6HPD

The structure of a beta-glucuronidase from glycoside hydrolase family 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan.

Reisky, L.Prechoux, A.Zuhlke, M.K.Baumgen, M.Robb, C.S.Gerlach, N.Roret, T.Stanetty, C.Larocque, R.Michel, G.Song, T.Markert, S.Unfried, F.Mihovilovic, M.D.Trautwein-Schult, A.Becher, D.Schweder, T.Bornscheuer, U.T.Hehemann, J.H.

(2019) Nat Chem Biol 15: 803-812

  • DOI: https://doi.org/10.1038/s41589-019-0311-9
  • Primary Citation of Related Structures:  
    6HHM, 6HHN, 6HPD, 6HR5

  • PubMed Abstract: 

    Marine seaweeds increasingly grow into extensive algal blooms, which are detrimental to coastal ecosystems, tourism and aquaculture. However, algal biomass is also emerging as a sustainable raw material for the bioeconomy. The potential exploitation of algae is hindered by our limited knowledge of the microbial pathways-and hence the distinct biochemical functions of the enzymes involved-that convert algal polysaccharides into oligo- and monosaccharides. Understanding these processes would be essential, however, for applications such as the fermentation of algal biomass into bioethanol or other value-added compounds. Here, we describe the metabolic pathway that enables the marine flavobacterium Formosa agariphila to degrade ulvan, the main cell wall polysaccharide of bloom-forming Ulva species. The pathway involves 12 biochemically characterized carbohydrate-active enzymes, including two polysaccharide lyases, three sulfatases and seven glycoside hydrolases that sequentially break down ulvan into fermentable monosaccharides. This way, the enzymes turn a previously unexploited renewable into a valuable and ecologically sustainable bioresource.


  • Organizational Affiliation

    Institute of Marine Biotechnology, Greifswald, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase (GH2)990Formosa agariphila KMM 3901Mutation(s): 0 
Gene Names: BN863_22060
EC: 3.2.1.23
UniProt
Find proteins for T2KN75 (Formosa agariphila (strain DSM 15362 / KCTC 12365 / LMG 23005 / KMM 3901 / M-2Alg 35-1))
Explore T2KN75 
Go to UniProtKB:  T2KN75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2KN75
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.929α = 90
b = 67.17β = 95.93
c = 96.72γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyHE 7217/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description