6jnk

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Current revision (10:38, 27 March 2024) (edit) (undo)
 
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<StructureSection load='6jnk' size='340' side='right'caption='[[6jnk]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='6jnk' size='340' side='right'caption='[[6jnk]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6jnk]] is a 4 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=6JNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6jnk]] is a 4 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=6JNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JNK FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
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<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=6jnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnk OCA], [http://pdbe.org/6jnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnk RCSB], [http://www.ebi.ac.uk/pdbsum/6jnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnk ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnk OCA], [https://pdbe.org/6jnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jnk RCSB], [https://www.ebi.ac.uk/pdbsum/6jnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[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>
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[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>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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<ref>PMID:31058311</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6jnk" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 29145]]
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[[Category: Azospirillum brasilense]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Iga, C]]
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[[Category: Iga C]]
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[[Category: Watanabe, S]]
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[[Category: Watanabe S]]
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[[Category: Watanabe, Y]]
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[[Category: Watanabe Y]]
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[[Category: Gfo/idh/moca protein family]]
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[[Category: L-arabinose metabolism]]
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[[Category: Nadp-dependent dehydrogenase]]
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[[Category: Oxidoreductase]]
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Current revision

Crystal structure of Azospirillum brasilense L-arabinose 1-dehydrogenase (NADP-bound form)

PDB ID 6jnk

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