1s3p: Difference between revisions

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-[[Image:1s3p.jpg|left|200px]]<br /><applet load="1s3p" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1s3p, resolution 2.00&Aring;" />
-'''Crystal structure of rat alpha-parvalbumin S55D/E59D mutant'''<br />
-==Overview==
+==Crystal structure of rat alpha-parvalbumin S55D/E59D mutant==
-In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs, containing four carboxylates positioned on the +x and -x and +z and -z, axes; introduction of a fifth carboxylate ligand reduces the affinity., However, in rat beta-parvalbumin, replacement of Ser-55 with aspartate, heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry, 35, 5856-5869]. The corresponding alpha-parvalbumin variant (S55D/E59D), likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal., Biochem. 319, 216-233]. To determine whether these mutations produce a, variation on the archetypal EF-hand coordination scheme, we have obtained, high-resolution X-ray crystallographic data for alpha S55D/E59D. As, anticipated, the aspartyl carboxylate replaces the serine hydroxyl at the, +z coordination position. Interestingly, the Asp-59 carboxylate abandons, the role it plays as an outer sphere ligand in wild-type rat beta, rotating away from the Ca2+ and, instead, forming a hydrogen bond with the, amide of Glu-62. Superficially, the coordination sphere in the CD site of, alpha S55D/E59D resembles that in the EF site. However, the orientation of, the Asp-59 side chain is predicted to stabilize the D-helix, which may, contribute to the heightened divalent ion affinity. DSC data indicate that, the alpha S55D/E59D variant retains the capacity to bind 1 equiv of Na+., Consistent with this finding, when binding measurements are conducted in, K(+)-containing buffer, divalent ion affinity is markedly higher. In 0.15, M KCl and 0.025 M Hepes-KOH (pH 7.4) at 5 degrees C, the macroscopic Ca2+, binding constants are 1.8 x 10(10) and 2.0 x 10(9) M(-1). The, corresponding Mg2+ binding constants are 2.7 x 10(6) and 1.2 x 10(5), M(-1).
+<StructureSection load='1s3p' size='340' side='right'caption='[[1s3p]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1s3p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S3P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S3P 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1s3p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s3p OCA], [https://pdbe.org/1s3p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s3p RCSB], [https://www.ebi.ac.uk/pdbsum/1s3p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s3p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRVA_RAT PRVA_RAT] In muscle, parvalbumin is thought to be involved in relaxation after contraction. It binds two calcium ions.
+== 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/s3/1s3p_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=1s3p ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs containing four carboxylates positioned on the +x and -x and +z and -z axes; introduction of a fifth carboxylate ligand reduces the affinity. However, in rat beta-parvalbumin, replacement of Ser-55 with aspartate heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry 35, 5856-5869]. The corresponding alpha-parvalbumin variant (S55D/E59D) likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal. Biochem. 319, 216-233]. To determine whether these mutations produce a variation on the archetypal EF-hand coordination scheme, we have obtained high-resolution X-ray crystallographic data for alpha S55D/E59D. As anticipated, the aspartyl carboxylate replaces the serine hydroxyl at the +z coordination position. Interestingly, the Asp-59 carboxylate abandons the role it plays as an outer sphere ligand in wild-type rat beta, rotating away from the Ca2+ and, instead, forming a hydrogen bond with the amide of Glu-62. Superficially, the coordination sphere in the CD site of alpha S55D/E59D resembles that in the EF site. However, the orientation of the Asp-59 side chain is predicted to stabilize the D-helix, which may contribute to the heightened divalent ion affinity. DSC data indicate that the alpha S55D/E59D variant retains the capacity to bind 1 equiv of Na+. Consistent with this finding, when binding measurements are conducted in K(+)-containing buffer, divalent ion affinity is markedly higher. In 0.15 M KCl and 0.025 M Hepes-KOH (pH 7.4) at 5 degrees C, the macroscopic Ca2+ binding constants are 1.8 x 10(10) and 2.0 x 10(9) M(-1). The corresponding Mg2+ binding constants are 2.7 x 10(6) and 1.2 x 10(5) M(-1).
-==About this Structure==
+Crystal structure of a high-affinity variant of rat alpha-parvalbumin.,Lee YH, Tanner JJ, Larson JD, Henzl MT Biochemistry. 2004 Aug 10;43(31):10008-17. PMID:15287728<ref>PMID:15287728</ref>
-S3P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with CA and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S3P OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of a high-affinity variant of rat alpha-parvalbumin., Lee YH, Tanner JJ, Larson JD, Henzl MT, Biochemistry. 2004 Aug 10;43(31):10008-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15287728 15287728]
+</div>
+<div class="pdbe-citations 1s3p" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Parvalbumin|Parvalbumin]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rattus norvegicus]]
-[[Category: Single protein]]
+[[Category: Henzl MT]]
-[[Category: Henzl, M.T.]]
+[[Category: Tanner JJ]]
-[[Category: Tanner, J.J.]]
-[[Category: CA]]
-[[Category: SO4]]
-[[Category: calcium-binding protein]]
-[[Category: ef-hand]]
-[[Category: parvalbumin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:04:42 2007''