1u9r: Difference between revisions

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OCA

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-[[Image:1u9r.gif|left|200px]]<br /><applet load="1u9r" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1u9r, resolution 2.10&Aring;" />
-'''Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature'''<br />
-==Overview==
+==Crystal Structure of Staphylococcal Nuclease mutant V66E/P117G/H124L/S128A at Room Temperature==
-The ionizable amino acid side chains of proteins are usually located at, the surface. However, in some proteins an ionizable group is embedded in, an apolar internal region. Such buried ionizable groups destabilize the, protein and may trigger conformational changes in response to pH, variations. Because of the prohibitive energetic cost of transferring a, charged group from water to an apolar medium, other stabilizing factors, must be invoked, such as ionization-induced water penetration or, structural changes. To examine the role of water penetration, we have, measured the 17O and 2H magnetic relaxation dispersions (MRD) for the V66E, and V66K mutants of staphylococcal nuclease, where glutamic acid and, lysine residues are buried in predominantly apolar environments. At, neutral pH, where these residues are uncharged, we find no evidence of, buried water molecules near the mutation site. This contrasts with a, previous cryogenic crystal structure of the V66E mutant, but is consistent, with the room-temperature crystal structure reported here. MRD, measurements at different pH values show that ionization of Glu-66 or, Lys-66 is not accompanied by penetration of long-lived water molecules. On, the other hand, the MRD data are consistent with a local conformational, change in response to ionization of the internal residues.
+<StructureSection load='1u9r' size='340' side='right'caption='[[1u9r]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1u9r]] 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=1U9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U9R FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1u9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u9r OCA], [https://pdbe.org/1u9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u9r RCSB], [https://www.ebi.ac.uk/pdbsum/1u9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u9r 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/u9/1u9r_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=1u9r ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-U9R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1U9R OCA].
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Stabilization of internal charges in a protein: water penetration or conformational change?, Denisov VP, Schlessman JL, Garcia-Moreno E B, Halle B, Biophys J. 2004 Dec;87(6):3982-94. Epub 2004 Sep 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15377517 15377517]
+[[Category: Large Structures]]
-[[Category: Micrococcal nuclease]]
-[[Category: Single protein]]
 [[Category: Staphylococcus aureus]]
-[[Category: Denisov, V.P.]]
+[[Category: Denisov VP]]
-[[Category: Garcia-Moreno, B.E.]]
+[[Category: Garcia-Moreno BE]]
-[[Category: Halle, B.]]
+[[Category: Halle B]]
-[[Category: Schlessman, J.L.]]
+[[Category: Schlessman JL]]
-[[Category: hyperstable variant]]
-[[Category: internal waters]]
-[[Category: nuclease]]
-[[Category: staphylococcal nuclease]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:56:55 2007''