Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 485407.22 
• Atom Count: 32968 
• Residue Count: 4208 
• Unique protein chains: 1

3VD9

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

• DOI: 10.2210/pdb3VD9/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2012-01-04 Released: 2012-04-11 
• Deposition Author(s): Wheatley, R.W., Kappelhoff, J.C., Hahn, J.N., Dugdale, M.L., Dutkoski, M.J., Tamman, S.D., Fraser, M.E., Huber, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.223 
• R-Value Work: 0.169 

Literature

Substitution for Asn460 cripples {beta}-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability.

Wheatley, R.W., Kappelhoff, J.C., Hahn, J.N., Dugdale, M.L., Dutkoski, M.J., Tamman, S.D., Fraser, M.E., Huber, R.E.

(2012) Arch.Biochem.Biophys. 521: 51-61

• PubMed: 22446164 
• DOI: 10.1016/j.abb.2012.03.014
• Primary Citation of Related Structures:  
  3VDC, 3VDB, 3VDA, 3VD7, 3VD5, 3VD4, 3VD3


• PubMed Abstract: 
  

Substrate initially binds to β-galactosidase (Escherichia coli) at a 'shallow' site. It then moves ∼3Å to a 'deep' site and the transition state forms. Asn460 interacts in both sites, forming a water bridge interaction with the O3 hydroxyl of the galactosyl moiety in the shallow site and a direct H-bond with the O2 hydroxyl of the transition state in the deep site. Structural and kinetic studies were done with β-galactosidases with substitutions for Asn460. The substituted enzymes have enhanced substrate affinity in the shallow site indicating lower E·substrate complex energy levels. They have poor transition state stabilization in the deep site that is manifested by increased energy levels of the E·transition state complexes. These changes in stability result in increased activation energies and lower k(cat) values. Substrate affinity to N460D-β-galactosidase was enhanced through greater binding enthalpy (stronger H-bonds through the bridging water) while better affinity to N460T-β-galactosidase occurred because of greater binding entropy. The transition states are less stable with N460S- and N460T-β-galactosidase because of the weakening or loss of the important bond to the O2 hydroxyl of the transition state. For N460D-β-galactosidase, the transition state is less stable due to an increased entropy penalty.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Beta-galactosidase	A, B, C, D	1052	Escherichia 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A, B, C, D	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
DMS	A, B, C, D	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IPT	A, B, C, D	ISOPROPYL-1-BETA-D-THIOGALACTOSIDE 1-(ISOPROPYLTHIO)-BETA-GALACTOPYRANSIDE C9 H18 O5 S BPHPUYQFMNQIOC-NXRLNHOXSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IPT	Ki: 76000 nM (99) BINDINGDB
IPT	Ki: 100000 nM BINDINGMOAD
IPT	Ki: 100000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.223 
• R-Value Work: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 151.537	α = 90.00
b = 162.550	β = 90.00
c = 203.440	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-04 
• Released Date: 2012-04-11 
• Deposition Author(s): Wheatley, R.W., Kappelhoff, J.C., Hahn, J.N., Dugdale, M.L., Dutkoski, M.J., Tamman, S.D., Fraser, M.E., Huber, R.E.

Revision History 

• Version 1.0: 2012-04-11
  Type: Initial release
• Version 1.1: 2013-06-19
  Type: Database references
• Version 1.2: 2019-07-17
  Type: Data collection, Refinement description