2oxp
From Proteopedia
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|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=THP:THYMIDINE-3',5'-DIPHOSPHATE'>THP</scene> | |LIGAND= <scene name='pdbligand=THP:THYMIDINE-3',5'-DIPHOSPHATE'>THP</scene> | ||
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxp OCA], [http://www.ebi.ac.uk/pdbsum/2oxp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oxp RCSB]</span> | ||
}} | }} | ||
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[[Category: Gittis, A G.]] | [[Category: Gittis, A G.]] | ||
[[Category: Karp, D A.]] | [[Category: Karp, D A.]] | ||
| - | [[Category: | + | [[Category: nuclease]] |
| - | [[Category: | + | [[Category: staphylococcal nuclease]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:24:47 2008'' |
Revision as of 01:24, 31 March 2008
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| , resolution 2.000Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Activity: | Micrococcal nuclease, with EC number 3.1.31.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Staphylococcal Nuclease mutant V66D/P117G/H124L/S128A
Overview
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.
About this Structure
2OXP is a Single protein structure of sequence from Staphylococcus aureus. Full crystallographic information is available from OCA.
Reference
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
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