5nhm | pdb_00005nhm

Crystal structure of apo xylose isomerase from Piromyces E2

spinqualitylabelsall models 5nhm, resolution 1.67Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5nhm is a 4 chain structure with sequence from Pirse. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACY, GOL, SO4 Gene: xylA (PIRSE) Activity: Xylose isomerase, with EC number 5.3.1.5 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Xylose isomerase from Piromyces sp. E2 (PirXI) can be used for equipping Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in E. coli, analyzed the metal-dependence of its catalytic properties and solved twelve crystal structures in the presence of different metals, substrates, and substrate analogs. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn2+ which was established by measuring the activation constants (Kact) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals which is determined by metal availability as well as the affinity, indicating that native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a D-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal-dependence of the isomerase activity. Metal-dependence of xylose isomerase from Piromyces sp. E2 explored by activity profiling and protein crystallography.,Lee M, Rozeboom HJ, de Waal P, de Jong R, Dudek HM, Janssen DB Biochemistry. 2017 Oct 18. doi: 10.1021/acs.biochem.7b00777. PMID:29045784 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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