Multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis: mannoimidazole complex

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 

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Structural and functional characterization of a multi-domain GH92 alpha-1,2-mannosidase from Neobacillus novalis.

Kolaczkowski, B.M.Moroz, O.V.Blagova, E.Davies, G.J.Moller, M.S.Meyer, A.S.Westh, P.Jensen, K.Wilson, K.S.Krogh, K.B.R.M.

(2023) Acta Crystallogr D Struct Biol 79: 387-400

  • DOI: https://doi.org/10.1107/S2059798323001663
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Many secreted eukaryotic proteins are N-glycosylated with oligosaccharides composed of a high-mannose N-glycan core and, in the specific case of yeast cell-wall proteins, an extended α-1,6-mannan backbone carrying a number of α-1,2- and α-1,3-mannose substituents of varying lengths. α-Mannosidases from CAZy family GH92 release terminal mannose residues from these N-glycans, providing access for the α-endomannanases, which then degrade the α-mannan backbone. Most characterized GH92 α-mannosidases consist of a single catalytic domain, while a few have extra domains including putative carbohydrate-binding modules (CBMs). To date, neither the function nor the structure of a multi-domain GH92 α-mannosidase CBM has been characterized. Here, the biochemical investigation and crystal structure of the full-length five-domain GH92 α-1,2-mannosidase from Neobacillus novalis (NnGH92) with mannoimidazole bound in the active site and an additional mannoimidazole bound to the N-terminal CBM32 are reported. The structure of the catalytic domain is very similar to that reported for the GH92 α-mannosidase Bt3990 from Bacteroides thetaiotaomicron, with the substrate-binding site being highly conserved. The function of the CBM32s and other NnGH92 domains was investigated by their sequential deletion and suggested that whilst their binding to the catalytic domain was crucial for the overall structural integrity of the enzyme, they appear to have little impact on the binding affinity to the yeast α-mannan substrate. These new findings provide a better understanding of how to select and optimize other multi-domain bacterial GH92 α-mannosidases for the degradation of yeast α-mannan or mannose-rich glycans.

  • Organizational Affiliation

    Department of Science and Environment, Roskilde University, Universitetsvej 1, Building 28, 4000 Roskilde, Denmark.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GH92 alpha-1,2-mannosidase
A, B
1,411Neobacillus novalisMutation(s): 0 
Find proteins for A0A7R9KAR8 (Neobacillus novalis)
Explore A0A7R9KAR8 
Go to UniProtKB:  A0A7R9KAR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R9KAR8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B3P

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]
C11 H26 N2 O6
Query on MVL

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G [auth A],
J [auth A],
O [auth B]
C8 H12 N2 O4
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.605α = 90
b = 151.937β = 94.63
c = 114.007γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
xia2data reduction
xia2data scaling
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-04-10
    Changes: Database references, Refinement description