1m3s: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1m3s.jpg|left|200px]]<br /><applet load="1m3s" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1m3s, resolution 1.95&Aring;" />
-'''Crystal structure of YckF from Bacillus subtilis'''<br />
-==Overview==
+==Crystal structure of YckF from Bacillus subtilis==
-The crystal structure of the YckF protein from Bacillus subtilis was, determined with MAD phasing and refined at 1.95A resolution. YckF forms a, tight tetramer both in crystals and in solution. Conservation of such, oligomerization in other phosphate sugar isomerases indicates that the, crystallographically observed tetramer is physiologically relevant. The, structure of YckF was compared to with its ortholog from Methanococcus, jannaschii, MJ1247. Both of these proteins have phosphate hexulose, isomerase activity, although neither of the organisms can utilize methane, or methanol as source of energy and/or carbon. Extensive sequence and, structural similarities with MJ1247 and with the isomerase domain of, glucosamine-6-phosphate synthase from Escherichia coli allowed us to group, residues contributing to substrate binding or catalysis. Few notable, differences among these structures suggest possible cooperativity of the, four active sites of the tetramer. Phylogenetic relationships between, obligatory and facultative methylotrophs along with B. subtilis and E., coli provide clues about the possible evolution of genes as they loose, their physiological importance.
+<StructureSection load='1m3s' size='340' side='right'caption='[[1m3s]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1m3s]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M3S FirstGlance]. <br>
-M3S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M3S OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#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=1m3s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3s OCA], [https://pdbe.org/1m3s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3s RCSB], [https://www.ebi.ac.uk/pdbsum/1m3s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3s ProSAT], [https://www.topsan.org/Proteins/MCSG/1m3s TOPSAN]</span></td></tr>
-==Reference==
+</table>
-Crystal structure of Bacillus subtilis YckF: structural and functional evolution., Sanishvili R, Wu R, Kim DE, Watson JD, Collart F, Joachimiak A, J Struct Biol. 2004 Oct;148(1):98-109. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15363790 15363790]
+== Function ==
+[https://www.uniprot.org/uniprot/PHI_BACSU PHI_BACSU] Catalyzes the isomerization between 3-hexulose 6-phosphate and fructose 6-phosphate. Together with HxlA, may act as a formaldehyde detoxification system.
+== 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/m3/1m3s_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=1m3s ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Collart, F.]]
+[[Category: Collart F]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: Kim, D.E.]]
+[[Category: Kim DE]]
-[[Category: MCSG, Midwest.Center.for.Structural.Genomics.]]
+[[Category: Sanishvili R]]
-[[Category: Sanishvili, R.]]
+[[Category: Wu R]]
-[[Category: Wu, R.]]
-[[Category: mcsg]]
-[[Category: midwest center for structural genomics]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomics]]
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