3OOJ

C1A mutant of E. coli GlmS in complex with glucose-6P and glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.220 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted G6QClick on this verticalbar to view detailsBest fitted G6PClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structural basis for morpheein-type allosteric regulation of Escherichia coli glucosamine-6-phosphate synthase: equilibrium between inactive hexamer and active dimer.

Mouilleron, S.Badet-Denisot, M.A.Pecqueur, L.Madiona, K.Assrir, N.Badet, B.Golinelli-Pimpaneau, B.

(2012) J Biol Chem 287: 34533-34546

  • DOI: https://doi.org/10.1074/jbc.M112.380378
  • Primary Citation of Related Structures:  
    3OOJ

  • PubMed Abstract: 

    The amino-terminal cysteine of glucosamine-6-phosphate synthase (GlmS) acts as a nucleophile to release and transfer ammonia from glutamine to fructose 6-phosphate through a channel. The crystal structure of the C1A mutant of Escherichia coli GlmS, solved at 2.5 Å resolution, is organized as a hexamer, where the glutaminase domains adopt an inactive conformation. Although the wild-type enzyme is active as a dimer, size exclusion chromatography, dynamic and quasi-elastic light scattering, native polyacrylamide gel electrophoresis, and ultracentrifugation data show that the dimer is in equilibrium with a hexameric state, in vitro and in cellulo. The previously determined structures of the wild-type enzyme, alone or in complex with glucosamine 6-phosphate, are also consistent with a hexameric assembly that is catalytically inactive because the ammonia channel is not formed. The shift of the equilibrium toward the hexameric form in the presence of cyclic glucosamine 6-phosphate, together with the decrease of the specific activity with increasing enzyme concentration, strongly supports product inhibition through hexamer stabilization. Altogether, our data allow us to propose a morpheein model, in which the active dimer can rearrange into a transiently stable form, which has the propensity to form an inactive hexamer. This would account for a physiologically relevant allosteric regulation of E. coli GlmS. Finally, in addition to cyclic glucose 6-phosphate bound at the active site, the hexameric organization of E. coli GlmS enables the binding of another linear sugar molecule. Targeting this sugar-binding site to stabilize the inactive hexameric state is therefore suggested for the development of specific antibacterial inhibitors.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosamine/fructose-6-phosphate aminotransferase, isomerizing
A, B, C, D, E
608Escherichia coliMutation(s): 1 
EC: 2.6.1.16
UniProt
Find proteins for P17169 (Escherichia coli (strain K12))
Explore P17169 
Go to UniProtKB:  P17169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17169
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6Q
Query on G6Q

Download Ideal Coordinates CCD File 
BA [auth E]
FA [auth F]
JA [auth G]
L [auth A]
NA [auth H]
GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
VFRROHXSMXFLSN-SLPGGIOYSA-N
G6P
Query on G6P

Download Ideal Coordinates CCD File 
DA [auth F]
HA [auth G]
J [auth A]
LA [auth H]
N [auth B]
6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
CA [auth F]
GA [auth G]
I [auth A]
KA [auth H]
M [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
IA [auth G]
K [auth A]
MA [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.220 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.599α = 90
b = 247.599β = 90
c = 630.862γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted G6QClick on this verticalbar to view detailsBest fitted G6PClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Structure summary