1U0F

Crystal structure of mouse phosphoglucose isomerase in complex with glucose 6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

The crystal structure of mouse phosphoglucose isomerase at 1.6A resolution and its complex with glucose 6-phosphate reveals the catalytic mechanism of sugar ring opening.

Graham Solomons, J.T.Zimmerly, E.M.Burns, S.Krishnamurthy, N.Swan, M.K.Krings, S.Muirhead, H.Chirgwin, J.Davies, C.

(2004) J Mol Biol 342: 847-860

  • DOI: https://doi.org/10.1016/j.jmb.2004.07.085
  • Primary Citation of Related Structures:  
    1U0E, 1U0F, 1U0G

  • PubMed Abstract: 

    Phosphoglucose isomerase (PGI) is an enzyme of glycolysis that interconverts glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P) but, outside the cell, is a multifunctional cytokine. High-resolution crystal structures of the enzyme from mouse have been determined in native form and in complex with the inhibitor erythrose 4-phosphate, and with the substrate glucose 6-phosphate. In the substrate-bound structure, the glucose sugar is observed in both straight-chain and ring forms. This structure supports a specific role for Lys518 in enzyme-catalyzed ring opening and we present a "push-pull" mechanism in which His388 breaks the O5-C1 bond by donating a proton to the ring oxygen atom and, simultaneously, Lys518 abstracts a proton from the C1 hydroxyl group. The reverse occurs in ring closure. The transition from ring form to straight-chain substrate is achieved through rotation of the C3-C4 bond, which brings the C1-C2 region into close proximity to Glu357, the base catalyst for the isomerization step. The structure with G6P also explains the specificity of PGI for glucose 6-phosphate over mannose 6-isomerase (M6P). To isomerize M6P to F6P requires a rotation of its C2-C3 bond but in PGI this is sterically blocked by Gln511.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate isomerase
A, B
564Mus musculusMutation(s): 0 
Gene Names: Gpi
EC: 5.3.1.9
UniProt
Find proteins for P06745 (Mus musculus)
Explore P06745 
Go to UniProtKB:  P06745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06745
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G6Q
Query on G6Q

Download Ideal Coordinates CCD File 
D [auth A]GLUCOSE-6-PHOSPHATE
C6 H13 O9 P
VFRROHXSMXFLSN-SLPGGIOYSA-N
G6P
Query on G6P

Download Ideal Coordinates CCD File 
C [auth A]6-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-DVKNGEFBSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
P [auth B]
Q [auth B]
R [auth B]
E [auth A],
F [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
W [auth B],
X [auth B],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
V [auth B]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.4α = 90
b = 116.8β = 101.6
c = 73.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Structure summary
  • Version 1.6: 2024-04-03
    Changes: Refinement description