• Home
  • Search Results
  • Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans.

Substrate recognition and hydrolysis by a family 50 exo-β-agarase, Aga50D, from the marine bacterium Saccharophagus degradans.

The Journal of biological chemistry (2013-08-08)
Benjamin Pluvinage, Jan-Hendrik Hehemann, Alisdair B Boraston
ABSTRACT

The bacteria that metabolize agarose use multiple enzymes of complementary specificities to hydrolyze the glycosidic linkages in agarose, a linear polymer comprising the repeating disaccharide subunit of neoagarobiose (3,6-anhydro-l-galactose-α-(1,3)-d-galactose) that are β-(1,4)-linked. Here we present the crystal structure of a glycoside hydrolase family 50 exo-β-agarase, Aga50D, from the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The crystal structure of Aga50D to 1.9 Å resolution reveals a (β/α)8-barrel fold that is elaborated with a β-sandwich domain and extensive loops. The structures of catalytically inactivated Aga50D in complex with non-hydrolyzed neoagarotetraose (2.05 Å resolution) and neoagarooctaose (2.30 Å resolution) provide views of Michaelis complexes for a β-agarase. In these structures, the d-galactose residue in the -1 subsite is distorted into a (1)S3 skew boat conformation. The relative positioning of the putative catalytic residues are most consistent with a retaining catalytic mechanism. Additionally, the neoagarooctaose complex showed that this extended substrate made substantial interactions with the β-sandwich domain, which resembles a carbohydrate-binding module, thus creating additional plus (+) subsites and funneling the polymeric substrate through the tunnel-shaped active site. A synthesis of these results in combination with an additional neoagarobiose product complex suggests a potential exo-processive mode of action of Aga50D on the agarose double helix.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Agarose, BioReagent, for molecular biology, low EEO
Sigma-Aldrich
Agarose, Type I, low EEO
Sigma-Aldrich
Agarose, for molecular biology
Sigma-Aldrich
Sepharose® 4B, 45-165 μm bead diameter
Sigma-Aldrich
Agarose, Low EEO
Sigma-Aldrich
Agarose, Ultra-low Gelling Temperature, molecular biology grade
Sigma-Aldrich
Agarose, Ultra-low Gelling Temperature
Sigma-Aldrich
Agarose, Medium EEO, for molecular biology
Sigma-Aldrich
Agarose, Type I-A, low EEO
Sigma-Aldrich
Agarose, High Gelling Temperature
Sigma-Aldrich
Agarose, For pulsed field electrophoresis running gel
Sigma-Aldrich
Sepharose® 6B, 6% Beaded Agarose, 45-165 μm (wet), fractionation range 10,000-1,000,000 Da (dextrans)
Sigma-Aldrich
Agarose, Type II-A, Medium EEO
Sigma-Aldrich
Agarose, Wide range, for molecular biology
Sigma-Aldrich
Agarose, Low EEO, for Immunoelectrophoresis
Sigma-Aldrich
Agarose, High EEO, for molecular biology
Sigma-Aldrich
Agarose, High EEO
Sigma-Aldrich
Agarase from Pseudomonas atlantica, lyophilized powder, ≥5,000 units/mg protein (Lowry)
Sigma-Aldrich
Agarose, BioReagent, for molecular biology, Wide range/Standard 3:1
Sigma-Aldrich
Agarose, Type IV, Special High EEO
Sigma-Aldrich
Agarose, Special High EEO

Social Media

LinkedIn icon
Twitter icon
Facebook Icon
Instagram Icon

MilliporeSigma

Research. Development. Production.

We are a leading supplier to the global Life Science industry with solutions and services for research, biotechnology development and production, and pharmaceutical drug therapy development and production.

© 2021 Merck KGaA, Darmstadt, Germany and/or its affiliates. All Rights Reserved.

Reproduction of any materials from the site is strictly forbidden without permission.