2VEZ | pdb_00002vez

AfGNA1 crystal structure complexed with Acetyl-CoA and Glucose-6P gives new insights into catalysis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.219 (Depositor) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

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This is version 1.5 of the entry. See complete history. 

Literature

Glucose-6-Phosphate as a Probe for the Glucosamine- 6-Phosphate N-Acetyltransferase Michaelis Complex.

Hurtado-Guerrero, R., Raimi, O., Shepherd, S., Van Aalten, D.M.F.

(2007) FEBS Lett 581: 5597

  • DOI: https://doi.org/10.1016/j.febslet.2007.10.065
  • Primary Citation Related Structures: 
    2VEZ

  • PubMed Abstract: 

    Glucosamine-6-phosphate N-acetyltransferase (GNA1) catalyses the N-acetylation of d-glucosamine-6-phosphate (GlcN-6P), using acetyl-CoA as an acetyl donor. The product GlcNAc-6P is an intermediate in the biosynthesis UDP-GlcNAc. GNA1 is part of the GCN5-related acetyl transferase family (GNATs), which employ a wide range of acceptor substrates. GNA1 has been genetically validated as an antifungal drug target. Detailed knowledge of the Michaelis complex and trajectory towards the transition state would facilitate rational design of inhibitors of GNA1 and other GNAT enzymes. Using the pseudo-substrate glucose-6-phosphate (Glc-6P) as a probe with GNA1 crystals, we have trapped the first GNAT (pseudo-)Michaelis complex, providing direct evidence for the nucleophilic attack of the substrate amine, and giving insight into the protonation of the thiolate leaving group.

    • Organizational Affiliation: 
    • Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.

Macromolecule Content 

  • Total Structure Weight: 22.29 kDa 
  • Atom Count: 1,662 
  • Modeled Residue Count: 165 
  • Deposited Residue Count: 190 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PUTATIVE GLUCOSAMINE 6-PHOSPHATE ACETYLTRANSFERASE190Aspergillus fumigatusMutation(s): 0 
EC: 2.3.1.4
UniProt
Find proteins for Q4WCU5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
Explore Q4WCU5 
Go to UniProtKB:  Q4WCU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4WCU5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.219 (Depositor) 
  • R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.677α = 90
b = 100.541β = 90
c = 55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Advisory
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Structure summary