2oxp | pdb_00002oxp

Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A

spinqualitylabelsall models 2oxp, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2oxp is a 1 chain structure with sequence from Staphylococcus aureus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: THP Activity: Micrococcal nuclease, with EC number 3.1.31.1 Resources: FirstGlance, OCA, RCSB, PDBsum Function [NUC_STAAW] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond (By similarity). Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed The dielectric properties of proteins are poorly understood and difficult to describe quantitatively. This limits the accuracy of methods for structure-based calculation of electrostatic energies and pK(a) values. The pK(a) values of many internal groups report apparent protein dielectric constants of 10 or higher. These values are substantially higher than the dielectric constants of 2-4 measured experimentally with dry proteins. The structural origins of these high apparent dielectric constants are not well understood. Here we report on structural and equilibrium thermodynamic studies of the effects of pH on the V66D variant of staphylococcal nuclease. In a crystal structure of this protein the neutral side chain of Asp-66 is buried in the hydrophobic core of the protein and hydrated by internal water molecules. Asp-66 titrates with a pK(a) value near 9. A decrease in the far UV-CD signal was observed, concomitant with ionization of this aspartic acid, and consistent with the loss of 1.5 turns of alpha-helix. These data suggest that the protein dielectric constant needed to reproduce the pK(a) value of Asp-66 with continuum electrostatics calculations is high because the dielectric constant has to capture, implicitly, the energetic consequences of the structural reorganization that are not treated explicitly in continuum calculations with static structures. High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp.,Karp DA, Gittis AG, Stahley MR, Fitch CA, Stites WE, Garcia-Moreno E B Biophys J. 2007 Mar 15;92(6):2041-53. Epub 2006 Dec 15. PMID:17172297 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Staphylococcal nuclease

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