This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2q1d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate

Structural highlights

2q1d is a 1 chain structure with sequence from Saccharolobus solfataricus P2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KDAD_SACS2 Participates in a pentose oxidation pathway that converts D-arabinonate to 2-oxoglutarate.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Brouns SJ, Walther J, Snijders AP, van de Werken HJ, Willemen HL, Worm P, de Vos MG, Andersson A, Lundgren M, Mazon HF, van den Heuvel RH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, van der Oost J. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J Biol Chem. 2006 Sep 15;281(37):27378-88. PMID:16849334 doi:10.1074/jbc.M605549200
↑ Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J. 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. J Mol Biol. 2008 May 30;379(2):357-71. Epub 2008 Apr 8. PMID:18448118 doi:10.1016/j.jmb.2008.03.064

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q1d"

@@ Line 1: / Line 1: @@
 ==2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate==
-<StructureSection load='2q1d' size='340' side='right' caption='[[2q1d]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='2q1d' size='340' side='right'caption='[[2q1d]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q1d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q1d]] 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=2Q1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2q18|2q18]], [[2q19|2q19]], [[2q1a|2q1a]], [[2q1c|2q1c]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO4:2,5-DIOXOPENTANOIC+ACID'>DO4</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">kdaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [https://pdbe.org/2q1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [https://www.ebi.ac.uk/pdbsum/2q1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1d ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1d OCA], [http://pdbe.org/2q1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q1d RCSB], [http://www.ebi.ac.uk/pdbsum/2q1d PDBsum]</span></td></tr>
 </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/q1/2q1d_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1d_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2q1d ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Sulso]]
+[[Category: Large Structures]]
-[[Category: Akerboom, J]]
+[[Category: Saccharolobus solfataricus P2]]
-[[Category: Barends, T]]
+[[Category: Akerboom J]]
-[[Category: Brouns, S]]
+[[Category: Barends T]]
-[[Category: Salmon, L]]
+[[Category: Brouns S]]
-[[Category: Turnbull, A]]
+[[Category: Salmon L]]
-[[Category: Worm, P]]
+[[Category: Turnbull A]]
-[[Category: Fah-family fold]]
+[[Category: Worm P]]
-[[Category: Lyase]]

2q1d

From Proteopedia

Current revision

2-keto-3-deoxy-D-arabinonate dehydratase complexed with magnesium and 2,5-dioxopentanoate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox