6YQ4

Crystal structure of Fusobacterium nucleatum tannase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance.

Mancheno, J.M.Atondo, E.Tomas-Cortazar, J.Luis Lavin, J.Plaza-Vinuesa, L.Martin-Ruiz, I.Barriales, D.Palacios, A.Daniel Navo, C.Sampedro, L.Pena-Cearra, A.Angel Pascual-Itoiz, M.Castelo, J.Carreras-Gonzalez, A.Castellana, D.Pellon, A.Delgado, S.Ruas-Madiedo, P.de Las Rivas, B.Abecia, L.Munoz, R.Jimenez-Oses, G.Anguita, J.Rodriguez, H.

(2022) Microb Biotechnol 15: 648-667

  • DOI: https://doi.org/10.1111/1751-7915.13732
  • Primary Citation of Related Structures:  
    6YQ4

  • PubMed Abstract: 

    Colorectal cancer pathogenesis and progression is associated with the presence of Fusobacterium nucleatum and the reduction of acetylated derivatives of spermidine, as well as dietary components such as tannin-rich foods. We show that a new tannase orthologue of F. nucleatum (TanBF nn ) has significant structural differences with its Lactobacillus plantarum counterpart affecting the flap covering the active site and the accessibility of substrates. Crystallographic and molecular dynamics analysis revealed binding of polyamines to a small cavity that connects the active site with the bulk solvent which interact with catalytically indispensable residues. As a result, spermidine and its derivatives, particularly N 8 -acetylated spermidine, inhibit the hydrolytic activity of TanBF nn and increase the toxicity of gallotannins to F. nucleatum. Our results support a model in which the balance between the detoxicant activity of TanBF nn and the presence of metabolic inhibitors can dictate either conducive or unfavourable conditions for the survival of F. nucleatum.


  • Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano" (IQFR-CSIC), Madrid, 28006, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tannase
A, B, C
495Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: FN0616
UniProt
Find proteins for Q8RFS1 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RFS1 
Go to UniProtKB:  Q8RFS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RFS1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.84α = 90
b = 91.067β = 101.7
c = 124.068γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainSAF2015-65327
Spanish Ministry of Science, Innovation, and UniversitiesSpainRTI2018-096494-B-100

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description