4PBG

6-PHOSPHO-BETA-GALACTOSIDASE FORM-CST


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.

Wiesmann, C.Hengstenberg, W.Schulz, G.E.

(1997) J.Mol.Biol. 269: 851-860

  • DOI: 10.1006/jmbi.1997.1084
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The initial structural model of 6-phospho-beta-galactosidase from Lactococcus lactis was refined to an R-factor of 16.4% (R[free] = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular re ...

    The initial structural model of 6-phospho-beta-galactosidase from Lactococcus lactis was refined to an R-factor of 16.4% (R[free] = 23.6%) to 2.3 A resolution (1 A = 0.1 nm), and the structures of three other crystal forms were solved by molecular replacement. The four structural models are essentially identical. The catalytic center of the enzyme is approximately at the mass center of the molecule and can only be reached through a 20 A long channel, which is observed with an "open" or "closed" entrance. The closed entrance is probably too small for the educt lactose-6-phosphate to enter, but large enough for the first product glucose to leave. Among the presented structures is a complex between an almost inactive mutant and the second product galactose-6-phosphate, which is exclusively bound at side-chains. A superposition (onto the native enzyme) of galactose-6-phosphate as bound to the mutant suggests the geometry of a postulated covalent intermediate. The binding mode of the educt was modeled, starting from the bound galactose-6-phosphate. A tightly fixed tryptophan is used as a chopping-board for splitting the disaccharide, and several other aromatic residues in the active center cavity are likely to participate in substrate transport/binding.


    Related Citations: 
    • 6-Phospho-Beta-Galactosidases of Gram-Positive and 6-Phospho-Beta-Glucosidase B of Gram-Negative Bacteria: Comparison of Structure and Function by Kinetic and Immunological Methods and Mutagenesis of the Lacg Gene of Staphylococcus Aureus
      Witt, E.,Frank, R.,Hengstenberg, W.
      (1993) Protein Eng. 6: 913
    • The Three-Dimensional Structure of 6-Phospho-Beta-Galactosidase from Lactococcus Lactis
      Wiesmann, C.,Beste, G.,Hengstenberg, W.,Schulz, G.E.
      (1995) Structure 3: 961
    • Identification of the Active-Site Nucleophile in 6-Phospho-Beta-Galactosidase from Staphylococcus Aureus by Labelling with Synthetic Inhibitors
      Staedtler, P.,Hoenig, S.,Frank, R.,Withers, S.G.,Hengstenberg, W.
      (1995) Eur.J.Biochem. 232: 658


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-PHOSPHO-BETA-D-GALACTOSIDASE
A, B
468Lactococcus lactis subsp. lactisMutation(s): 1 
Gene Names: lacG
EC: 3.2.1.85
Find proteins for P11546 (Lactococcus lactis subsp. lactis)
Go to UniProtKB:  P11546
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGP
Query on BGP

Download SDF File 
Download CCD File 
A, B
BETA-GALACTOSE-6-PHOSPHATE
C6 H13 O9 P
NBSCHQHZLSJFNQ-FPRJBGLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.700α = 90.00
b = 174.300β = 90.00
c = 60.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
BIOMOLdata scaling
XDSdata reduction
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance