3vny | pdb_00003vny

Crystal structure of beta-glucuronidase from Acidobacterium capsulatum

spinqualitylabelsall models 3vny, resolution 1.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3vny is a 1 chain structure with sequence from Acic5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, PO4 Related: 3vnz, 3vo0 Gene: ACP_2665 (ACIC5) Activity: Beta-glucuronidase, with EC number 3.2.1.31 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed We present the first structure of a glycoside hydrolase family 79 beta-glucuronidase from Acidobacterium capsulatum, both as a product complex with beta-D-glucuronic acid (GlcA) and as its trapped covalent 2-fluoroglucuronyl intermediate. This enzyme consists of a catalytic (beta/alpha)(8)-barrel domain and a beta-domain with irregular Greek key motifs that is of unknown function. The enzyme showed beta-glucuronidase activity and trace levels of beta-glucosidase and beta-xylosidase activities. In conjunction with mutagenesis studies, these structures identify the catalytic residues as Glu(173) (acid base) and Glu(287) (nucleophile), consistent with the retaining mechanism demonstrated by (1)H NMR analysis. Glu(45), Tyr(243), Tyr(292)-Gly(294), and Tyr(334) form the catalytic pocket and provide substrate discrimination. Consistent with this, the Y292A mutation, which affects the interaction between the main chains of Gln(293) and Gly(294) and the GlcA carboxyl group, resulted in significant loss of beta-glucuronidase activity while retaining the side activities at wild-type levels. Likewise, although the beta-glucuronidase activity of the Y334F mutant is ~200-fold lower (k(cat)/K(m)) than that of the wild-type enzyme, the beta-glucosidase activity is actually 3 times higher and the beta-xylosidase activity is only 2.5-fold lower than the equivalent parameters for wild type, consistent with a role for Tyr(334) in recognition of the C6 position of GlcA. The involvement of Glu(45) in discriminating against binding of the O-methyl group at the C4 position of GlcA is revealed in the fact that the E45D mutant hydrolyzes PNP-beta-GlcA approximately 300-fold slower (k(cat)/K(m)) than does the wild-type enzyme, whereas 4-O-methyl-GlcA-containing oligosaccharides are hydrolyzed only 7-fold slower. Structural and biochemical characterization of glycoside hydrolase family 79 beta-glucuronidase from Acidobacterium capsulatum.,Michikawa M, Ichinose H, Momma M, Biely P, Jongkees S, Yoshida M, Kotake T, Tsumuraya Y, Withers SG, Fujimoto Z, Kaneko S J Biol Chem. 2012 Apr 20;287(17):14069-77. Epub 2012 Feb 24. PMID:22367201 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Glucuronidase

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