Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E517Q in complex with galactose

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Mapping the Transglycosylation Relevant Sites of Cold-Adapted beta-d-Galactosidase fromArthrobactersp. 32cB.

Rutkiewicz, M.Wanarska, M.Bujacz, A.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21155354
  • Primary Citation of Related Structures:  
    6ZJP, 6ZJQ, 6ZJR, 6ZJS, 6ZJT, 6ZJU, 6ZJV, 6ZJW, 6ZJX

  • PubMed Abstract: 

    β-Galactosidase from Arthrobacter sp. 32cB ( Arth βDG) is a cold-adapted enzyme able to catalyze hydrolysis of β-d-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of Arth βDG: D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to shed light onto the structural basis of the transglycosylation reaction. The catalytic assays proved loss of function mutation E517 into glutamine and a significant drop of activity for mutation of D207 into alanine. Solving crystal structures of two new mutants, and new complex structures of previously presented mutant E441Q enables description of introduced changes within active site of enzyme and determining the importance of mutated residues for active site size and character. Furthermore, usage of mutants with diminished and abolished enzymatic activity enabled solving six complex structures with galactose, lactulose or sucrose bounds. As a result, not only the galactose binding sites were mapped on the enzyme's surface but also the mode of lactulose, product of transglycosylation reaction, and binding within the enzyme's active site were determined and the glucopyranose binding site in the distal of active site was discovered. The latter two especially show structural details of transglycosylation, providing valuable information that may be used for engineering of Arth βDG or other analogous galactosidases belonging to GH2 family.

  • Organizational Affiliation

    Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase1,012Arthrobacter sp. 32cBMutation(s): 1 
Find proteins for A0A023UGN9 (Arthrobacter sp. 32cB)
Explore A0A023UGN9 
Go to UniProtKB:  A0A023UGN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A023UGN9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL (Subject of Investigation/LOI)
Query on GAL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
C6 H12 O6
Query on MLI

Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
EA [auth A]
FA [auth A]
GA [auth A]
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A]
C3 H2 O4
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
I [auth A]
J [auth A]
K [auth A]
AA [auth A],
BA [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C2 H3 O2
Query on NA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.608α = 90
b = 138.608β = 90
c = 127.656γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2016/21/B/ST5/00555
Polish National Science CentrePoland2018/28/T/ST5/00233

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description