1JXA | pdb_00001jxa

GLUCOSAMINE 6-PHOSPHATE SYNTHASE WITH GLUCOSE 6-PHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1JXA/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-06 Released: 2001-11-21 
• Deposition Author(s): Teplyakov, A., Obmolova, G., Badet, B., Badet-Denisot, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.280 (Depositor) 
• R-Value Work: 
  0.200 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Models: experimental

Literature

Channeling of ammonia in glucosamine-6-phosphate synthase.

Teplyakov, A., Obmolova, G., Badet, B., Badet-Denisot, M.A.

(2001) J Mol Biology 313: 1093-1102

• PubMed: 11700065 
• DOI: https://doi.org/10.1006/jmbi.2001.5094
• Primary Citation Related Structures: 
  1JXA


• PubMed Abstract: 
  

  Glucosamine-6-phosphate synthase catalyses the first and rate-limiting step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate in the presence of glutamine. The crystal structure of the Escherichia coli enzyme reveals the domain organisation of the homodimeric molecule. The 18 A hydrophobic channel sequestered from the solvent connects the glutaminase and isomerase active sites, and provides a means of ammonia transfer from glutamine to sugar phosphate. The C-terminal decapeptide sandwiched between the two domains plays a central role in the transfer. Based on the structure, a mechanism of enzyme action and self-regulation is proposed. It involves large domain movements triggered by substrate binding that lead to the formation of the channel.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Notkestr. 85, D-22603 Hamburg, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 200.97 kDa 
• Atom Count: 14,156 
• Modeled Residue Count: 1,824 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glucosamine 6-phosphate synthase	A, B, C	608	Escherichia coli	Mutation(s): 0  EC: 2.6.1.16
UniProt
Find proteins for P17169 (Escherichia coli (strain K12)) Explore P17169  Go to UniProtKB:  P17169

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6Q	D [auth A], E [auth B]	GLUCOSE-6-PHOSPHATE C6 H13 O9 P VFRROHXSMXFLSN-SLPGGIOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.280 (Depositor) 
• R-Value Work:  0.200 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.4	α = 90
b = 112.4	β = 96.4
c = 185.1	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-11-21 
Deposition Author(s): Teplyakov, A., Obmolova, G., Badet, B., Badet-Denisot, M.A.

Revision History  

• Version 1.0: 2001-11-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-10-03
  Changes: Data collection
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary