PDBsum entry: 1rkn

Hydrolase

PDB id: 1rkn

Contents

Protein chain

110 a.a. *

* Residue conservation analysis

PDB id:

1rkn

Name:

Hydrolase

Title:

Solution structure of 1-110 fragment of staphylococcal nuclease with g88w mutation

Structure:

Thermonuclease. Chain: a. Fragment: residues 1-110. Synonym: staphylococcal nuclease, tnase. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

12 models

Authors:

D.S.Liu,Y.G.Feng,K.Q.Ye,L.Shan,J.F.Wang

Key ref:

T.Xie et al. (2007). Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease. Biophys J, 92, 2090-2107. PubMed id: 17172296 DOI: 10.1529/biophysj.106.092155

Date:

22-Nov-03 Release date: 07-Dec-04

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease

Seq: 231 a.a.

Struc: 110 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.31.1 - Micrococcal nuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

DOI no: 10.1529/biophysj.106.092155

Biophys J 92:2090-2107 (2007)

PubMed id: 17172296

Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease.

T.Xie, D.Liu, Y.Feng, L.Shan, J.Wang.

ABSTRACT

Folding stability and cooperativity of the three forms of 1-110 residues fragment of staphylococcal nuclease (SNase110) have been studied by various biophysical and NMR methods. Samples of G-88W- and V-66W-mutant SNase110, namely G-88W110 and V-66W110, in aqueous solution and SNase110 in 2.0 M TMAO are adopted in this study. The unfolding transitions and folded conformations of the three SNase fragments were detected by far- and near-ultraviolet circular dichroism and intrinsic tryptophan fluorescence measurements. The tertiary structures and internal motions of the fragments were determined by NMR spectroscopy. Both G-88W and V-66W single mutations as well as a small organic osmolyte (Trimethylamine N-oxide, TMAO) can fold the fragment into a native-like conformation. However, the tertiary structures of the three fragments exhibit different degrees of folding stability and compactness. G-88W110 adopts a relatively rigid structure representing a most stable native-like beta-subdomain conformation of the three fragments. V-66W110- and TMAO-stabilized SNase110 produce less compact structures having a less stable "beta-barrel" structural region. The different folding status accounts for the different backbone dynamic and urea-unfolding transition features of the three fragments. The G-20I/G-29I-mutant variants of the three fragments have provided the evidence that the folding status is correlated closely to the packing of the beta-strands in the beta-barrel of the fragments. The native-like beta-barrel structural region acts as a nonlocal nucleus for folding the fragment. The tertiary folding of the three fragments is initiated by formation of the local nucleation sites at two beta-turn regions, I-18-D-21 and Y-27-Q-30, and developed by the formation of a nonlocal nucleation site at the beta-barrel region. The formation of beta-barrel and overall structure is concerted, but the level of cooperativity is different for the three 1-110 residues SNase fragments.