7B5V

The carbohydrate binding module family 48 (CBM48) and carboxy-terminal carbohydrate esterase family 1 (CE1) domains of the multidomain esterase DmCE1B from Dysgonomonas mossii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A polysaccharide utilization locus from the gut bacterium Dysgonomonas mossii encodes functionally distinct carbohydrate esterases.

Kmezik, C.Mazurkewich, S.Meents, T.McKee, L.S.Idstrom, A.Armeni, M.Savolainen, O.Branden, G.Larsbrink, J.

(2021) J Biol Chem 296: 100500-100500

  • DOI: https://doi.org/10.1016/j.jbc.2021.100500
  • Primary Citation of Related Structures:  
    7B5V, 7B6B

  • PubMed Abstract: 

    The gut microbiota plays a central role in human health by enzymatically degrading dietary fiber and concomitantly excreting short chain fatty acids that are associated with manifold health benefits. The polysaccharide xylan is abundant in dietary fiber but noncarbohydrate decorations hinder efficient cleavage by glycoside hydrolases (GHs) and need to be addressed by carbohydrate esterases (CEs). Enzymes from carbohydrate esterase families 1 and 6 (CE1 and 6) perform key roles in xylan degradation by removing feruloyl and acetate decorations, yet little is known about these enzyme families especially with regard to their diversity in activity. Bacteroidetes bacteria are dominant members of the microbiota and often encode their carbohydrate-active enzymes in multigene polysaccharide utilization loci (PULs). Here we present the characterization of three CEs found in a PUL encoded by the gut Bacteroidete Dysgonomonas mossii. We demonstrate that the CEs are functionally distinct, with one highly efficient CE6 acetyl esterase and two CE1 enzymes with feruloyl esterase activities. One multidomain CE1 enzyme contains two CE1 domains: an N-terminal domain feruloyl esterase, and a C-terminal domain with minimal activity on model substrates. We present the structure of the C-terminal CE1 domain with the carbohydrate-binding module that bridges the two CE1 domains, as well as a complex of the same protein fragment with methyl ferulate. The investment of D. mossii in producing multiple CEs suggests that improved accessibility of xylan for GHs and cleavage of covalent polysaccharide-polysaccharide and lignin-polysaccharide bonds are important enzyme activities in the gut environment.


  • Organizational Affiliation

    Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbohydrate Esterase family 1 protein with an N-terminal carbohydrate binding module family 48
A, B
386Dysgonomonas mossii DSM 22836Mutation(s): 0 
Gene Names: HMPREF9456_02279
UniProt
Find proteins for F8X1N1 (Dysgonomonas mossii DSM 22836)
Explore F8X1N1 
Go to UniProtKB:  F8X1N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8X1N1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.962α = 90
b = 80.966β = 105.666
c = 107.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
MoRDaphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03931
Novo Nordisk FoundationSwedenNNF17OC0027648
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2021-07-21
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Advisory, Data collection, Database references, Refinement description