1YQ2

beta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1)

• PDB DOI:  https://doi.org/10.2210/pdb1YQ2/pdb

• Classification: HYDROLASE
• Organism(s): Arthrobacter sp. C2-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-01 Released: 2005-10-04 
• Deposition Author(s): Skalova, T., Dohnalek, J., Spiwok, V., Lipovova, P., Vondrackova, E., Petrokova, H., Strnad, H., Kralova, B., Hasek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 

Literature

Cold-active beta-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660kDa Hexamers: Crystal Structure at 1.9A Resolution

Skalova, T., Dohnalek, J., Spiwok, V., Lipovova, P., Vondrackova, E., Petrokova, H., Duskova, J., Strnad, H., Kralova, B., Hasek, J.

(2005) J Mol Biol 353: 282-294

• PubMed: 16171818 
• DOI: https://doi.org/10.1016/j.jmb.2005.08.028
• Primary Citation of Related Structures:  
  1YQ2


• PubMed Abstract: 
  

The X-ray structure of cold-active beta-galactosidase (isoenzyme C-2-2-1) from an Antarctic bacterium Arthrobacter sp. C2-2 was solved at 1.9A resolution. The enzyme forms 660 kDa hexamers with active sites opened to the central cavity of the hexamer and connected by eight channels with exterior solvent. To our best knowledge, this is the first cold-active beta-galactosidase with known structure and also the first known beta-galactosidase structure in the form of compact hexamers. The hexamer organization regulates access of substrates and ligands to six active sites and this unique packing, present also in solution, raises questions about its purpose and function. This enzyme belongs to glycosyl hydrolase family 2, similarly to Escherichia coli beta-galactosidase, forming tetramers necessary for its enzymatic function. However, we discovered significant differences between these two enzymes affecting the ability of tetramer/hexamer formation and complementation of the active site. This structure reveals new insights into the cold-adaptation mechanisms of enzymatic pathways of extremophiles.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 1606 Praha 6, Czech Republic. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 669.2 kDa 
• Atom Count: 53,897 
• Modelled Residue Count: 6,120 
• Deposited Residue Count: 6,144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-galactosidase	A, B, C, D, E, F	1,024	Arthrobacter sp. C2-2	Mutation(s): 1  Gene Names: lacZ EC: 3.2.1.23

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	GA [auth D], M [auth A], NA [auth E], T [auth B], UA [auth F], Z [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	EA [auth D], FA [auth D], K [auth A], L [auth A], LA [auth E], MA [auth E], R [auth B], S [auth B], SA [auth F], TA [auth F], Y [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	DA [auth D], J [auth A], KA [auth E], Q [auth B], RA [auth F], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AA [auth D], G [auth A], HA [auth E], N [auth B], OA [auth F], U [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	BA [auth D], CA [auth D], H [auth A], I [auth A], IA [auth E], JA [auth E], O [auth B], P [auth B], PA [auth F], QA [auth F], V [auth C], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.15785/SBGRID/855

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.091	α = 90
b = 205.698	β = 102.34
c = 140.458	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Skalova, T., Dohnalek, J., Spiwok, V., Lipovova, P., Vondrackova, E., Petrokova, H., Strnad, H., Kralova, B., Hasek, J.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description