2q19: 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:2q19.jpg|left|200px]]
-<!--
+==2-keto-3-deoxy-D-arabinonate dehydratase apo form==
-The line below this paragraph, containing "STRUCTURE_2q19", creates the "Structure Box" on the page.
+<StructureSection load='2q19' size='340' side='right'caption='[[2q19]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2q19]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q19 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q19 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#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=2q19 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q19 OCA], [https://pdbe.org/2q19 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q19 RCSB], [https://www.ebi.ac.uk/pdbsum/2q19 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q19 ProSAT]</span></td></tr>
-{{STRUCTURE_2q19|  PDB=2q19  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KDAD_SACS2 KDAD_SACS2] Participates in a pentose oxidation pathway that converts D-arabinonate to 2-oxoglutarate.<ref>PMID:16849334</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/q1/2q19_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=2q19 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The archaeon Sulfolobus solfataricus converts d-arabinose to 2-oxoglutarate by an enzyme set consisting of two dehydrogenases and two dehydratases. The third step of the pathway is catalyzed by a novel 2-keto-3-deoxy-D-arabinonate dehydratase (KdaD). In this study, the crystal structure of the enzyme has been solved to 2.1 A resolution. The enzyme forms an oval-shaped ring of four subunits, each consisting of an N-terminal domain with a four-stranded beta-sheet flanked by two alpha-helices, and a C-terminal catalytic domain with a fumarylacetoacetate hydrolase (FAH) fold. Crystal structures of complexes of the enzyme with magnesium or calcium ions and either a substrate analog 2-oxobutyrate, or the aldehyde enzyme product 2,5-dioxopentanoate revealed that the divalent metal ion in the active site is coordinated octahedrally by three conserved carboxylate residues, a water molecule, and both the carboxylate and the oxo groups of the substrate molecule. An enzymatic mechanism for base-catalyzed dehydration is proposed on the basis of the binding mode of the substrate to the metal ion, which suggests that the enzyme enhances the acidity of the protons alpha to the carbonyl group, facilitating their abstraction by glutamate 114. A comprehensive structural comparison of members of the FAH superfamily is presented and their evolution is discussed, providing a basis for functional investigations of this largely unexplored protein superfamily.
-'''2-keto-3-deoxy-D-arabinonate dehydratase apo form'''
+Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.,Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J J Mol Biol. 2008 May 30;379(2):357-71. Epub 2008 Apr 8. PMID:18448118<ref>PMID:18448118</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-Q19 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q19 OCA].
+<div class="pdbe-citations 2q19" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
-[[Category: Sulfolobus solfataricus]]
+<references/>
-[[Category: Akerboom, J.]]
+__TOC__
-[[Category: Barends, T.]]
+</StructureSection>
-[[Category: Brouns, S.]]
+[[Category: Large Structures]]
-[[Category: Salmon, L.]]
+[[Category: Saccharolobus solfataricus P2]]
-[[Category: Turnbull, A.]]
+[[Category: Akerboom J]]
-[[Category: Worm, P.]]
+[[Category: Barends T]]
-[[Category: Fah-family fold]]
+[[Category: Brouns S]]
-[[Category: Lyase]]
+[[Category: Salmon L]]
+[[Category: Turnbull A]]
+[[Category: Worm P]]