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 6HPD | pdb_00006hpd

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 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6HPD

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 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: 
    • Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University Greifswald, Greifswald, Germany.

Macromolecule Content 

  • Total Structure Weight: 112.96 kDa 
  • Atom Count: 8,066 
  • Modeled Residue Count: 955 
  • Deposited Residue Count: 990 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (PDB Primary Data), 3.2.1.31 (UniProt)
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 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
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