1a3u: Difference between revisions

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OCA

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-[[Image:1a3u.gif|left|200px]]<br /><applet load="1a3u" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1a3u, resolution 2.05&Aring;" />
-'''STAPHYLOCOCCAL NUCLEASE, CYCLOHEXANE THIOL DISULFIDE TO V23C VARIANT'''<br />
-==Overview==
+==STAPHYLOCOCCAL NUCLEASE, CYCLOHEXANE THIOL DISULFIDE TO V23C VARIANT==
-We have determined by X-ray crystallography the structures of several, variants of staphylococcal nuclease with long flexible straight chain and, equivalent length cyclic unnatural amino acid side chains embedded in the, protein core. The terminal atoms in the straight side chains are not well, defined by the observed electron density even though they remain buried, within the protein interior. We have previously observed this behavior and, have suggested that it may arise from the addition of side-chain, vibrational and oscillational motions with each bond as a side chain grows, away from the relatively rigid protein main chain and/or the population of, multiple rotamers (Wynn R, Harkins P, Richards FM. Fox RO. 1996. Mobile, unnatural amino acid side chains in the core of staphylococcal nuclease., Protein Sci 5:1026-1031). Reduction of the number of degrees of freedom by, cyclization of a side chain would be expected to constrain these motions., These side chains are in fact well defined in the structures described, here. Over-packing of the protein core results in a 1.0 A shift of helix 1, away from the site of mutation. Additionally, we have determined the, structure of a side chain containing a single hydrogen to fluorine atom, replacement on a methyl group. A fluorine atom is intermediate in size, between methyl group and a hydrogen atom. The fluorine atom is observed in, a single position indicating it does not rotate like methyl hydrogen, atoms. This change also causes subtle differences in the packing, interactions.
+<StructureSection load='1a3u' size='340' side='right'caption='[[1a3u]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1a3u]] 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=1A3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A3U 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]] 2.05&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C6C:S-CYCLOHEXYL+THIOCYSTEINE'>C6C</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</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=1a3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a3u OCA], [https://pdbe.org/1a3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a3u RCSB], [https://www.ebi.ac.uk/pdbsum/1a3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a3u 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/a3/1a3u_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=1a3u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have determined by X-ray crystallography the structures of several variants of staphylococcal nuclease with long flexible straight chain and equivalent length cyclic unnatural amino acid side chains embedded in the protein core. The terminal atoms in the straight side chains are not well defined by the observed electron density even though they remain buried within the protein interior. We have previously observed this behavior and have suggested that it may arise from the addition of side-chain vibrational and oscillational motions with each bond as a side chain grows away from the relatively rigid protein main chain and/or the population of multiple rotamers (Wynn R, Harkins P, Richards FM. Fox RO. 1996. Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci 5:1026-1031). Reduction of the number of degrees of freedom by cyclization of a side chain would be expected to constrain these motions. These side chains are in fact well defined in the structures described here. Over-packing of the protein core results in a 1.0 A shift of helix 1 away from the site of mutation. Additionally, we have determined the structure of a side chain containing a single hydrogen to fluorine atom replacement on a methyl group. A fluorine atom is intermediate in size between methyl group and a hydrogen atom. The fluorine atom is observed in a single position indicating it does not rotate like methyl hydrogen atoms. This change also causes subtle differences in the packing interactions.
-==About this Structure==
+Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.,Wynn R, Harkins PC, Richards FM, Fox RO Protein Sci. 1997 Aug;6(8):1621-6. PMID:9260275<ref>PMID:9260275</ref>
-A3U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus] with CA and THP as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1A3U OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease., Wynn R, Harkins PC, Richards FM, Fox RO, Protein Sci. 1997 Aug;6(8):1621-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9260275 9260275]
+</div>
-[[Category: Micrococcal nuclease]]
+<div class="pdbe-citations 1a3u" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+==See Also==
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Staphylococcus aureus]]
-[[Category: Fox, R.O.]]
+[[Category: Fox RO]]
-[[Category: Harkins, P.C.]]
+[[Category: Harkins PC]]
-[[Category: Richards, F.M.]]
+[[Category: Richards FM]]
-[[Category: Wynn, R.]]
+[[Category: Wynn R]]
-[[Category: CA]]
-[[Category: THP]]
-[[Category: endonuclease]]
-[[Category: hydrolase]]
-[[Category: nuclease]]
-[[Category: unnatural amino acid]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:35:31 2007''