3BDC

Crystal structure of Staphylococcal nuclease variant Delta+PHS at cryogenic temperature

Summary for 3BDC

• Entry DOI: 10.2210/pdb3bdc/pdb
• Related: 2rbm 3c1e 3c1f 3d4d 3d6c 3dmu 3e5s 3eji 3ero 3erq 3evq
• Descriptor: Thermonuclease, CALCIUM ION, THYMIDINE-3',5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: staphylococcal nuclease, hyperstable variant, hydrolase, pdtp
• Biological source: Staphylococcus aureus
• Cellular location: Nuclease A: Secreted. Nuclease B: Membrane: P00644
• Total number of polymer chains: 1
• Total formula weight: 16585.73

Authors

Khangulov, V.,Schlessman, J.L.,Garcia-Moreno, B.E. (deposition date: 2007-11-14, release date: 2008-11-04, Last modification date: 2023-08-30)

Primary citation

Castaneda, C.A.,Fitch, C.A.,Majumdar, A.,Khangulov, V.,Schlessman, J.L.,Garcia-Moreno, B.E.
Molecular determinants of the pK(a) values of Asp and Glu residues in staphylococcal nuclease.
Proteins, 77:570-588, 2009

PubMed Abstract: Prior computational studies of the acid-unfolding behavior of staphylococcal nuclease (SNase) suggest that the pK(a) values of its carboxylic groups are difficult to reproduce with electrostatics calculations with continuum methods. To examine the molecular determinants of the pK(a) values of carboxylic groups in SNase, the pK(a) values of all 20 Asp and Glu residues were measured with multidimensional and multinuclear NMR spectroscopy in an acid insensitive variant of SNase. The crystal structure of the protein was obtained to describe the microenvironments of the carboxylic groups. Fourteen Asp and Glu residues titrate with relatively normal pK(a) values that are depressed by less than 1.1 units relative to the normal pK(a) of Asp and Glu in water. Only six residues have pK(a) values shifted by more than 1.5 units. Asp-21 has an unusually high pK(a) of 6.5, which is probably the result of interactions with other carboxylic groups at the active site. The most perturbed pK(a) values appear to be governed by hydrogen bonding and not by Coulomb interactions. The pK(a) values calculated with standard continuum electrostatics methods applied to static structures are more depressed than the measured values because Coulomb effects are exaggerated in the calculations. The problems persist even when the protein is treated with the dielectric constant of water. This can be interpreted to imply that structural relaxation is an important determinant of the pK(a) values; however, no major pH-sensitive conformational reorganization of the backbone was detected using NMR spectroscopy.

PubMed: 19533744
DOI: 10.1002/prot.22470

Experimental method

X-RAY DIFFRACTION (1.8 Å)