6SE8

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA1010Arthrobacter sp. 32cBMutation(s): 1 
EC: 3.2.1.23
UniProt
Find proteins for A0A023UGN9 (Arthrobacter sp. 32cB)
Explore A0A023UGN9 
Go to UniProtKB:  A0A023UGN9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
EA [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A] , C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , 
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
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
FA [auth A], GA [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 136.859α = 90
b = 136.859β = 90
c = 127.082γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



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