4DUW

E. coli (lacZ) beta-galactosidase (G974A) in complex with allolactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Explanation for Allolactose (lac operon inducer) Synthesis by lacZ beta-Galactosidase and the Evolutionary Relationship between Allolactose synthesis and the lac Repressor

Wheatley, R.W.Lo, S.Jancewicz, L.J.Dugdale, M.L.Huber, R.E.

(2013) J.Biol.Chem. 288: 12993-13005

  • DOI: 10.1074/jbc.M113.455436
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of ...

    β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2',2″-nitrilotriethanol) and L-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795-803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution.


    Organizational Affiliation

    Division of Biochemistry, Faculty of Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
1052Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: lacZ
EC: 3.2.1.23
Find proteins for P00722 (Escherichia coli (strain K12))
Go to UniProtKB:  P00722
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LAK
Query on LAK

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-GALACTOPYRANOSYL-1-6-BETA-D-GLUCOPYRANOSE
ALLOLACTOSE
C12 H22 O11
DLRVVLDZNNYCBX-VHBGUFLRSA-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
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 151.826α = 90.00
b = 162.635β = 90.00
c = 203.692γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
ADSCdata collection
CNSrefinement
SCALAdata scaling
CNSphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-07-10
    Type: Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Refinement description