5O9X | pdb_00005o9x

Crystal structure of Aspergillus fumigatus N-acetylphosphoglucosamine mutate S69A in complex with glucose1,6bisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Evidence for substrate-assisted catalysis inN-acetylphosphoglucosamine mutase.

Raimi, O.G.Hurtado-Guerrero, R.van Aalten, D.M.F.

(2018) Biochem J 475: 2547-2557

  • DOI: https://doi.org/10.1042/BCJ20180172
  • Primary Citation Related Structures: 
    5O9X, 5OAW

  • PubMed Abstract: 

    N -acetylphosphoglucosamine mutase (AGM1) is a key component of the hexosamine biosynthetic pathway that produces UDP-GlcNAc, an essential precursor for a wide range of glycans in eukaryotes. AGM belongs to the α-d-phosphohexomutase metalloenzyme superfamily and catalyzes the interconversion of N -acetylglucosamine-6-phosphate (GlcNAc-6P) to N -acetylglucosamine-1-phosphate (GlcNAc-1P) through N -acetylglucosamine-1,6-bisphosphate (GlcNAc-1,6-bisP) as the catalytic intermediate. Although there is an understanding of the phosphoserine-dependent catalytic mechanism at enzymatic and structural level, the identity of the requisite catalytic base in AGM1/phosphoglucomutases is as yet unknown. Here, we present crystal structures of a Michaelis complex of AGM1 with GlcNAc-6P and Mg 2+ , and a complex of the inactive Ser69Ala mutant together with glucose-1,6-bisphosphate (Glc-1,6-bisP) that represents key snapshots along the reaction co-ordinate. Together with mutagenesis, these structures reveal that the phosphate group of the hexose-1,6-bisP intermediate may act as the catalytic base.


  • Organizational Affiliation
    • Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.

Macromolecule Content 

  • Total Structure Weight: 60.51 kDa 
  • Atom Count: 4,657 
  • Modeled Residue Count: 541 
  • Deposited Residue Count: 549 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoacetylglucosamine mutase549Aspergillus lentulusMutation(s): 1 
Gene Names: ALT_8497
EC: 5.4.2.3

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.86α = 90
b = 87.574β = 90
c = 91.867γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Structure summary