5WU7

Crystal structure of GH57-type branching enzyme from hyperthermophilic archaeon Pyrococcus horikoshii

Summary for 5WU7

• Entry DOI: 10.2210/pdb5wu7/pdb
• Descriptor: Uncharacterized protein, GLYCEROL (3 entities in total)
• Functional Keywords: enzyme, amylase, glycogen branching enzyme, hydrolase
• Biological source: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
• Total number of polymer chains: 2
• Total formula weight: 134061.20

Authors

Na, S.,Jo, I.,Ha, N.-C. (deposition date: 2016-12-16, release date: 2017-03-08, Last modification date: 2023-11-08)

Primary citation

Na, S.,Park, M.,Jo, I.,Cha, J.,Ha, N.C.
Structural basis for the transglycosylase activity of a GH57-type glycogen branching enzyme from Pyrococcus horikoshii.
Biochem. Biophys. Res. Commun., 484:850-856, 2017

PubMed Abstract: Glycogen branching enzyme (GBE) catalyzes the formation of α-1,6-branching points during glycogenesis by cleaving α-1,4 bonds and making new α-1,6 bonds. Most GBEs belong to the glycoside hydrolase 13 family (GH13), but new GBEs in the GH57 family have been isolated from Archaea. Here, we determined the crystal structure of a GH57 GBE from the hyperthermophilic archaeon Pyrococcus horikoshii (PhGBE) at a resolution of 2.3 Å. PhGBE exhibits both α-1,6-branching activity and endo-α-1,4 hydrolytic activity. PhGBE has a central (β/α)-barrel domain that contains an embedded helix domain and an α-helix-rich C-terminal domain. The active-site cleft is located at the interface of the central and C-terminal domains. Amino acid substitution at Trp22, which is separate from the catalytic nucleophilic residue, abolished both enzymatic activities, indicating that Trp22 might be responsible for substrate recognition. We also observed that shortening of the flexible loop near the catalytic residue changed branched chain lengths of the reaction products with increased hydrolytic activity. Taken together, our findings propose a molecular mechanism for how GH57 GBEs exhibit the two activities and where the substrate binds the enzyme.

PubMed: 28163025
DOI: 10.1016/j.bbrc.2017.02.002

Experimental method

X-RAY DIFFRACTION (2.31 Å)