1Z4N

Structure of beta-phosphoglucomutase with inhibitor bound alpha-galactose 1-phosphate cocrystallized with Fluoride

• PDB DOI: https://doi.org/10.2210/pdb1Z4N/pdb

• Classification: ISOMERASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-16 Released: 2005-04-19 
• Deposition Author(s): Tremblay, L.W., Zhang, G., Dai, J., Dunaway-Mariano, D., Allen, K.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Chemical Confirmation of a Pentavalent Phosphorane in Complex with beta-Phosphoglucomutase

Tremblay, L.W., Zhang, G., Dai, J., Dunaway-Mariano, D., Allen, K.N.

(2005) J Am Chem Soc 127: 5298-5299

• PubMed: 15826149 
• DOI: https://doi.org/10.1021/ja0509073
• Primary Citation of Related Structures:  
  1Z4N, 1Z4O


• PubMed Abstract: 
  

  This communication reports the X-ray crystal structure of the alpha-d-galactose-1-phosphate complex with that of Lactococcus lactis beta-phosphoglucomutase (beta-PGM) crystallized in the presence of Mg2+ cofactor and the enzyme-to-phosphorus ratio determined by protein and phosphate analyses of the crystalline complex. The 1:1 ratio determined for this complex was compared to the 1:2 ratio determined for the crystals of beta-PGM grown in the presence of substrate and Mg2+ cofactor. This result verifies the published structure assignment of this latter complex as the phosphorane adduct formed by covalent bonding between the active site Asp8 carboxylate to the C(1)phosphorus of the beta-glucose 1,6-bisphosphate ligand and rules out the proposal of a beta-PGM-glucose-6-phosphate-1-MgF3- complex.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.05 kDa 
• Atom Count: 3,700 
• Modelled Residue Count: 423 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A, B	221	Lactococcus lactis	Mutation(s): 0  Gene Names: pgmB 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
GL1	D [auth A], F [auth B]	1-O-phosphono-alpha-D-galactopyranose C6 H13 O9 P HXXFSFRBOHSIMQ-FPRJBGLDSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GL1	PDBBind:  1Z4N	Ki: 3.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.239 
• R-Value Work: 0.207 
• R-Value Observed: 0.236 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.143	α = 90
b = 36.451	β = 94.35
c = 105.119	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Tremblay, L.W., Zhang, G., Dai, J., Dunaway-Mariano, D., Allen, K.N.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary