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| | <StructureSection load='6jnj' size='340' side='right'caption='[[6jnj]], [[Resolution|resolution]] 1.50Å' scene=''> | | <StructureSection load='6jnj' size='340' side='right'caption='[[6jnj]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jnj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29145 Atcc 29145]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jnj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JNJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">araA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 ATCC 29145])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=6jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnj OCA], [http://pdbe.org/6jnj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnj RCSB], [http://www.ebi.ac.uk/pdbsum/6jnj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnj 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=6jnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnj OCA], [https://pdbe.org/6jnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jnj RCSB], [https://www.ebi.ac.uk/pdbsum/6jnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ARAA_AZOBR ARAA_AZOBR]] Catalyzes the NAD(P)(+)-dependent conversion of L-arabinose to L-arabino-gamma-lactone. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NADP(+) to NAD(+) as electron acceptor. Displays high catalytic efficiency for both L-arabinose and D-galactose in vitro. However, the enzyme appears to be involved in the metabolism of L-arabinose but not D-galactose in vivo. To a lesser extent, is also active on D-talose and D-xylose as substrates in vitro, but not with D-arabinose, D-glucose, D-ribose, L-xylose, L-mannose, L-lyxose, and D-fructose.<ref>PMID:16326697</ref> | + | [https://www.uniprot.org/uniprot/ARAA_AZOBR ARAA_AZOBR] Catalyzes the NAD(P)(+)-dependent conversion of L-arabinose to L-arabino-gamma-lactone. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NADP(+) to NAD(+) as electron acceptor. Displays high catalytic efficiency for both L-arabinose and D-galactose in vitro. However, the enzyme appears to be involved in the metabolism of L-arabinose but not D-galactose in vivo. To a lesser extent, is also active on D-talose and D-xylose as substrates in vitro, but not with D-arabinose, D-glucose, D-ribose, L-xylose, L-mannose, L-lyxose, and D-fructose.<ref>PMID:16326697</ref> |
| | <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: Atcc 29145]] | + | [[Category: Azospirillum brasilense]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Iga, C]] | + | [[Category: Iga C]] |
| - | [[Category: Watanabe, S]] | + | [[Category: Watanabe S]] |
| - | [[Category: Watanabe, Y]] | + | [[Category: Watanabe Y]] |
| - | [[Category: Gfo/idh/moca protein family]]
| + | |
| - | [[Category: L-arabinose metabolism]]
| + | |
| - | [[Category: Nadp-dependent dehydrogenase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
Function
ARAA_AZOBR Catalyzes the NAD(P)(+)-dependent conversion of L-arabinose to L-arabino-gamma-lactone. Is involved in a degradation pathway of L-arabinose that allows A.brasilense to grow on L-arabinose as a sole carbon source. Prefers NADP(+) to NAD(+) as electron acceptor. Displays high catalytic efficiency for both L-arabinose and D-galactose in vitro. However, the enzyme appears to be involved in the metabolism of L-arabinose but not D-galactose in vivo. To a lesser extent, is also active on D-talose and D-xylose as substrates in vitro, but not with D-arabinose, D-glucose, D-ribose, L-xylose, L-mannose, L-lyxose, and D-fructose.[1]
Publication Abstract from PubMed
In Azospirillum brasilense, a gram-negative nitrogen-fixing bacterium, l-arabinose is converted to alpha-ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway, l-arabinose is oxidized to l-arabino-gamma-lactone by NAD(P)-dependent l-arabinose 1-dehydrogenase (AraDH) belonging to the glucose-fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo- and NADP-bound AraDH at 1.5 and 2.2 A resolutions, respectively. A docking model of l-arabinose and NADP-bound AraDH and structure-based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination between l-arabinose and d-xylose, the C4 epimer of l-arabinose.
Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase.,Watanabe Y, Iga C, Watanabe Y, Watanabe S FEBS Lett. 2019 May 6. doi: 10.1002/1873-3468.13424. PMID:31058311[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Watanabe S, Kodaki T, Makino K. Cloning, expression, and characterization of bacterial L-arabinose 1-dehydrogenase involved in an alternative pathway of L-arabinose metabolism. J Biol Chem. 2006 Feb 3;281(5):2612-23. Epub 2005 Dec 2. PMID:16326697 doi:http://dx.doi.org/M506477200
- ↑ Watanabe Y, Iga C, Watanabe Y, Watanabe S. Structural insights into the catalytic and substrate recognition mechanisms of bacterial l-arabinose 1-dehydrogenase. FEBS Lett. 2019 May 6. doi: 10.1002/1873-3468.13424. PMID:31058311 doi:http://dx.doi.org/10.1002/1873-3468.13424
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