6a3f
From Proteopedia
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<StructureSection load='6a3f' size='340' side='right' caption='[[6a3f]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='6a3f' size='340' side='right' caption='[[6a3f]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6a3f]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A3F FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6a3f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_phenanthrenivorans Arthrobacter phenanthrenivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A3F FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Asphe3_10730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=930171 Arthrobacter phenanthrenivorans])</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=6a3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a3f OCA], [http://pdbe.org/6a3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a3f RCSB], [http://www.ebi.ac.uk/pdbsum/6a3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a3f 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=6a3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a3f OCA], [http://pdbe.org/6a3f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a3f RCSB], [http://www.ebi.ac.uk/pdbsum/6a3f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a3f ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| - | + | Levoglucosan is the 1,6-anhydrosugar of D-glucose formed by pyrolysis of glucans and is found in the environment and industrial waste. Two types of microbial levoglucosan metabolic pathways are known. Although the eukaryotic pathway involving levoglucosan kinase has been well studied, the bacterial pathway involving levoglucosan dehydrogenase (LGDH) has not been well investigated. Here, we identified and cloned the lgdh gene from the bacterium Pseudarthrobacter phenanthrenivorans and characterized the recombinant protein. The enzyme exhibited high substrate specificity toward levoglucosan and NAD(+) for the oxidative reaction and was confirmed to be LGDH. LGDH also showed weak activities (~4%) toward L-sorbose and 1,5-anhydro-D-glucitol. The reverse (reductive) reaction using 3-keto levoglucosan and NADH exhibited significantly lower Km and higher kcat values than those of the forward reaction. The crystal structures of LGDH in the apo and complex forms with NADH, NADH + levoglucosan, and NADH + L-sorbose revealed that LGDH has a typical fold of Gfo/Idh/MocA family proteins, similar to those of scyllo-inositol dehydrogenase, aldose-aldose oxidoreductase, 1,5-anhydro-D-fructose reductase, and glucose-fructose oxidoreductase. The crystal structures also disclosed that the active site of LGDH is distinct from those of these enzymes. The LGDH active site extensively recognized the levoglucosan molecule with six hydrogen bonds, and the C3 atom of levoglucosan was closely located to the C4 atom of NADH nicotinamide. Our study is the first molecular characterization of LGDH, providing evidence for C3-specific oxidation, and representing a starting point for future biotechnological use of LGDH and levoglucosan-metabolizing bacteria. | |
| - | + | Identification, functional characterization, and crystal structure determination of bacterial levoglucosan dehydrogenase.,Sugiura M, Nakahara M, Yamada C, Arakawa T, Kitaoka M, Fushinobu S J Biol Chem. 2018 Sep 17. pii: RA118.004963. doi: 10.1074/jbc.RA118.004963. PMID:30224354<ref>PMID:30224354</ref> | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Arthrobacter phenanthrenivorans]] | ||
[[Category: Arakawa, T]] | [[Category: Arakawa, T]] | ||
[[Category: Fushinobu, S]] | [[Category: Fushinobu, S]] | ||
Revision as of 08:38, 3 October 2018
Levoglucosan dehydrogenase, apo form
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