2GL9

Crystal Structure of Glycosylasparaginase-Substrate Complex

Summary for 2GL9

• Entry DOI: 10.2210/pdb2gl9/pdb
• Descriptor: Glycosylasparaginase alpha chain, Glycosylasparaginase beta chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: glycosylasparaginase, enzyme-substrate complex, catalytic mechanism, proton-relay network, electron-pair transfer, nucleophilic attack, oxyanion hole, enzyme-acyl intermediate, ntn-hydrolase, hydrolase
• Biological source: Elizabethkingia meningoseptica; More
• Cellular location: Periplasm: Q47898 Q47898
• Total number of polymer chains: 4
• Total formula weight: 65106.03

Authors

Wang, Y.,Guo, H.C. (deposition date: 2006-04-04, release date: 2007-02-13, Last modification date: 2023-08-30)

Primary citation

Wang, Y.,Guo, H.C.
Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.
J.Mol.Biol., 366:82-92, 2007

PubMed Abstract: Glycosylasparaginase (GA) plays an important role in asparagine-linked glycoprotein degradation. A deficiency in the activity of human GA leads to a lysosomal storage disease named aspartylglycosaminuria. GA belongs to a superfamily of N-terminal nucleophile hydrolases that autoproteolytically generate their mature enzymes from inactive single chain protein precursors. The side-chain of the newly exposed N-terminal residue then acts as a nucleophile during substrate hydrolysis. By taking advantage of mutant enzyme of Flavobacterium meningosepticum GA with reduced enzymatic activity, we have obtained a crystallographic snapshot of a productive complex with its substrate (NAcGlc-Asn), at 2.0 A resolution. This complex structure provided us an excellent model for the Michaelis complex to examine the specific contacts critical for substrate binding and catalysis. Substrate binding induces a conformational change near the active site of GA. To initiate catalysis, the side-chain of the N-terminal Thr152 is polarized by the free alpha-amino group on the same residue, mediated by the side-chain hydroxyl group of Thr170. Cleavage of the amide bond is then accomplished by a nucleophilic attack at the carbonyl carbon of the amide linkage in the substrate, leading to the formation of an acyl-enzyme intermediate through a negatively charged tetrahedral transition state.

PubMed: 17157318
DOI: 10.1016/j.jmb.2006.09.051

Experimental method

X-RAY DIFFRACTION (2 Å)