From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada and.
J Biol Chem. 2013 Sep 27;288(39):28078-88. doi: 10.1074/jbc.M113.491068. Epub 2013 Aug 6.
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.
能代谢琼脂糖的细菌使用多种具有互补特异性的酶来水解琼脂糖的糖苷键,琼脂糖是一种线性聚合物,由新琼二糖(3,6-脱水-l-半乳糖-α-(1,3)-d-半乳糖)的重复二糖亚基组成,这些亚基通过β-(1,4)-键连接。在这里,我们展示了一种来自海洋微生物 Saccharophagus degradans 的糖苷水解酶家族 50 外切-β-琼脂酶 Aga50D 的晶体结构。该酶通过将琼脂糖寡聚物切割成新琼二糖产物,从而催化琼脂糖代谢的关键步骤,这些产物可以进一步加工成单体。Aga50D 的晶体结构分辨率达到 1.9 Å,揭示了一个(β/α)8-桶折叠结构,该结构通过β-夹心结构域和广泛的环进行了修饰。与未水解的新琼四糖(2.05 Å 分辨率)和新琼八糖(2.30 Å 分辨率)复合物中催化失活的 Aga50D 的结构提供了β-琼脂酶的 Michaelis 复合物的视图。在这些结构中,-1 亚基中的 d-半乳糖残基被扭曲成(1)S3 斜船构象。假定催化残基的相对定位最符合保留催化机制。此外,新琼八糖复合物表明,这种扩展的底物与β-夹心结构域有实质性相互作用,该结构域类似于碳水化合物结合模块,从而创造了额外的加号(+)亚基,并将聚合物底物通过隧道形活性位点引导。将这些结果与另一个新琼二糖产物复合物相结合的综合分析表明,Aga50D 对琼脂糖双螺旋可能具有潜在的外向作用模式。