5NOA

Polysaccharide Lyase BACCELL_00875


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.

Munoz-Munoz, J.Cartmell, A.Terrapon, N.Basle, A.Henrissat, B.Gilbert, H.J.

(2017) J Biol Chem 292: 13271-13283

  • DOI: 10.1074/jbc.M117.794578
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represent ...

    The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta , and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-α1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Δ4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-β-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (α/α) 6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the β-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.


    Related Citations: 
    • Rhamnose Capping in Complex Arabinogalactan Proteins
      Munoz-Munoz, J., Cartmell, A., Terrapon, N., Basle, A., Henrissat, B.
      () To be published --: --

    Organizational Affiliation

    From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom, harry.gilbert@ncl.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Family 88 glycosyl hydrolaseA381Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: yteR_9BJP75_03260Btheta7330_04609
EC: 3.2.1.172
Find proteins for Q8A1H4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Explore Q8A1H4 
Go to UniProtKB:  Q8A1H4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.123 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.398α = 90
b = 88.398β = 90
c = 215.857γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
MrBUMPphasing
PHASERphasing
BUCCANEERmodel building
ARPmodel building
WARPmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCUnited Kingdom322820

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Database references