Crystal structure of Tomato beta-galactosidase (TBG) 4 with beta-1,4-galactobiose

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

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Substrate-recognition mechanism of tomato beta-galactosidase 4 using X-ray crystallography and docking simulation.

Matsuyama, K.Kondo, T.Igarashi, K.Sakamoto, T.Ishimaru, M.

(2020) Planta 252: 72-72

  • DOI: https://doi.org/10.1007/s00425-020-03481-4
  • Primary Citation of Related Structures:  
    6IK5, 6IK6, 6IK7, 6IK8

  • PubMed Abstract: 

    TBG4 recognize multiple linkage types substrates due to having a spatially wide subsite + 1. This feature allows the degradation of AGI, AGII, and AGP leading to the fruit ripening. β-galactosidase (EC 3. 2. 1. 23) catalyzes the hydrolysis of β-galactan and release of D-galactose. Tomato has at least 17 β-galactosidases (TBGs), of which, TBG 4 is responsible for fruit ripening. TBG4 hydrolyzes not only β-1,4-bound galactans, but also β-1,3- and β-1,6-galactans. In this study, we compared each enzyme-substrate complex using X-ray crystallography, ensemble refinement, and docking simulation to understand the broad substrate-specificity of TBG4. In subsite - 1, most interactions were conserved across each linkage type of galactobioses; however, some differences were seen in subsite + 1, owing to the huge volume of catalytic pocket. In addition to this, docking simulation indicated TBG4 to possibly have more positive subsites to recognize and hydrolyze longer galactans. Taken together, our results indicated that during tomato fruit ripening, TBG4 plays an important role by degrading arabinogalactan I (AGI), arabinogalactan II (AGII), and the carbohydrate moiety of arabinogalactan protein (AGP).

  • Organizational Affiliation

    Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo, 113-8657, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
718Solanum lycopersicumMutation(s): 1 
Gene Names: TBG4
Find proteins for O81100 (Solanum lycopersicum)
Explore O81100 
Go to UniProtKB:  O81100
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO81100
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F
Glycosylation Resources
GlyTouCan:  G08806VI
GlyCosmos:  G08806VI
GlyGen:  G08806VI
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.032α = 90
b = 110.73β = 90
c = 162.141γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-12-23
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description