8T9W

Crystal structure of a GH140 apiosidase derived from a lignocellulolytic enriched mangrove metagenome.

  • Classification: HYDROLASE
  • Organism(s): metagenome
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-06-26 Released: 2024-02-07 
  • Deposition Author(s): Liberato, M.V., Squina, F.
  • Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community.

Liberato, M.V.Paixao, D.A.A.Tomazetto, G.Ndeh, D.Bolam, D.N.Squina, F.M.

(2024) Biotechnol Lett 46: 201-211

  • DOI: https://doi.org/10.1007/s10529-023-03460-1
  • Primary Citation of Related Structures:  
    8T9W

  • PubMed Abstract: 

    Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase.


  • Organizational Affiliation

    Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apiosidase
A, B, C, D
434metagenomeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.093α = 90
b = 113.391β = 90
c = 158.156γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/04105-4
Sao Paulo Research Foundation (FAPESP)Brazil2015/14009-5
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil306279/2020-7

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references