4DUX | pdb_00004dux

E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose

• PDB DOI: https://doi.org/10.2210/pdb4DUX/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-02-22 Released: 2013-03-20 
• Deposition Author(s): Wheatley, R.W., Lo, S., Janzcewicz, L.J., Dugdale, M.L., Huber, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

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 Biological Chem 288: 12993-13005

• PubMed: 23486479 
• DOI: https://doi.org/10.1074/jbc.M113.455436
• Primary Citation Related Structures: 
  4DUW, 4DUX


• 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 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.

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Organizational Affiliation: 
• Division of Biochemistry, Faculty of Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 485.81 kDa 
• Atom Count: 35,621 
• Modeled Residue Count: 4,060 
• Deposited Residue Count: 4,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,052	Escherichia coli K-12	Mutation(s): 1  Gene Names: b0344, JW0335, lacZ EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0MK	AB [auth C], BB [auth C], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], XB [auth D], YB [auth D]	beta-L-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-FCAWWPLPSA-N
DMS	AA [auth A], BA [auth A], CA [auth A], EC [auth D], FC [auth D], GC [auth D], HC [auth D], IB [auth C], IC [auth D], JB [auth C], JC [auth D], KB [auth C], KC [auth D], L [auth A], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RA [auth B], RB [auth C], RC [auth D], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	AC [auth D], CB [auth C], DB [auth C], G [auth A], GA [auth B], H [auth A], HA [auth B], ZB [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	BC [auth D], CC [auth D], DC [auth D], EB [auth C], FB [auth C], GB [auth C], HB [auth C], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], LA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.648	α = 90
b = 168.103	β = 90
c = 201.881	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Wheatley, R.W., Lo, S., Janzcewicz, L.J., Dugdale, M.L., Huber, R.E.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary