4IUG

Crystal structure of beta-galactosidase from Aspergillus oryzae in complex with galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The crystal structure of acidic beta-galactosidase from Aspergillus oryzae.

Maksimainen, M.M.Lampio, A.Mertanen, M.Turunen, O.Rouvinen, J.

(2013) Int.J.Biol.Macromol. 60C: 109-115

  • DOI: 10.1016/j.ijbiomac.2013.05.003

  • PubMed Abstract: 
  • The crystal structure of the industrially important Aspergillus oryzae β-galactosidase has been determined at 2.60 Å resolution. The Ao-β-gal is a large (985 residues) monomeric multi-domain enzyme that has a catalytic (α/β)8-barrel domain. An electr ...

    The crystal structure of the industrially important Aspergillus oryzae β-galactosidase has been determined at 2.60 Å resolution. The Ao-β-gal is a large (985 residues) monomeric multi-domain enzyme that has a catalytic (α/β)8-barrel domain. An electron density map revealed extensive N-glycosylation between the domain interfaces suggesting that the oligosaccharide-chains would have a stabilizing role for the structure of Ao-β-gal. Comparison of structure with other β-galactosidase structures of glycoside hydrolase family 35 revealed a number of hydrophobic residues, which may contribute favorably to the stabilization of the structure. The role of a high number of acidic residues in Ao-β-gal is also discussed.


    Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, P.O. Box 111, 80100 Joensuu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase A
A
1005Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Gene Names: lacA
EC: 3.2.1.23
Find proteins for Q2UCU3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  Q2UCU3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
M6D
Query on M6D

Download SDF File 
Download CCD File 
A
6-O-phosphono-beta-D-mannopyranose
beta-D-mannose-6-phosphate
C6 H13 O9 P
NBSCHQHZLSJFNQ-RWOPYEJCSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.380α = 90.00
b = 146.380β = 90.00
c = 136.330γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement
EDNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release