2h6e: Difference between revisions

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<StructureSection load='2h6e' size='340' side='right'caption='[[2h6e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='2h6e' size='340' side='right'caption='[[2h6e]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2h6e]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H6E FirstGlance]. <br>
<table><tr><td colspan='2'>[[2h6e]] 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=2H6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H6E FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Adh-4 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-arabinose_1-dehydrogenase_(NAD(P)(+)) D-arabinose 1-dehydrogenase (NAD(P)(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.117 1.1.1.117] </span></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=2h6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h6e OCA], [https://pdbe.org/2h6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h6e RCSB], [https://www.ebi.ac.uk/pdbsum/2h6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h6e ProSAT]</span></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=2h6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h6e OCA], [https://pdbe.org/2h6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h6e RCSB], [https://www.ebi.ac.uk/pdbsum/2h6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h6e ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q97YM2_SACS2 Q97YM2_SACS2]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2h6e 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=2h6e ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Sulfolobus solfataricus metabolizes the five-carbon sugar d-arabinose to 2-oxoglutarate by an inducible pathway consisting of dehydrogenases and dehydratases. Here we report the crystal structure and biochemical properties of the first enzyme of this pathway: the d-arabinose dehydrogenase. The AraDH structure was solved to a resolution of 1.80 A by single-wavelength anomalous diffraction and phased using the two endogenous zinc ions per subunit. The structure revealed a catalytic and cofactor binding domain, typically present in mesophilic and thermophilic alcohol dehydrogenases. Cofactor modeling showed the presence of a phosphate binding pocket sequence motif (SRS-X2-H), which is likely to be responsible for the enzyme's preference for NADP+. The homo-tetrameric enzyme is specific for d-arabinose, l-fucose, l-galactose and d-ribose, which could be explained by the hydrogen bonding patterns of the C3 and C4 hydroxyl groups observed in substrate docking simulations. The enzyme optimally converts sugars at pH 8.2 and 91 degrees C, and displays a half-life of 42 and 26 min at 85 and 90 degrees C, respectively, indicating that the enzyme is thermostable at physiological operating temperatures of 80 degrees C. The structure represents the first crystal structure of an NADP+-dependent member of the medium-chain dehydrogenase/reductase (MDR) superfamily from Archaea.
Crystal structure and biochemical properties of the D-arabinose dehydrogenase from Sulfolobus solfataricus.,Brouns SJ, Turnbull AP, Willemen HL, Akerboom J, van der Oost J J Mol Biol. 2007 Aug 31;371(5):1249-60. Epub 2007 Jun 8. PMID:17610898<ref>PMID:17610898</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2h6e" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sulso]]
[[Category: Saccharolobus solfataricus P2]]
[[Category: Akerboom, J]]
[[Category: Akerboom J]]
[[Category: Brouns, S J.J]]
[[Category: Brouns SJJ]]
[[Category: Oost, J Van der]]
[[Category: De Vos WM]]
[[Category: Turnbull, A P]]
[[Category: Turnbull AP]]
[[Category: Vos, W M.De]]
[[Category: Van der Oost J]]
[[Category: Willemen, H L.D M]]
[[Category: Willemen HLDM]]
[[Category: Medium chain alcohol dehydrogenase]]
[[Category: Oxidoreductase]]
[[Category: Rossmann fold]]

Latest revision as of 09:31, 14 February 2024

Crystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus

2h6e, resolution 1.80Å

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