1stb: Difference between revisions

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OCA

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-[[Image:1stb.jpg|left|200px]]<br /><applet load="1stb" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1stb, resolution 2.00&Aring;" />
-'''ACCOMMODATION OF INSERTION MUTATIONS ON THE SURFACE AND IN THE INTERIOR OF STAPHYLOCOCCAL NUCLEASE'''<br />
-==Overview==
+==ACCOMMODATION OF INSERTION MUTATIONS ON THE SURFACE AND IN THE INTERIOR OF STAPHYLOCOCCAL NUCLEASE==
-Alignment of homologous amino acid sequences reveals that insertion, mutations are fairly common in evolution. Hitherto, the structural, consequences of insertion mutations on the surface and in the interior of, proteins of known structures have received little attention. We report, here the high-resolution X-ray crystal structures of 2 site-directed, insertion mutants of staphylococcal nuclease. The structure of the first, insertion mutant, in which 2 glycine residues were inserted on the protein, surface in the amino-terminal beta-strand, has been solved to 1.70 A, resolution and refined to a crystallographic R value of 0.182. The, inserted residues are accommodated in a special 3-residue beta-bulge. A, bridging water molecule in the newly created cavity satisfies the hydrogen, bonding requirements of the beta-sheet by forming a bifurcated hydrogen, bond to 1 beta-strand, and a single hydrogen bond to the other, beta-strand. The second insertion mutant contains a single leucine residue, inserted at the end of the third beta-strand. The structure was solved to, 2.0 A resolution and refined to a final R value of 0.196. The insertion is, accommodated in a register shift that changes the conformation of the, flexible loop portion of the molecule, relaxing and widening the omega, turn. This structural alteration results in changes in position and, coordination of a bound calcium ion important for catalysis. These, structures illustrate important differences in how amino acid insertions, are accommodated: as localized bulges, and as extensive register shifts.
+<StructureSection load='1stb' size='340' side='right'caption='[[1stb]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1stb]] 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=1STB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1STB 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=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=1stb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1stb OCA], [https://pdbe.org/1stb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1stb RCSB], [https://www.ebi.ac.uk/pdbsum/1stb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1stb 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/st/1stb_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=1stb ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-STB 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=1STB OCA].
+*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease., Keefe LJ, Quirk S, Gittis A, Sondek J, Lattman EE, Protein Sci. 1994 Mar;3(3):391-401. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8019410 8019410]
+[[Category: Large Structures]]
-[[Category: Micrococcal nuclease]]
-[[Category: Single protein]]
 [[Category: Staphylococcus aureus]]
-[[Category: Gittis, A.]]
+[[Category: Gittis A]]
-[[Category: Keefe, L.J.]]
+[[Category: Keefe LJ]]
-[[Category: Lattman, E.E.]]
+[[Category: Lattman EE]]
-[[Category: Quirk, S.]]
+[[Category: Quirk S]]
-[[Category: CA]]
-[[Category: THP]]
-[[Category: hydrolase(phosphoric diester)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:38:53 2007''