3w5n
Crystal Structure of Streptomyces avermitilis alpha-L-rhamnosidase complexed with L-rhamnose
Structural highlights
FunctionRHA78_STRAW Alpha-L-rhamnosidase which is able to degrade p-nitrophenyl-alpha-L-rhamnopyranoside (PNP-Rha) in vitro. Releases L-rhamnose from citrus flavonoids such as naringin, rutin and hesperidin, and the arabinogalactan-protein (AGP) gum arabic. AGPs are a family of proteoglycans that are localized on the cell surfaces of higher plants. Cleaves both the alpha-1,6 and the alpha-1,2-linked rhamnosyl residues.[1] Publication Abstract from PubMedalpha-L-rhamnosidases hydrolyze alpha-linked L-rhamnosides from oligosaccharides or polysaccharides. We determined the crystal structure of the glycoside hydrolase family 78 Streptomyces avermitilis alpha-L-rhamnosidase (SaRha78A) in its free and L-rhamnose complexed forms, which revealed the presence of six domains N, D, E, F, A, and C. In the ligand complex, L-rhamnose was bound in the proposed active site of the catalytic module, revealing the likely catalytic mechanism of SaRha78A. Glu(636) is predicted to donate protons to the glycosidic oxygen, and Glu(895) is the likely catalytic general base, activating the nucleophilic water, indicating that the enzyme operates through an inverting mechanism. Replacement of Glu(636) and Glu(895) resulted in significant loss of alpha-rhamnosidase activity. Domain D also bound L-rhamnose in a calcium-dependent manner, with a KD of 135 mum. Domain D is thus a non-catalytic carbohydrate binding module (designated SaCBM67). Mutagenesis and structural data identified the amino acids in SaCBM67 that target the features of L-rhamnose that distinguishes it from the other major sugars present in plant cell walls. Inactivation of SaCBM67 caused a substantial reduction in the activity of SaRha78A against the polysaccharide composite gum arabic, but not against aryl rhamnosides, indicating that SaCBM67 contributes to enzyme function against insoluble substrates. The structure of a Streptomyces avermitilis alpha-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement.,Fujimoto Z, Jackson A, Michikawa M, Maehara T, Momma M, Henrissat B, Gilbert HJ, Kaneko S J Biol Chem. 2013 Apr 26;288(17):12376-85. doi: 10.1074/jbc.M113.460097. Epub, 2013 Mar 13. PMID:23486481[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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