3OB8 | pdb_00003ob8

Structure of the beta-galactosidase from Kluyveromyces lactis in complex with galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.246 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3OB8

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis of specificity in tetrameric Kluyveromyces lactis beta-galactosidase.

Pereira-Rodriguez, A.Fernandez-Leiro, R.Gonzalez-Siso, M.I.Cerdan, M.E.Becerra, M.Sanz-Aparicio, J.

(2012) J Struct Biol 177: 392-401

  • DOI: https://doi.org/10.1016/j.jsb.2011.11.031
  • Primary Citation Related Structures: 
    3OB8, 3OBA

  • PubMed Abstract: 

    β-Galactosidase or lactase is a very important enzyme in the food industry, being that from the yeast Kluyveromyces lactis the most widely used. Here we report its three-dimensional structure both in the free state and complexed with the product galactose. The monomer folds into five domains in a pattern conserved with the prokaryote enzymes of the GH2 family, although two long insertions in domains 2 and 3 are unique and related to oligomerization and specificity. The tetrameric enzyme is a dimer of dimers, with higher dissociation energy for the dimers than for its assembly. Two active centers are located at the interface within each dimer in a narrow channel. The insertion at domain 3 protrudes into this channel and makes putative links with the aglycone moiety of docked lactose. In spite of common structural features related to function, the determinants of the reaction mechanism proposed for Escherichia coli β-galactosidase are not found in the active site of the K. lactis enzyme. This is the first X-ray crystal structure for a β-galactosidase used in food processing.


  • Organizational Affiliation
    • Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira s/n, 15071-A Coruña, Spain. apereira@udc.es

Macromolecule Content 

  • Total Structure Weight: 475.95 kDa 
  • Atom Count: 34,419 
  • Modeled Residue Count: 4,096 
  • Deposited Residue Count: 4,128 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidaseA,
B,
C [auth D],
D [auth C]
1,032Kluyveromyces lactisMutation(s): 0 
Gene Names: KLLA0B14883gLAC4
EC: 3.2.1.23
UniProt
Find proteins for P00723 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Explore P00723 
Go to UniProtKB:  P00723
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00723
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GAL

Query on GAL



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
S [auth D],
Z [auth C]
beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
EA [auth C],
J [auth A],
Q [auth B],
X [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth C],
F [auth A],
M [auth B],
T [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BA [auth C]
CA [auth C]
DA [auth C]
FA [auth C]
G [auth A]
BA [auth C],
CA [auth C],
DA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
R [auth B],
U [auth D],
V [auth D],
W [auth D],
Y [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.246 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.381α = 90
b = 153.454β = 90
c = 217.166γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2012-02-08
    Changes: Database references
  • Version 1.2: 2013-06-26
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Refinement description, Structure summary