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.

doi:10.2210/pdb1jz3/pdb

Macromolecule Content

Total Structure Weight: 476894.31
Atom Count: 33075
Residue Count: 4092
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 (strain K12)
Expression System: Escherichia coli

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

Experimental Data Snapshot

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

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
Primary Citation of Related Structures:
4V45, 4V44, 1JZ8, 1JZ7, 1JZ6, 1JZ5, 1JZ4, 1JZ2, 1JZ1, 1JZ0, 1JYZ, 1JYY, 1JYX, 1JYW, 1JYV, 1JYN

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.

Related Citations:

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

Organizational Affiliation:

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

Macromolecules

Find similar proteins by: Sequence | Structure

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
2DG Query on 2DG Download SDF File Download CCD File	A, B, C, D	2-DEOXY-BETA-D-GALACTOSE C₆ H₁₂ O₅ PMMURAAUARKVCB-ARQDHWQXSA-N		Ligand Interaction
NA Query on NA Download SDF File Download CCD File	A, B, C, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
BTB Query on BTB Download SDF File Download CCD File	A, B, C, D	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL BIS-TRIS BUFFER C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Ligand Interaction
DMS Query on DMS Download SDF File Download CCD File	A, B, C, D	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction