3IAQ

E. coli (lacz) beta-galactosidase (E416V)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate optimization of active site chemistry

Lo, S.Dugdale, M.L.Jeerh, N.Ku, T.Roth, N.J.Huber, R.E.

(2010) Protein J. 29: 26-31

  • DOI: 10.1007/s10930-009-9216-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Variants of beta-galactosidase with Valine and with Glutamine replacing Glutamate-416 did not have a Mg(2+) bound at the active site even at high Mg(2+) concentrations (200 mM). They had low catalytic activity and the pH profiles were very different ...

    Variants of beta-galactosidase with Valine and with Glutamine replacing Glutamate-416 did not have a Mg(2+) bound at the active site even at high Mg(2+) concentrations (200 mM). They had low catalytic activity and the pH profiles were very different from those of the native enzyme. In addition, substrates, substrate analogs, transition state analogs and galactose bound very poorly. However, the orientation and conformation of the Mg(2+) ligands (residues 416, 418, and 461) as well as the B-factors of these three side chains did not change significantly. The structures, conformations and B-factors of other active site residues were also essentially unchanged. These studies show that the active site Mg(2+) is not necessary for structure and is, therefore, mainly important for modulating the chemistry and mediating the interactions between the active site components.


    Organizational Affiliation

    Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase
A, B, C, D
1023Escherichia 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

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

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Download CCD File 
A, B, C, D
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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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: 2.7 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 149.380α = 90.00
b = 168.300β = 90.00
c = 200.730γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
ADSCdata collection
REFMACrefinement
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance