Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB in complex with IPTG

Experimental Data Snapshot

  • Resolution: 2.27 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.4 of the entry. See complete history


Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase fromArthrobactersp. 32cB.

Rutkiewicz, M.Bujacz, A.Wanarska, M.Wierzbicka-Wos, A.Cieslinski, H.

(2019) Int J Mol Sci 20

  • DOI: https://doi.org/10.3390/ijms20174301
  • Primary Citation of Related Structures:  
    6SE8, 6SE9, 6SEA, 6SEB, 6SEC, 6SED

  • PubMed Abstract: 

    Arth βDG is a dimeric, cold-adapted β-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its Arth βDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The Arth βDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: Arth βDG_E441Q/LACs and Arth βDG/IPTG (ligand bound in shallow mode) and structures of complexes Arth βDG_E441Q/LACd, Arth βDG/ONPG (ligands bound in deep mode), and galactose Arth βDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 βDGs, in Arth βDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation.

  • Organizational Affiliation

    Institute of Technical Biochemistry, 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-galactosidase1,010Arthrobacter sp. 32cBMutation(s): 0 
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
IPT (Subject of Investigation/LOI)
Query on IPT

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
1-methylethyl 1-thio-beta-D-galactopyranoside
C9 H18 O5 S
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
C2 H3 O2
Query on FMT

Download Ideal Coordinates CCD File 
C H2 O2
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.27 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.069α = 90
b = 137.069β = 90
c = 126.795γ = 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

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Structure summary
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary