3VD7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.abb.2012.03.014
  • Primary Citation of Related Structures:  

  • 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 gal ...

    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.


    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
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
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
GTZ
Query on GTZ

Download SDF File 
Download CCD File 
A, B, C, D
(5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6,7,8-TRIHYDROXY-TETRAZOLO[1,5-A]PIPERIDINE
C6 H10 N4 O4
UCJXQRFJERKPOZ-MGCNEYSASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GTZKi: 33000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 128.460α = 90.00
b = 152.370β = 104.25
c = 135.110γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references