7S06

Cryo-EM structure of human GlcNAc-1-phosphotransferase A2B2 subcomplex

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Cricetulus griseus
  • Mutation(s): No 

  • Deposited: 2021-08-30 Released: 2022-03-30 
  • Deposition Author(s): Li, H., Li, H.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the human GlcNAc-1-phosphotransferase alpha beta subunits reveals regulatory mechanism for lysosomal enzyme glycan phosphorylation.

Li, H.Lee, W.S.Feng, X.Bai, L.Jennings, B.C.Liu, L.Doray, B.Canfield, W.M.Kornfeld, S.Li, H.

(2022) Nat Struct Mol Biol 29: 348-356

  • DOI: https://doi.org/10.1038/s41594-022-00748-0
  • Primary Citation of Related Structures:  
    7S05, 7S06

  • PubMed Abstract: 

    Vertebrates use the mannose 6-phosphate (M6P)-recognition system to deliver lysosomal hydrolases to lysosomes. Key to this pathway is N-acetylglucosamine (GlcNAc)-1-phosphotransferase (PTase) that selectively adds GlcNAc-phosphate (P) to mannose residues of hydrolases. Human PTase is an α 2 β 2 γ 2 heterohexamer with a catalytic core and several peripheral domains that recognize and bind substrates. Here we report a cryo-EM structure of the catalytic core of human PTase and the identification of a hockey stick-like motif that controls activation of the enzyme. Movement of this motif out of the catalytic pocket is associated with a rearrangement of part of the peripheral domains that unblocks hydrolase glycan access to the catalytic site, thereby activating PTase. We propose that PTase fluctuates between inactive and active states in solution, and selective substrate binding of a lysosomal hydrolase through its protein-binding determinant to PTase locks the enzyme in the active state to permit glycan phosphorylation. This mechanism would help ensure that only N-linked glycans of lysosomal enzymes are phosphorylated.


  • Organizational Affiliation

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
A, B
1,179Homo sapiensMutation(s): 0 
Gene Names: GNPTABGNPTAKIAA1208
EC: 2.7.8.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q3T906 (Homo sapiens)
Explore Q3T906 
Go to UniProtKB:  Q3T906
PHAROS:  Q3T906
GTEx:  ENSG00000111670 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3T906
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F
2N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-03-30 
  • Deposition Author(s): Li, H., Li, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA231466

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-06
    Changes: Database references
  • Version 1.2: 2022-04-13
    Changes: Database references
  • Version 1.3: 2022-04-27
    Changes: Database references