4AG7

C. elegans glucosamine-6-phosphate N-acetyltransferase (GNA1): coenzyme A adduct

• PDB DOI: https://doi.org/10.2210/pdb4AG7/pdb

• Classification: TRANSFERASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-24 Released: 2012-07-25 
• Deposition Author(s): Dorfmueller, H.C., Fang, W., Rao, F.V., Blair, D.E., Attrill, H., Shepherd, S.M., van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Structural and Biochemical Characterization of a Trapped Coenzyme a Adduct of Caenorhabditis Elegans Glucosamine-6-Phosphate N-Acetyltransferase 1.

Dorfmueller, H.C., Fang, W., Rao, F.V., Blair, D.E., Attrill, H., Van Aalten, D.M.F.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1019

• PubMed: 22868768 
• DOI: https://doi.org/10.1107/S0907444912019592
• Primary Citation of Related Structures:  
  4AG7, 4AG9


• PubMed Abstract: 
  

  Glucosamine-6-phosphate N-acetyltransferase 1 (GNA1) produces GlcNAc-6-phosphate from GlcN-6-phosphate and acetyl coenzyme A. Early mercury-labelling experiments implicated a conserved cysteine in the reaction mechanism, whereas recent structural data appear to support a mechanism in which this cysteine plays no role. Here, two crystal structures of Caenorhabditis elegans GNA1 are reported, revealing an unusual covalent complex between this cysteine and the coenzyme A product. Mass-spectrometric and reduction studies showed that this inactive covalent complex can be reactivated through reduction, yet mutagenesis of the cysteine supports a previously reported bi-bi mechanism. The data unify the apparently contradictory earlier reports on the role of a cysteine in the GNA1 active site.

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Organizational Affiliation: 

Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

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)

Macromolecule Content

• Total Structure Weight: 38.5 kDa 
• Atom Count: 3,035 
• Modelled Residue Count: 329 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOSAMINE-6-PHOSPHATE N-ACETYLTRANSFERASE	A, B	165	Caenorhabditis elegans	Mutation(s): 0  EC: 2.3.1.4
UniProt
Find proteins for Q17427 (Caenorhabditis elegans) Explore Q17427  Go to UniProtKB:  Q17427

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], D [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.072	α = 90
b = 86.072	β = 90
c = 77.285	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-25 
Deposition Author(s): Dorfmueller, H.C., Fang, W., Rao, F.V., Blair, D.E., Attrill, H., Shepherd, S.M., van Aalten, D.M.F.

Revision History  

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary