1O03

Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl transfer Reaction observed on cocrystallization with Glucose 6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The pentacovalent phosphorus intermediate of a phosphoryl transfer reaction.

Lahiri, S.D.Zhang, G.Dunaway-Mariano, D.Allen, K.N.

(2003) Science 299: 2067-2071

  • DOI: 10.1126/science.1082710
  • Primary Citation of Related Structures:  1O08
  • Also Cited By: 3FM9

  • PubMed Abstract: 
  • Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a h ...

    Enzymes provide enormous rate enhancements, unmatched by any other type of catalyst. The stabilization of high-energy states along the reaction coordinate is the crux of the catalytic power of enzymes. We report the atomic-resolution structure of a high-energy reaction intermediate stabilized in the active site of an enzyme. Crystallization of phosphorylated beta-phosphoglucomutase in the presence of the Mg(II) cofactor and either of the substrates glucose 1-phosphate or glucose 6-phosphate produced crystals of the enzyme-Mg(II)-glucose 1,6-(bis)phosphate complex, which diffracted x-rays to 1.2 and 1.4 angstroms, respectively. The structure reveals a stabilized pentacovalent phosphorane formed in the phosphoryl transfer from the C(1)O of glucose 1,6-(bis)phosphate to the nucleophilic Asp8 carboxylate.


    Organizational Affiliation

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118-2394, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
beta-phosphoglucomutase
A
221Lactococcus lactis subsp. lactis (strain IL1403)Gene Names: pgmB
EC: 5.4.2.6
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403))
Go to UniProtKB:  P71447
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
G16
Query on G16

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE
C6 H13 O12 P2
RWHOZGRAXYWRNX-VFUOTHLCSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.311α = 90.00
b = 54.173β = 90.00
c = 104.446γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance