6PKH | pdb_00006pkh

Zebrafish N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase (NAGPA) catalytic domain auto-inhibited by pro-peptide

• PDB DOI: https://doi.org/10.2210/pdb6PKH/pdb

• Classification: HYDROLASE
• Organism(s): Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-06-29 Released: 2020-02-19 
• Deposition Author(s): Gorelik, A., Illes, K., Nagar, B.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.

Gorelik, A., Illes, K., Nagar, B.

(2020) Structure 28: 426-436.e3

• PubMed: 32109365 
• DOI: https://doi.org/10.1016/j.str.2020.02.001
• Primary Citation Related Structures: 
  6PKG, 6PKH, 6PKI, 6PKU, 6PKY, 6U11


• 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 ¹ 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.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Room 464, 3649 Promenade Sir-William-Osler, Montreal, QC H3G 0B1, Canada.
Department of Biochemistry, McGill University, Room 464, 3649 Promenade Sir-William-Osler, Montreal, QC H3G 0B1, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.53 kDa 
• Atom Count: 2,879 
• Modeled Residue Count: 307 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	A	321	Danio rerio	Mutation(s): 0  Gene Names: nagpa
UniProt
Find proteins for F1QSF9 (Danio rerio) Explore F1QSF9  Go to UniProtKB:  F1QSF9
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.954	α = 90
b = 73.954	β = 90
c = 109.288	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Gorelik, A., Illes, K., Nagar, B.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP-133535

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-03-11
  Changes: Database references
• Version 1.2: 2020-04-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary