4V44

E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH 2-F-LACTOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase

Juers, D.H.Heightman, T.D.Vasella, A.McCarter, J.D.Mackenzie, L.Withers, S.G.Matthews, B.W.

(2001) Biochemistry 40: 14781-14794

  • Primary Citation of Related Structures:  1JYN, 1JYV, 1JYW, 1JYX, 1JYY, 1JYZ, 1JZ0, 1JZ1, 1JZ2, 1JZ3, 1JZ4, 1JZ5, 1JZ6, 1JZ7, 1JZ8, 4V45

  • PubMed Abstract: 
  • The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu ...

    The structures of a series of complexes designed to mimic intermediates along the reaction coordinate for beta-galactosidase are presented. These complexes clarify and enhance previous proposals regarding the catalytic mechanism. The nucleophile, Glu537, is seen to covalently bind to the galactosyl moiety. Of the two potential acids, Mg(2+) and Glu461, the latter is in better position to directly assist in leaving group departure, suggesting that the metal ion acts in a secondary role. A sodium ion plays a part in substrate binding by directly ligating the galactosyl 6-hydroxyl. The proposed reaction coordinate involves the movement of the galactosyl moiety deep into the active site pocket. For those ligands that do bind deeply there is an associated conformational change in which residues within loop 794-804 move up to 10 A closer to the site of binding. In some cases this can be inhibited by the binding of additional ligands. The resulting restricted access to the intermediate helps to explain why allolactose, the natural inducer for the lac operon, is the preferred product of transglycosylation.


    Related Citations: 
    • Crystallization of beta-galactosidase from Escherichia coli
      Jacobson, R.H.,Matthews, B.W.
      (1992) J.Mol.Biol. 223: 1177
    • Three-Dimensional Structure of Beta-Galactosidase from E. Coli
      Jacobson, R.H.,Zhang, X.J.,Dubose, R.F.,Matthews, B.W.
      (1994) Nature 369: 761
    • High Resolution Structure of Beta-Galactosidase in a New Crystal Form Reveals Multiple Metal-Binding Sites and Provides a Structural Basis for Alpha-Complementation
      Juers, D.H.,Jacobson, R.H.,Wigley, D.,Zhang, X.J.,Huber, R.E.,Tronrud, D.E.,Matthews, B.W.
      (2000) Protein Sci. 9: 1685
    • Structural Comparisons of Tim Barrel Proteins Suggest Functional and Evolutionary Relationships between Beta-Galactosidase and Other Glycohydrolases
      Juers, D.H.,Huber, R.E.,Matthews, B.W.
      (1999) Protein Sci. 8: 122


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, Oregon 97403-1229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-Galactosidase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
1023Escherichia coli (strain K12)Gene Names: lacZ
EC: 3.2.1.23
Find proteins for P00722 (Escherichia coli (strain K12))
Go to UniProtKB:  P00722
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
2FL
Query on 2FL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
2-FLUORO-2-DEOXY-LACTOSE
2-FLUORO-2-DEOXY-BETA-D-GALACTOPYRANOSYL-BETA-D-GLUCOPYRANOSE
C12 H21 F O10
KWMZPXRIEZDXAQ-QRZGKKJRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.600α = 90.00
b = 207.300β = 95.00
c = 510.300γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
TNTphasing
WEISdata reduction
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other