1YQ2

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 1606 Praha 6, Czech Republic. skalova@imc.cas.cz



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
beta-galactosidaseA, B, C, D, E, F1024Arthrobacter sp. C2-2Mutation(s): 1 
Gene Names: lacZ
EC: 3.2.1.23
UniProt
Find proteins for Q8KRF6 (Arthrobacter sp. C2-2)
Explore Q8KRF6 
Go to UniProtKB:  Q8KRF6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth D] , FA [auth D] , K [auth A] , L [auth A] , LA [auth E] , MA [auth E] , R [auth B] , S [auth B] , 
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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
DA [auth D], J [auth A], KA [auth E], Q [auth B], RA [auth F], X [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D], G [auth A], HA [auth E], N [auth B], OA [auth F], U [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , H [auth A] , I [auth A] , IA [auth E] , JA [auth E] , O [auth B] , P [auth B] , 
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
 Ligand Interaction
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 DOI: 10.15785/SBGRID/855 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.091α = 90
b = 205.698β = 102.34
c = 140.458γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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