7dfn | pdb_00007dfn

Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86 in complex with alpha-L-arabinofuranosyl xylotetraose

spinqualitylabelsall models 7dfn, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7dfn is a 4 chain structure with sequence from Streptomyces olivaceoviridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: AHR, CL, NA, XYP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A7G1MBT0_STROI Publication Abstract from PubMed Although many xylanases have been studied, many of the characteristics of xylanases toward branches in xylan remain unclear. In this study, the substrate specificity of a GH11 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn11B) was elucidated based on its three-dimensional structure. Subsite mapping suggests that SoXyn11B has seven subsites (four subsites on the - side and three subsites on the + side), and it is one longer than the GH10 xylanase from S. olivaceoviridis (SoXyn10A). SoXyn11B has no affinity for the subsites at either end of the scissile glycosidic bond, and the sugar-binding energy at subsite - 2 was the highest, followed by subsite + 2. These properties were very similar to those of SoXyn10A. In contrast, SoXyn11B produced different branched oligosaccharides from bagasse compared with those of SoXyn10A. These branched oligosaccharides were identified as O-beta-D-xylopyranosyl-(1-->4)-[O-alpha-L-arabinofuranosyl-(1-->3)]-O-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranose (Ara(3)Xyl(4)) and O-beta-D-xylopyranosyl-(1-->4)-[O-4-O-methyl-alpha-D-glucuronopyranosyl-(l-->2)]-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranosyl-(1-->4)-beta-D-xylopyranose (MeGlcA(3)Xyl(4)) by nuclear magnetic resonance (NMR) and electrospray ionization mass spectrometry (ESI-MS) and confirmed by crystal structure analysis of SoXyn11B in complex with these branched xylooligosaccharides. SoXyn11B has a beta-jerryroll fold structure, and the catalytic cleft is located on the inner beta-sheet of the fold. The ligand-binding structures revealed seven subsites of SoXyn11B. The 2- and 3-hydroxy groups of xylose at the subsites + 3, + 2, and - 3 face outwards, and an arabinose or a glucuronic acid side chain can be linked to these positions. These subsite structures appear to cause the limited substrate specificity of SoXyn11B for branched xylooligosaccharides. KEY POINTS: * Crystal structure of family 11 beta-xylanase from Streptomyces olivaceoviridis was determined. * Topology of substrate-binding cleft of family 11 beta-xylanase from Streptomyces olivaceoviridis was characterized. * Mode of action of family 11 beta-xylanase from Streptomyces olivaceoviridis for substitutions in xylan was elucidated. Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.,Fujimoto Z, Kishine N, Teramoto K, Tsutsui S, Kaneko S Appl Microbiol Biotechnol. 2021 Mar;105(5):1943-1952. doi: , 10.1007/s00253-021-11098-0. Epub 2021 Feb 10. PMID:33564921 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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