2nuy: Difference between revisions

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-[[Image:2nuy.gif|left|200px]]<br /><applet load="2nuy" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2nuy, resolution 2.500&Aring;" />
-'''2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate'''<br />
-==Overview==
+==2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate==
-Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present, study, the genomes of Sulfolobus species were screened for aldolases. Two, new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from, Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were, found to have biochemical properties similar to the previously, characterized S. solfataricus KDGA, including the condensation of pyruvate, and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The, crystal structure of S. acidocaldarius KDGA revealed the presence of a, novel phosphate-binding motif that allows the formation of multiple, hydrogen-bonding interactions with the acceptor substrate, and enables, high activity with glyceraldehyde 3-phosphate. Activity analyses with, unnatural substrates revealed that these three KDGAs readily accept, aldehydes with two to four carbon atoms, and that even aldoses with five, carbon atoms are accepted to some extent. Water-mediated interactions, permit binding of substrates in multiple conformations in the spacious, hydrophilic binding site, and correlate with the observed broad substrate, specificity.
+<StructureSection load='2nuy' size='340' side='right'caption='[[2nuy]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2nuy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_DSM_639 Sulfolobus acidocaldarius DSM 639]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUY 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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=2nuy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nuy OCA], [https://pdbe.org/2nuy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nuy RCSB], [https://www.ebi.ac.uk/pdbsum/2nuy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nuy ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDGA_SULAC KDGA_SULAC] Involved in the degradation of glucose and galactose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal).<ref>PMID:17176250</ref>
+== 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/nu/2nuy_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=2nuy ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-NUY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=PYR:'>PYR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/2-dehydro-3-deoxy-phosphogluconate_aldolase 2-dehydro-3-deoxy-phosphogluconate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.14 4.1.2.14] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUY OCA].
+*[[Aldolase 3D structures|Aldolase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases., Wolterink-van Loo S, van Eerde A, Siemerink MA, Akerboom J, Dijkstra BW, van der Oost J, Biochem J. 2007 May 1;403(3):421-30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17176250 17176250]
+__TOC__
-[[Category: 2-dehydro-3-deoxy-phosphogluconate aldolase]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Sulfolobus acidocaldarius]]
+[[Category: Sulfolobus acidocaldarius DSM 639]]
-[[Category: Dijkstra, B.W.]]
+[[Category: Dijkstra BW]]
-[[Category: Eerde, A.van.]]
+[[Category: Van Eerde A]]
-[[Category: MG]]
-[[Category: PYR]]
-[[Category: tim barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:59:53 2008''