Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 476.89 kDa 
• Atom Count: 37369 
• Residue Count: 4044 
• Unique protein chains: 1

1JZ3

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE

• DOI: 10.2210/pdb1JZ3/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-13 Released: 2001-12-07 
• Deposition Author(s): Juers, D.H., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.222 
• R-Value Work: 0.158 

Literature

A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase

Juers, D.H., Heightman, T.D., Vasella, A., McCarter, J.D., Mackenzie, L., Withers, S.G., Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

• PubMed: 11732897 
• DOI: 10.1021/bi011727i
• Primary Citation of Related Structures:  
  4V44, 4V45, 1JYW, 1JZ8, 1JYV, 1JZ7, 1JZ6, 1JZ5, 1JZ4, 1JZ3


• PubMed Abstract: 
  

The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.

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Related Citations: 

• High Resolution Structure of Beta-Galactosidase in a New Crystal Form Reveals Multiple Metal-Binding Sites and Provides a Structural Basis for Alpha-Complementation
  Juers, D.H., Jacobson, R.H., Wigley, D., Zhang, X.J., Huber, R.E., Tronrud, D.E., Matthews, B.W.
  (2000) Protein Sci 9: 1685

• Structural Comparisons of Tim Barrel Proteins Suggest Functional and Evolutionary Relationships between Beta-Galactosidase and Other Glycohydrolases
  Juers, D.H., Huber, R.E., Matthews, B.W.
  (1999) Protein Sci 8: 122

• Three-Dimensional Structure of Beta-Galactosidase from E. Coli
  Jacobson, R.H., Zhang, X.J., Dubose, R.F., Matthews, B.W.
  (1994) Nature 369: 761

• Crystallization of beta-galactosidase from Escherichia coli
  Jacobson, R.H., Matthews, B.W.
  (1992) J Mol Biol 223: 1177

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Organizational Affiliation: 

Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-Galactosidase	A, B, C, D	1023	Escherichia coli	Mutation(s): 0  Gene Names: lacZ EC: 3.2.1.23
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	A, B, C, D	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
2DG	A, B, C, D	2-deoxy-alpha-D-galactopyranose C6 H12 O5 PMMURAAUARKVCB-ARQDHWQXSA-N
DMS	A, B, C, D	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	A, B, C, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.222 
• R-Value Work: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.56	α = 90
b = 168.19	β = 90
c = 200.69	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement
MOSFLM	data reduction
CCP4	data scaling
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-13 
• Released Date: 2001-12-07 
Deposition Author(s): Juers, D.H., Matthews, B.W.

Revision History 

• Version 1.0: 2001-12-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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, Database references, Derived calculations, Structure summary