Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 111.89 kDa 
• Atom Count: 8,760 
• Modelled Residue Count: 1,001 
• Deposited Residue Count: 1,010 
• Unique protein chains: 1

 6SE8

Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E441Q

• PDB DOI:  https://doi.org/10.2210/pdb6SE8/pdb

• Classification: HYDROLASE
• Organism(s): Arthrobacter sp. 32cB
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-29 Released: 2019-09-11 
• Deposition Author(s): Rutkiewicz, M., Bujacz, A., Bujacz, G.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.165 
• R-Value Work: 0.135 
• R-Value Observed: 0.135 

Literature

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

• PubMed: 31484304 
• 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.

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Related Citations: 

• Structural features of cold-adapted dimeric GH2 beta-D-galactosidase from Arthrobacter sp. 32cB.
  Rutkiewicz, M., Bujacz, A., Bujacz, G.
  (2019) Biochim Biophys Acta Proteins Proteom 1867: 776

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Organizational Affiliation: 

Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A	1,010	Arthrobacter sp. 32cB	Mutation(s): 1  EC: 3.2.1.23
UniProt
Find proteins for A0A023UGN9 (Arthrobacter sp. 32cB) Explore A0A023UGN9  Go to UniProtKB:  A0A023UGN9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	EA [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MLI	AA [auth A], BA [auth A], CA [auth A], DA [auth A], X [auth A], Y [auth A], Z [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
ACT	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [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]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	FA [auth A], GA [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.165 
• R-Value Work: 0.135 
• R-Value Observed: 0.135 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.859	α = 90
b = 136.859	β = 90
c = 127.082	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Rutkiewicz, M., Bujacz, A., Bujacz, G.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2016/21/B/ST5/00555

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references