9FYM

Lacto-N-biosidase from Treponema denticola ATCC 35405


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of Lacto-N-biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights.

Vuillemin, M.Muschiol, J.Zhang, Y.Holck, J.Barrett, K.Morth, J.P.Meyer, A.S.Zeuner, B.

(2024) Chembiochem : e202400710-e202400710

  • DOI: https://doi.org/10.1002/cbic.202400710
  • Primary Citation of Related Structures:  
    9FYL, 9FYM, 9FYN, 9FYO

  • PubMed Abstract: 

    The glycoside hydrolase family 20 (GH20) predominantly features N-acetylhexosaminidases (EC 3.2.1.52), with only few known lacto-N-biosidases (EC 3.2.1.140; LNBases). LNBases catalyze the degradation of lacto-N-tetraose (LNT), a prominent component of human milk oligosaccharides, thereby supporting a healthy infant gut microbiome development. We investigated GH20 diversity to discover novel enzymes that release disaccharides such as lacto-N-biose (LNB). Our approach combined peptide clustering, sequence analysis, and 3D structure model evaluation to assess active site topologies, focusing on the presence of a subsite -2. Five LNBases were active on pNP-LNB and four showed activity on LNT. One enzyme displayed activity on both pNP-LacNAc and pNP-LNB, establishing the first report of N-acetyllactosaminidase (LacNAcase) activity. Exploration of this enzyme cluster led to the identification of four additional enzymes sharing this dual substrate specificity. Comparing the determined crystal structure of a specific LNBase (TrpyGH20) and the first crystal structure of an enzyme with dual LacNAcase/LNBase activity (TrdeGH20) revealed a highly conserved subsite -1, common to GH20 enzymes, while the -2 subsites varied significantly. TrdeGH20 had a wider subsite -2, accommodating Gal with both β1,4- and β1,3-linkages to the GlcNAc in subsite -1. Biotechnological applications of these enzymes may include structural elucidation of complex carbohydrates and glycoengineering.


  • Organizational Affiliation

    Technical University of Denmark, Department of Biotechnology and Biomedicine, DENMARK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 20 catalytic domain-containing protein330Treponema denticola ATCC 35405Mutation(s): 0 
Gene Names: TDE_1723
UniProt
Find proteins for Q73LY9 (Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104))
Explore Q73LY9 
Go to UniProtKB:  Q73LY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ73LY9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.954α = 90
b = 50.701β = 90
c = 153.656γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Independent Research Fund Denmark - Technology and Production SciencesDenmark9068-00006B

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release