3T0D

E.coli (lacZ) beta-galactosidase (S796T) in complex with galactonolactone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Ser-796 of Beta-galactosidase (E. coli) plays a Key role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop

Jancewicz, L.J., Wheatley, R.W., Sutendra, G., Lee, M., Fraser, M.E., Huber, R.E.

(2012) Arch.Biochem.Biophys. 517: 111-122

  • DOI: 10.1016/j.abb.2011.11.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • A loop (residues 794-803) at the active site of β-galactosidase (Escherichia coli) opens and closes during catalysis. The α and β carbons of Ser-796 form a hydrophobic connection to Phe-601 when the loop is closed while a connection via two H-bonds w ...

    A loop (residues 794-803) at the active site of β-galactosidase (Escherichia coli) opens and closes during catalysis. The α and β carbons of Ser-796 form a hydrophobic connection to Phe-601 when the loop is closed while a connection via two H-bonds with the Ser hydroxyl occurs with the loop open. β-Galactosidases with substitutions for Ser-796 were investigated. Replacement by Ala strongly stabilizes the closed conformation because of greater hydrophobicity and loss of H-bonding ability while replacement with Thr stabilizes the open form through hydrophobic interactions with its methyl group. Upon substitution with Asp much of the defined loop structure is lost. The different open-closed equilibria cause differences in the stabilities of the enzyme·substrate and enzyme·transition state complexes and of the covalent intermediate that affect the activation thermodynamics. With Ala, large changes of both the galactosylation (k(2)) and degalactosylation (k(3)) rates occur. With Thr and Asp, the k(2) and k(3) were not changed as much but large ΔH(‡) and TΔS(‡) changes showed that the substitutions caused mechanistic changes. Overall, the hydrophobic and H-bonding properties of Ser-796 result in interactions strong enough to stabilize the open or closed conformations of the loop but weak enough to allow loop movement during the reaction.

    Organizational Affiliation: 

    Division of Biochemistry, University of Calgary, Calgary, Alberta, 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
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
149
Query on 149
Download SDF File 
Download CCD File 
A, B, C, D
D-galactonolactone
(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-one
C6 H10 O6
PHOQVHQSTUBQQK-MGCNEYSASA-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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
149Ki: 4300000 nM BINDINGMOAD
149Ki: 4300000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 151.930α = 90.00
b = 162.710β = 90.00
c = 203.910γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
CNSrefinement
SCALAdata scaling
MOSFLMdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Refinement description