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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41589-019-0311-9
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany.,Sorbonne Université, CNRS, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France.,Max Planck-Institute for Marine Microbiology, Bremen, Germany.,Max Planck-Institute for Marine Microbiology, Bremen, Germany. jhhehemann@marum.de.,Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany.,Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria.,Institute of Microbiology, University Greifswald, Greifswald, Germany.,Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Greifswald, Germany. schweder@uni-greifswald.de.,Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France.,University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany. jhhehemann@marum.de.,Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany. uwe.bornscheuer@uni-greifswald.de.,Institute of Marine Biotechnology, Greifswald, Germany. schweder@uni-greifswald.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactosidase (GH2)
A
990Formosa agariphila KMM 3901Mutation(s): 0 
EC: 3.2.1.23
Find proteins for T2KN75 (Formosa agariphila KMM 3901)
Go to UniProtKB:  T2KN75
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.929α = 90.00
b = 67.170β = 95.93
c = 96.720γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyHE 7217/1-1

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references