3QED

The structure and function of an arabinan-specific alpha-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases

Summary for 3QED

• Entry DOI: 10.2210/pdb3qed/pdb
• Related: 3QEE 3QEF
• Descriptor: Beta-xylosidase/alpha-L-arabinfuranosidase, gly43N, SULFATE ION, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: 5-bladed beta propeller, hydrolase
• Biological source: Cellvibrio japonicus (Pseudomonas fluorescens subsp. cellulosa)
• Total number of polymer chains: 4
• Total formula weight: 147297.17

Authors

Cartmell, A.,Mckee, L.S.,Pena, M.,Larsbrink, J.,Brumer, H.,Lewis, R.J.,Viks-Nielsen, A.,Gilbert, H.J.,Marles-Wright, J. (deposition date: 2011-01-20, release date: 2011-02-16, Last modification date: 2024-10-16)

Primary citation

Cartmell, A.,McKee, L.S.,Pena, M.J.,Larsbrink, J.,Brumer, H.,Kaneko, S.,Ichinose, H.,Lewis, R.J.,Vikso-Nielsen, A.,Gilbert, H.J.,Marles-Wright, J.
The Structure and Function of an Arabinan-specific {alpha}-1,2-Arabinofuranosidase Identified from Screening the Activities of Bacterial GH43 Glycoside Hydrolases.
J.Biol.Chem., 286:15483-15495, 2011

PubMed Abstract: Reflecting the diverse chemistry of plant cell walls, microorganisms that degrade these composite structures synthesize an array of glycoside hydrolases. These enzymes are organized into sequence-, mechanism-, and structure-based families. Genomic data have shown that several organisms that degrade the plant cell wall contain a large number of genes encoding family 43 (GH43) glycoside hydrolases. Here we report the biochemical properties of the GH43 enzymes of a saprophytic soil bacterium, Cellvibrio japonicus, and a human colonic symbiont, Bacteroides thetaiotaomicron. The data show that C. japonicus uses predominantly exo-acting enzymes to degrade arabinan into arabinose, whereas B. thetaiotaomicron deploys a combination of endo- and side chain-cleaving glycoside hydrolases. Both organisms, however, utilize an arabinan-specific α-1,2-arabinofuranosidase in the degradative process, an activity that has not previously been reported. The enzyme can cleave α-1,2-arabinofuranose decorations in single or double substitutions, the latter being recalcitrant to the action of other arabinofuranosidases. The crystal structure of the C. japonicus arabinan-specific α-1,2-arabinofuranosidase, CjAbf43A, displays a five-bladed β-propeller fold. The specificity of the enzyme for arabinan is conferred by a surface cleft that is complementary to the helical backbone of the polysaccharide. The specificity of CjAbf43A for α-1,2-l-arabinofuranose side chains is conferred by a polar residue that orientates the arabinan backbone such that O2 arabinose decorations are directed into the active site pocket. A shelflike structure adjacent to the active site pocket accommodates O3 arabinose side chains, explaining how the enzyme can target O2 linkages that are components of single or double substitutions.

PubMed: 21339299
DOI: 10.1074/jbc.M110.215962

Experimental method

X-RAY DIFFRACTION (2.99 Å)