3OGR

Complex structure of beta-galactosidase from Trichoderma reesei with galactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site

Maksimainen, M.Hakulinen, N.Kallio, J.M.Timoharju, T.Turunen, O.Rouvinen, J.

(2011) J Struct Biol 174: 156-163

  • DOI: https://doi.org/10.1016/j.jsb.2010.11.024
  • Primary Citation of Related Structures:  
    3OG2, 3OGR, 3OGS, 3OGV

  • PubMed Abstract: 

    We have determined the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal) at a 1.2Å resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4Å resolutions, respectively. Tr-β-gal is a potential enzyme for lactose hydrolysis in the dairy industry and belongs to family 35 of the glycoside hydrolases (GH-35). The high resolution crystal structures of this six-domain enzyme revealed interesting features about the structure of Tr-β-gal. We discovered conformational changes in the two loop regions in the active site, implicating a conformational selection-mechanism for the enzyme. In addition, the Glu200, an acid/base catalyst showed two different conformations which undoubtedly affect the pK(a) value of this residue and the catalytic mechanism. The electron density showed extensive glycosylation, suggesting a structure stabilizing role for glycans. The longest glycan showed an electron density that extends to the eighth monosaccharide unit in the extended chain. The Tr-β-gal structure also showed a well-ordered structure for a unique octaserine motif on the surface loop of the fifth domain.


  • Organizational Affiliation

    Department of Chemistry, University of Eastern Finland, P.O. Box 111, FIN-80101 Joensuu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase1,003Trichoderma reeseiMutation(s): 0 
EC: 3.2.1.23
UniProt
Find proteins for Q70SY0 (Hypocrea jecorina)
Explore Q70SY0 
Go to UniProtKB:  Q70SY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70SY0
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G16404YH
GlyCosmos:  G16404YH
GlyGen:  G16404YH
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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
C
10N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32149KV
GlyCosmos:  G32149KV
GlyGen:  G32149KV
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.43α = 109.03
b = 69.28β = 97.34
c = 81.5γ = 114.38
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary