2rks: Difference between revisions

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==Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature==
The line below this paragraph, containing "STRUCTURE_2rks", creates the "Structure Box" on the page.
<StructureSection load='2rks' size='340' side='right'caption='[[2rks]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2rks]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKS FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
{{STRUCTURE_2rks| PDB=2rks |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rks OCA], [https://pdbe.org/2rks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rks RCSB], [https://www.ebi.ac.uk/pdbsum/2rks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rks ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/2rks_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2rks ConSurf].
<div style="clear:both"></div>


'''Crystal structure of Staphylococcal nuclease variant PHS L38K at cryogenic temperature'''
==See Also==
 
*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pK(a) values shifted by up to 5 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a) . The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pK(a) of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pK(a) of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pK(a) value of Lys-38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native-like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys-38 and Glu-122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys-38. This illustrates both the important roles of local flexibility and water penetration as determinants of pK(a) values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pK(a) calculations in reproducing these effects.
[[Category: Large Structures]]
 
==About this Structure==
2RKS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKS OCA].
 
==Reference==
A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values., Harms MJ, Schlessman JL, Chimenti MS, Sue GR, Damjanovic A, Garcia-Moreno E B, Protein Sci. 2008 Mar 27;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18369193 18369193]
[[Category: Micrococcal nuclease]]
[[Category: Single protein]]
[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
[[Category: Garcia-Moreno, E B.]]
[[Category: Garcia-Moreno EB]]
[[Category: Harms, M J.]]
[[Category: Harms MJ]]
[[Category: Schlessman, J L.]]
[[Category: Schlessman JL]]
[[Category: Hydrolase]]
[[Category: Hyperstable variant]]
[[Category: Internal ion pair]]
[[Category: Staphylococcal nuclease]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 16 23:06:12 2008''
Retrieved from "https://proteopedia.org/2rks"