1YQ2 | pdb_00001yq2

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 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1YQ2

This is version 1.4 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 Biology 353: 282-294

  • DOI: https://doi.org/10.1016/j.jmb.2005.08.028
  • Primary Citation 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.


  • 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

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
beta-galactosidase
A, B, C, D, E
A, B, C, D, E, F
1,024Arthrobacter 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KRF6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / 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]
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

Query on SO4



Download:Ideal Coordinates CCD File
EA [auth D]
FA [auth D]
K [auth A]
L [auth A]
LA [auth E]
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

Query on CL



Download:Ideal Coordinates CCD File
DA [auth D]
J [auth A]
KA [auth E]
Q [auth B]
RA [auth F]
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

Query on MG



Download:Ideal Coordinates CCD File
AA [auth D]
G [auth A]
HA [auth E]
N [auth B]
OA [auth F]
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

Query on NA



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
H [auth A]
I [auth A]
IA [auth E]
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 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 1 21 1
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
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description