5bvc

Crystal structure of Lipomyces starkeyi levoglucosan kinase bound to ADP, magnesium and levoglucosan in an alternate orientation.

spinqualitylabelsall models 5bvc, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5bvc is a 1 chain structure with sequence from Lipomyces starkeyi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: 4PW, ADP, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function 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). Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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