21ji | pdb_000021ji

Crystal structure of isoprimeverose-producing enzyme from Phaeoacremonium minimum

spinqualitylabelsall models 21ji, resolution 2.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 21ji is a 3 chain structure with sequence from Phaeoacremonium minimum and Rattus rattus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.8Å Ligands: ACT, BMA, CA, NAG, P6G, PG4, PGE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Isoprimeverose-producing oligoxyloglucan hydrolases (IPases), which belong to glycoside hydrolase family 3 (GH3), release isoprimeverose (alpha-d-xylopyranosyl-(1-->6)-d-glucopyranose) from the non-reducing end of xyloglucan oligosaccharides. The IPase from Phaeoacremonium minimum (PmIPase) exhibits distinctive features compared to its homologous IPase in Aspergillus oryzae, IpeA. The hydrolytic activity of A. oryzae IpeA was inhibited by galactosylation of the second xylopyranosyl residue at the nonreducing end of the substrate, whereas PmIPase was unaffected. To elucidate the structural basis of the unique features of PmIPase, its crystal structure was determined. PmIPase forms a homo-dimer, and its active site is formed by two monomers. Structural comparison with IpeA revealed that the active-site structures are highly conserved between both enzymes, but with some differences, including Phe172 at subsite -1 and Trp624 at a positive subsite in PmIPase (Met173 and Ile625 in IpeA, respectively). Trp624 is from the adjacent monomer and seems to be located at the putative binding position of the galactose residue at subsite +1. When the substrate was a mixture of XXXG, XXLG/XLXG, and XLLG, the W624I mutant showed lower specificity for XLLG than XXXG and XXLG/XLXG, although the wild-type enzyme degraded all three substrates with equal efficiency. This result indicates that Trp624 in PmIPase is involved in the recognition of the galactose residue at subsite +1. These findings provide structural insights into the characteristics and diversity of IPases that adapt to the side chain structures of xyloglucan. Structural basis for galactose side-chain recognition in isoprimeverose-producing oligoxyloglucan hydrolase from Phaeoacremonium minimum.,Nakamichi Y, Watanabe M, Yaoi K, Matsuzawa T Int J Biol Macromol. 2026 Mar 26;357:151665. doi: 10.1016/j.ijbiomac.2026.151665. PMID:41903633 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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