6RV9

Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor inactive S270A variant in complex with the aldouronic acid XUXXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

The structural basis of fungal glucuronoyl esterase activity on natural substrates.

Ernst, H.A.Mosbech, C.Langkilde, A.E.Westh, P.Meyer, A.S.Agger, J.W.Larsen, S.

(2020) Nat Commun 11: 1026-1026

  • DOI: https://doi.org/10.1038/s41467-020-14833-9
  • Primary Citation of Related Structures:  
    6RTV, 6RU1, 6RU2, 6RV7, 6RV8, 6RV9

  • PubMed Abstract: 

    Structural and functional studies were conducted of the glucuronoyl esterase (GE) from Cerrena unicolor (CuGE), an enzyme catalyzing cleavage of lignin-carbohydrate ester bonds. CuGE is an α/β-hydrolase belonging to carbohydrate esterase family 15 (CE15). The enzyme is modular, comprised of a catalytic and a carbohydrate-binding domain. SAXS data show CuGE as an elongated rigid molecule where the two domains are connected by a rigid linker. Detailed structural information of the catalytic domain in its apo- and inactivated form and complexes with aldouronic acids reveal well-defined binding of the 4-O-methyl-a-D-glucuronoyl moiety, not influenced by the nature of the attached xylo-oligosaccharide. Structural and sequence comparisons within CE15 enzymes reveal two distinct structural subgroups. CuGE belongs to the group of fungal CE15-B enzymes with an open and flat substrate-binding site. The interactions between CuGE and its natural substrates are explained and rationalized by the structural results, microscale thermophoresis and isothermal calorimetry.


  • Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-O-methyl-glucuronoyl methylesterase
A, B
401Cerrena unicolorMutation(s): 1 
EC: 3.1.1 (PDB Primary Data), 3.1.1.117 (UniProt)
UniProt
Find proteins for A0A0A7EQR3 (Cerrena unicolor)
Explore A0A0A7EQR3 
Go to UniProtKB:  A0A0A7EQR3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A7EQR3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol
C
5N/A
Glycosylation Resources
GlyTouCan:  G92772TT
GlyCosmos:  G92772TT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.481α = 90
b = 84.481β = 90
c = 261.732γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary