6PKI

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain (C56S C230S) in complex with N-acetyl-alpha-D-glucosamine (alpha-GlcNAc) and mannose 6-phosphate (M6P)

Summary for 6PKI

• Entry DOI: 10.2210/pdb6pki/pdb
• Descriptor: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-alpha-D-glucopyranose, ... (7 entities in total)
• Functional Keywords: uncovering enzyme, mannose 6-phosphate, glycosidase, n-acetylglucosamine, hydrolase
• Biological source: Danio rerio (Zebrafish)
• Total number of polymer chains: 4
• Total formula weight: 140530.50

Authors

Gorelik, A.,Illes, K.,Nagar, B. (deposition date: 2019-06-29, release date: 2020-02-19, Last modification date: 2023-10-11)

Primary citation

Gorelik, A.,Illes, K.,Nagar, B.
Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.
Structure, 28:426-436.e3, 2020

PubMed Abstract: Most lysosomal hydrolytic enzymes reach their destination via the mannose-6-phosphate (M6P) pathway. The enzyme N-acetylglucosamine-1-phosphodiester α-N-acetylglucosaminidase (NAGPA, or "uncovering enzyme") catalyzes the second step in the M6P tag formation, namely the removal of the masking N-acetylglucosamine (GlcNAc) portion. Defects in this protein are associated with non-syndromic stuttering. To gain a better understanding of the function and regulation of this enzyme, we determined its crystal structure. The propeptide binds in a groove on the globular catalytic domain, blocking active site access. High-affinity substrate binding is enabled by a conformational switch in an active site loop. The protein recognizes the GlcNAc and phosphate portions of its substrate, but not the mannose moiety of the glycan. Based on enzymatic and H-NMR analysis, a catalytic mechanism is proposed. Crystallographic and solution scattering analyses suggest that the C-terminal domain forms a long flexible stem that extends the enzyme away from the Golgi membrane.

PubMed: 32109365
DOI: 10.1016/j.str.2020.02.001

Experimental method

X-RAY DIFFRACTION (2.293 Å)