6HR5

Structure of the S1_25 family sulfatase module of the rhamnosidase FA22250 from Formosa agariphila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.324 

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: 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 ...

    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

    University of Bremen, Center for Marine Environmental Sciences, Bremen, Germany. jhhehemann@marum.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-L-rhamnosidase/sulfatase (GH78)A467Formosa agariphila KMM 3901Mutation(s): 0 
Gene Names: BN863_22250
EC: 3.1.6 (UniProt), 3.2.1.40 (UniProt)
UniProt
Find proteins for T2KM26 (Formosa agariphila (strain DSM 15362 / KCTC 12365 / LMG 23005 / KMM 3901 / M-2Alg 35-1))
Explore T2KM26 
Go to UniProtKB:  T2KM26
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT2KM26
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.361 
  • R-Value Work: 0.322 
  • R-Value Observed: 0.324 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.879α = 90
b = 48.871β = 105.64
c = 92.651γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-14-CE19- 0020-01
French National Research AgencyFranceANR-10-BTBR-04

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references