5EUV

Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d.

Rutkiewicz-Krotewicz, M.Pietrzyk-Brzezinska, A.J.Sekula, B.Cieslinski, H.Wierzbicka-Wos, A.Kur, J.Bujacz, A.

(2016) Acta Crystallogr D Struct Biol 72: 1049-1061

  • DOI: 10.1107/S2059798316012535
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of a novel dimeric β-D-galactosidase from Paracoccus sp. 32d (ParβDG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to gly ...

    The crystal structure of a novel dimeric β-D-galactosidase from Paracoccus sp. 32d (ParβDG) was solved in space group P212121 at a resolution of 2.4 Å by molecular replacement with multiple models using the BALBES software. This enzyme belongs to glycoside hydrolase family 2 (GH2), similar to the tetrameric and hexameric β-D-galactosidases from Escherichia coli and Arthrobacter sp. C2-2, respectively. It is the second known structure of a cold-active GH2 β-galactosidase, and the first in the form of a functional dimer, which is also present in the asymmetric unit. Cold-adapted β-D-galactosidases have been the focus of extensive research owing to their utility in a variety of industrial technologies. One of their most appealing applications is in the hydrolysis of lactose, which not only results in the production of lactose-free dairy, but also eliminates the `sandy effect' and increases the sweetness of the product, thus enhancing its quality. The determined crystal structure represents the five-domain architecture of the enzyme, with its active site located in close vicinity to the dimer interface. To identify the amino-acid residues involved in the catalytic reaction and to obtain a better understanding of the mechanism of action of this atypical β-D-galactosidase, the crystal structure in complex with galactose (ParβDG-Gal) was also determined. The catalytic site of the enzyme is created by amino-acid residues from the central domain 3 and from domain 4 of an adjacent monomer. The crystal structure of this dimeric β-D-galactosidase reveals significant differences in comparison to other β-galactosidases. The largest difference is in the fifth domain, named Bgal_windup domain 5 in ParβDG, which contributes to stabilization of the functional dimer. The location of this domain 5, which is unique in size and structure, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme.


    Related Citations: 
    • In Situ Random Microseeding and Streak Seeding Used for Growth of Crystals of Cold-Adapted Beta-D-Galactosidases: Crystal Structure of BetaDG from Arthrobacter sp. 32cB
      Rutkiewicz-Krotewicz, M.,Pietrzyk-Brzezinska, A.J.,Wanarska, M.,Cieslinski, H.,Bujacz, A.
      (2018) Crystals 8: --


    Organizational Affiliation

    Department of Molecular Biotechnology, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.,Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, Stefanowskiego 4/10, 90-924 Lodz, Poland.,Department of Microbiology, Faculty of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-D-galactosidase
A, B
731Paracoccus sp. 32dMutation(s): 0 
Find proteins for D1LZK0 (Paracoccus sp. 32d)
Go to UniProtKB:  D1LZK0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BTB
Query on BTB

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

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.490α = 90.00
b = 106.240β = 90.00
c = 199.390γ = 90.00
Software Package:
Software NamePurpose
BALBESphasing
XDSdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Data collection, Database references
  • Version 1.2: 2018-01-10
    Type: Database references