4IUG | pdb_00004iug

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

• PDB DOI: https://doi.org/10.2210/pdb4IUG/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae
• Expression System: Kluyveromyces lactis
• Mutation(s): No 


• Deposited: 2013-01-21 Released: 2013-07-31 
• Deposition Author(s): Maksimainen, M., Rouvinen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

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

• PubMed: 23688418 
• DOI: https://doi.org/10.1016/j.ijbiomac.2013.05.003
• Primary Citation Related Structures: 
  4IUG


• 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 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Eastern Finland, P.O. Box 111, 80100 Joensuu, Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 120.15 kDa 
• Atom Count: 8,208 
• Modeled Residue Count: 957 
• Deposited Residue Count: 1,005 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase A	A	1,005	Aspergillus oryzae	Mutation(s): 0  Gene Names: lacA EC: 3.2.1.23
UniProt
Find proteins for Q2UCU3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2UCU3  Go to UniProtKB:  Q2UCU3
Glycosylation
Glycosylation Sites: 6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	10		N-Glycosylation
Glycosylation Resources
GlyTouCan: G27421EI GlyCosmos: G27421EI GlyGen: G27421EI

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-6-O-phosphono-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	G	9		N/A
Glycosylation Resources
GlyTouCan: G30402WE GlyCosmos: G30402WE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	LA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GAL	KA [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
CD	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.38	α = 90
b = 146.38	β = 90
c = 136.33	γ = 120

Software Package:

Software Name	Purpose
EDNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Maksimainen, M., Rouvinen, J.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary