6HH9

Crystal structure of a two-domain esterase (CEX) active on acetylated mannans co-crystallized with mannopentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex beta-mannans.

Michalak, L.La Rosa, S.L.Leivers, S.Lindstad, L.J.Rohr, A.K.Lillelund Aachmann, F.Westereng, B.

(2020) Proc Natl Acad Sci U S A 117: 7122-7130

  • DOI: 10.1073/pnas.1915376117
  • Primary Citation of Related Structures:  
    6HFZ, 6HH9

  • PubMed Abstract: 
  • β-mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods ...

    β-mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods. There are many fully characterized acetylxylan esterases (AcXEs); however, the enzymes deacetylating mannans are less understood. Here we present two carbohydrate esterases, Ri CE2 and Ri CE17, from the Firmicute Roseburia intestinalis , which together deacetylate complex galactoglucomannan (GGM). The three-dimensional (3D) structure of Ri CE17 with a mannopentaose in the active site shows that the CBM35 domain of Ri CE17 forms a confined complex, where the axially oriented C2-hydroxyl of a mannose residue points toward the Ser41 of the catalytic triad. Cavities on the Ri CE17 surface may accept galactosylations at the C6 positions of mannose adjacent to the mannose residue being deacetylated (subsite -1 and +1). In-depth characterization of the two enzymes using time-resolved NMR, high-performance liquid chromatography (HPLC), and mass spectrometry demonstrates that they work in a complementary manner. Ri CE17 exclusively removes the axially oriented 2- O -acetylations on any mannose residue in an oligosaccharide, including double acetylated mannoses, while the Ri CE2 is active on 3- O- , 4- O- , and 6- O- acetylations. Activity of Ri CE2 is dependent on Ri CE17 removing 2- O -acetylations from double acetylated mannose. Furthermore, transacetylation of oligosaccharides with the 2- O -specific Ri CE17 provided insight into how temperature and pH affects acetyl migration on manno-oligosaccharides.


    Organizational Affiliation

    Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432 Ås, Norway; bjorge.westereng@nmbu.no.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GDSL-like proteinA, B, C, D378Roseburia intestinalis L1-82Mutation(s): 0 
Gene Names: ROSINTL182_05471
UniProt
Find proteins for C7G6F8 (Roseburia intestinalis L1-82)
Explore C7G6F8 
Go to UniProtKB:  C7G6F8
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranoseE4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G51338PC
GlyCosmos:  G51338PC
GlyGen:  G51338PC
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranoseF, G, H3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G26320VF
GlyCosmos:  G26320VF
GlyGen:  G26320VF
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.482α = 90
b = 136.69β = 113.86
c = 85.411γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway244259
Research Council of NorwayNorway240967
Research Council of NorwayNorway226244/F50

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Data collection, Database references
  • Version 1.2: 2020-04-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary