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| | ==Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with NADPH== | | ==Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with NADPH== |
| - | <StructureSection load='4ijr' size='340' side='right' caption='[[4ijr]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='4ijr' size='340' side='right'caption='[[4ijr]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4ijr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IJR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IJR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4ijr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IJR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IJR FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ijc|4ijc]]</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=4ijr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ijr OCA], [https://pdbe.org/4ijr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ijr RCSB], [https://www.ebi.ac.uk/pdbsum/4ijr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ijr ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARA1, YBR1127, YBR149W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-arabinose_1-dehydrogenase_(NAD(P)(+)) D-arabinose 1-dehydrogenase (NAD(P)(+))], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ijr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ijr OCA], [http://pdbe.org/4ijr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ijr RCSB], [http://www.ebi.ac.uk/pdbsum/4ijr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ijr ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ARA1_YEAST ARA1_YEAST]] Catalyzes the oxidation of D-arabinose, L-xylose, L-fucose and L-galactose in the presence of NADP(+). | + | [https://www.uniprot.org/uniprot/ARA1_YEAST ARA1_YEAST] Catalyzes the oxidation of D-arabinose, L-xylose, L-fucose and L-galactose in the presence of NADP(+). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | + | [[Category: Large Structures]] |
| - | [[Category: Guo, P C]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Hu, X Q]] | + | [[Category: Guo PC]] |
| - | [[Category: Li, W F]] | + | [[Category: Hu XQ]] |
| - | [[Category: Zhou, C Z]] | + | [[Category: Li WF]] |
| - | [[Category: Cytosol]] | + | [[Category: Zhou CZ]] |
| - | [[Category: Dehydrogenase]]
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| - | [[Category: Nadph binding]]
| + | |
| - | [[Category: Oxidoreductase]]
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| - | [[Category: Tim barrel]]
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| Structural highlights
Function
ARA1_YEAST Catalyzes the oxidation of D-arabinose, L-xylose, L-fucose and L-galactose in the presence of NADP(+).
Publication Abstract from PubMed
The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic alpha,beta-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 A resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (alpha/beta)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.
Structures of Saccharomyces cerevisiaeD-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.,Hu XQ, Guo PC, Ma JD, Li WF Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Nov;69(Pt 11):1190-5. doi:, 10.1107/S1744309113026857. Epub 2013 Oct 26. PMID:24192347[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hu XQ, Guo PC, Ma JD, Li WF. Structures of Saccharomyces cerevisiaeD-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2013 Nov;69(Pt 11):1190-5. doi:, 10.1107/S1744309113026857. Epub 2013 Oct 26. PMID:24192347 doi:http://dx.doi.org/10.1107/S1744309113026857
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