1O08 | pdb_00001o08

Structure of Pentavalent Phosphorous Intermediate of an Enzyme Catalyzed Phosphoryl transfer Reaction observed on cocrystallization with Glucose 1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb1O08/pdb

• Classification: ISOMERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-02-20 Released: 2003-03-18 
• Deposition Author(s): Lahiri, S.D., Zhang, G., Dunaway-Mariano, D., Allen, K.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.179 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

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

• PubMed: 12637673 
• DOI: https://doi.org/10.1126/science.1082710
• Primary Citation Related Structures: 
  1O03, 1O08


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.6 kDa 
• Atom Count: 2,218 
• Modeled Residue Count: 221 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-phosphoglucomutase	A	221	Lactococcus lactis	Mutation(s): 0  EC: 5.4.2.6
UniProt
Find proteins for P71447 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore P71447  Go to UniProtKB:  P71447

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G16	B [auth A]	1,6-di-O-phosphono-alpha-D-glucopyranose C6 H13 O12 P2 RWHOZGRAXYWRNX-VFUOTHLCSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.179 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.939	α = 90
b = 54.297	β = 90
c = 104.68	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-18 
Deposition Author(s): Lahiri, S.D., Zhang, G., Dunaway-Mariano, D., Allen, K.N.

Revision History  

• Version 1.0: 2003-03-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 2.0: 2024-04-03
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-10-16
  Changes: Structure summary