1MOS

ISOMERASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH 2-AMINO-2-DEOXYGLUCITOL 6-PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Observed: 0.244 

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This is version 1.2 of the entry. See complete history


Literature

The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.

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

(1999) Protein Sci 8: 596-602

  • DOI: 10.1110/ps.8.3.596
  • Primary Citation of Related Structures:  
    1MOR, 1MOS

  • PubMed Abstract: 
  • Glucosamine 6-phosphate synthase converts fructose-6P into glucosamine-6P or glucose-6P depending on the presence or absence of glutamine. The isomerase activity is associated with a 40-kDa C-terminal domain, which has already been characterized crystallographically ...

    Glucosamine 6-phosphate synthase converts fructose-6P into glucosamine-6P or glucose-6P depending on the presence or absence of glutamine. The isomerase activity is associated with a 40-kDa C-terminal domain, which has already been characterized crystallographically. Now the three-dimensional structures of the complexes with the reaction product glucose-6P and with the transition state analog 2-amino-2-deoxyglucitol-6P have been determined. Glucose-6P binds in a cyclic form whereas 2-amino-2-deoxyglucitol-6P is in an extended conformation. The information on ligand-protein interactions observed in the crystal structures together with the isotope exchange and site-directed mutagenesis data allow us to propose a mechanism of the isomerase activity of glucosamine-6P synthase. The sugar phosphate isomerization involves a ring opening step catalyzed by His504 and an enolization step with Glu488 catalyzing the hydrogen transfer from C1 to C2 of the substrate. The enediol intermediate is stabilized by a helix dipole and the epsilon-amino group of Lys603. Lys485 may play a role in deprotonating the hydroxyl O1 of the intermediate.


    Related Citations: 
    • Involvement of the C Terminus in Intramolecular Nitrogen Channeling in Glucosamine 6-Phosphate Synthase: Evidence from a 1.6 A Crystal Structure of the Isomerase Domain
      Teplyakov, A., Obmolova, G., Badet-Denisot, M.A., Badet, B., Polikarpov, I.
      (1998) Structure 6: 1047
    • Erratum. Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase
      Isupov, M.N., Obmolova, G., Butterworth, S., Badet-Denisot, M.A., Badet, B., Polikarpov, I., Littlechild, J.A., Teplyakov, A.
      (1997) Structure 5: 723
    • Substrate Binding is Required for Assembly of the Active Conformation of the Catalytic Site in Ntn Amidotransferases: Evidence from the 1.8 A Crystal Structure of the Glutaminase Domain of Glucosamine 6-Phosphate Synthase
      Isupov, M.N., Obmolova, G., Butterworth, S., Badet-Denisot, M.A., Badet, B., Polikarpov, I., Littlechild, J.A., Teplyakov, A.
      (1996) Structure 4: 801
    • Crystallization and Preliminary X-Ray Analysis of the Two Domains of Glucosamine-6-Phosphate Synthase from Escherichia Coli
      Obmolova, G., Badet-Denisot, M.A., Badet, B., Teplyakov, A.
      (1994) J Mol Biol 242: 703

    Organizational Affiliation

    Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. alext@gm-mv.niddk.nih.gov



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSAMINE 6-PHOSPHATE SYNTHASEA368Escherichia coliMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGP
Query on AGP

Download Ideal Coordinates CCD File 
F [auth A]2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
C6 H16 N O8 P
LBNVXZROMBUNNQ-SLPGGIOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.287 
  • R-Value Observed: 0.244 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.9α = 90
b = 143.9β = 90
c = 172.8γ = 120
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance