5GKD

Structure of PL6 family alginate lyase AlyGC

Summary for 5GKD

• Entry DOI: 10.2210/pdb5gkd/pdb
• Descriptor: AlyGC, CALCIUM ION, GLYCEROL, ... (6 entities in total)
• Functional Keywords: alginate lyase, pl6, lyase
• Biological source: Glaciecola chathamensis
• Total number of polymer chains: 4
• Total formula weight: 324514.75

Authors

Zhang, Y.Z.,Wang, P.,Xu, F. (deposition date: 2016-07-04, release date: 2017-02-08, Last modification date: 2024-03-20)

Primary citation

Xu, F.,Dong, F.,Wang, P.,Cao, H.Y.,Li, C.Y.,Li, P.Y.,Pang, X.H.,Zhang, Y.Z.,Chen, X.L.
Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6
J. Biol. Chem., 292:4457-4468, 2017

PubMed Abstract: Alginate lyases that degrade alginate via a β-elimination reaction fall into seven polysaccharide lyase (PL) families. Although the structures and catalytic mechanisms of alginate lyases in the other PL families have been clarified, those in family PL6 have yet to be revealed. Here, the crystal structure of AlyGC, a PL6 alginate lyase from marine bacterium S18K6, was solved, and its catalytic mechanism was illustrated. AlyGC is a homodimeric enzyme and adopts a structure distinct from other alginate lyases. Each monomer contains a catalytic N-terminal domain and a functionally unknown C-terminal domain. A combined structural and mutational analysis using the structures of AlyGC and of an inactive mutant R241A in complex with an alginate tetrasaccharide indicates that conformational changes occur in AlyGC when a substrate is bound and that the two active centers in AlyGC may not bind substrates simultaneously. The C-terminal domain is shown to be essential for the dimerization and the catalytic activity of AlyGC. Residues Tyr, Arg, His, Arg, and Tyr in the active center are also important for the activity of AlyGC. In catalysis, Lys and Arg function as the Brønsted base and acid, respectively, and a Ca in the active center neutralizes the negative charge of the C5 carboxyl group of the substrate. Finally, based on our data, we propose a metal ion-assisted catalytic mechanism of AlyGC for alginate cleavage with a state change mode, which provides a better understanding for polysaccharide lyases and alginate degradation.

PubMed: 28154171
DOI: 10.1074/jbc.M116.766030

Experimental method

X-RAY DIFFRACTION (2.194 Å)