2M00

Solution structure of staphylococcal nuclease E43S mutant in the presence of ssDNA and Cd2+

Summary for 2M00

• Entry DOI: 10.2210/pdb2m00/pdb
• NMR Information: BMRB: 18788
• Descriptor: Thermonuclease (1 entity in total)
• Functional Keywords: hydrolase
• Biological source: Staphylococcus aureus
• Cellular location: Secreted (By similarity): Q8NXI6
• Total number of polymer chains: 1
• Total formula weight: 16776.31

Authors

Xie, T.,Feng, Y.,Shan, L.,Wang, J. (deposition date: 2012-10-14, release date: 2013-03-06, Last modification date: 2024-05-15)

Primary citation

Xie, T.,Feng, Y.,Shan, L.,Wang, J.
Modeling of the [E43S]SNase-ssDNA-Cd(2+) complex: Structural insight into the action of nuclease on ssDNA.
Arch.Biochem.Biophys., 532:103-113, 2013

PubMed Abstract: Staphylococcal nuclease (SNase) catalyzes the hydrolysis of the phosphate backbone of DNA and RNA leaving 3'-phosphate mononucleotides and dinucleotides. SNase has been extensively used as a model protein for investigating enzymatic mechanism, thermodynamic stability, and protein folding. An unanswered question regarding enzymatic structure-function relationship is how SNase is capable of binding DNA and catalyzing the DNA hydrolysis. For understanding the mechanism of SNase-DNA interaction at the structural level, we have investigated the interactions between the E43S-mutant SNase ([E43S]SNase) and ssDNA in the presence of Cd(2+) using various NMR techniques including pulsed field gradient diffusion measurement, NMR titration and affinity measurement, chemical shift mapping, backbone dynamics, and three dimensional structural determination. [E43S]SNase retains the similar DNA-binding ability to the native SNase but loses its catalytic activity, and binding of ssDNA/Cd(2+) to [E43S]SNase induced certain degree backbone conformational exchange motion in the ssDNA and Cd(2+) binding regions, which might account for the preferential binding of DNA. Based on the NMR-derived structure of ssDNA/Cd(2+)-bound [E43S]SNase, we have built a three-dimensional model of the [E43S]SNase-ssDNA-Cd(2+) complex. The resulting model enabled the functional roles of SNase to be discussed, in particular the action of nuclease on ssDNA.

PubMed: 23416741
DOI: 10.1016/j.abb.2013.02.003

Experimental method

SOLUTION NMR