dHcal pH:6.0, prot_conc:0.5 mg/mL ; Experimental Assay: Tm pH:6.0, prot_conc:0.5 mg/mL ; Experimental Assay: dHvH pH:6.0, prot_conc:0.5 mg/mL ; Experimental Assay: dHcal pH:5.6 ; Experimental Assay: Tm pH:5.6 ; Experimental Assay: dHvH pH:5.6 ; Experimental Assay: dHcal pH:4.8 ; Experimental Assay: Tm pH:4.8 ; Experimental Assay: dHvH pH:4.8 ; Experimental Assay: dHcal pH:4.2 ; Experimental Assay: Tm pH:4.2 ; Experimental Assay: dHvH pH:4.2 ; Experimental Assay: dHcal pH:3.2 ; Experimental Assay: Tm pH:3.2 ; Experimental Assay: dHvH pH:3.2
Libraries Mutations for sequence MTEKLNEIVVRKTKNVEDHVLDVIVLFNQGIDEVILKGTGREISKAVDVYNSLKDRLGDGVQLVNVQTGSEVRDRRRISYILLRLKRVY

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
2A2Y 2005-11-08 NMR Structue of Sso10b2 from Sulfolobus solfataricus
2BKY 2005-07-14 1.7 Crystal structure of the Alba1:Alba2 heterodimer from sulfolobus solfataricus
1UDV 2003-08-05 1.85 Crystal structure of the hyperthermophilic archaeal dna-binding protein Sso10b2 at 1.85 A

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
97.8 DNA/RNA-binding protein Alba 2 P74762 ALBA2_SACSH
100.0 DNA/RNA-binding protein Alba 2 Q97ZF4 ALBA2_SACS2