Structure of the GH76A alpha-1,6-mannanase from Salegentibacter sp. HEL1_6

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

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Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi.

Solanki, V.Kruger, K.Crawford, C.J.Pardo-Vargas, A.Danglad-Flores, J.Hoang, K.L.M.Klassen, L.Abbott, D.W.Seeberger, P.H.Amann, R.I.Teeling, H.Hehemann, J.H.

(2022) ISME J 

  • DOI: https://doi.org/10.1038/s41396-022-01223-w
  • Primary Citation of Related Structures:  
    6SHD, 6SHM, 6Y8F

  • PubMed Abstract: 

    Microbial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α) 6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms.

  • Organizational Affiliation

    Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
390Salegentibacter sp. Hel_I_6Mutation(s): 0 
Gene Names: GH76A
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.261α = 90
b = 37.507β = 100.95
c = 187.457γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description