4yh5

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==Lipomyces starkeyi levoglucosan kinase bound to ADP and Manganese==
==Lipomyces starkeyi levoglucosan kinase bound to ADP and Manganese==
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<StructureSection load='4yh5' size='340' side='right' caption='[[4yh5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='4yh5' size='340' side='right'caption='[[4yh5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4yh5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YH5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YH5 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4yh5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lipomyces_starkeyi Lipomyces starkeyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YH5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YH5 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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zfv|4zfv]]</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=4yh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh5 OCA], [http://pdbe.org/4yh5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yh5 RCSB], [http://www.ebi.ac.uk/pdbsum/4yh5 PDBsum]</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=4yh5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yh5 OCA], [https://pdbe.org/4yh5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yh5 RCSB], [https://www.ebi.ac.uk/pdbsum/4yh5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yh5 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/LGK_LIPST LGK_LIPST] Levoglucosan kinase that catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP (Ref.1, PubMed:21719279, PubMed:26354439). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom (Ref.1, PubMed:21719279, PubMed:26354439).<ref>PMID:21719279</ref> <ref>PMID:26354439</ref> <ref>PMID:21719279</ref>
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The most abundant carbohydrate product of cellulosic biomass pyrolysis is the anhydrosugar levoglucosan (1,6-anhydro-beta-D-glucopyranose), which can be converted to glucose-6-phosphate (G6P) by levoglucosan kinase (LGK). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O6 atom. Using X-ray crystallography we show that LGK binds two magnesium ions in the active site that are additionally coordinated with the nucleotide and water molecules to result in ideal octahedral coordination. To further verify the metal binding sites, we co-crystallized LGK in the presence of manganese instead of magnesium and solved the structure de novo using the anomalous signal from four manganese atoms in the dimeric structure. The first metal is required for catalysis while our work suggests the second is either required or significantly promotes the catalytic rate. Although the enzyme binds its sugar substrate in a similar orientation to the structurally related AnmK, it forms markedly fewer bonding interactions with the substrate. In this orientation, the sugar is in an optimal position to couple phosphorylation with ring cleavage. We also observed a second alternate binding orientation for levoglucosan, and in these structures ADP was found to bind with lower affinity. These combined observations provide an explanation for the high Km of LGK for levoglucosan. Greater knowledge of the factors that contribute to the catalytic efficiency of LGK can be used to improve applications of this enzyme for levoglucosan-derived biofuel production.
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Producing glucose-6-phosphate from cellulosic biomass: structural insights into levoglucosan bioconversion.,Bacik JP, Klesmith JR, Whitehead TA, Jarboe LR, Unkefer CJ, Mark BL, Michalczyk R J Biol Chem. 2015 Sep 9. pii: jbc.M115.674614. PMID:26354439<ref>PMID:26354439</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 4yh5" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacik, J P]]
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[[Category: Large Structures]]
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[[Category: Atp-binding]]
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[[Category: Lipomyces starkeyi]]
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[[Category: Carbohydrate metabolism]]
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[[Category: Bacik JP]]
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[[Category: Sugar kinase]]
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[[Category: Transferase]]
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Current revision

Lipomyces starkeyi levoglucosan kinase bound to ADP and Manganese

PDB ID 4yh5

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