6RV8

Crystal Structure of Glucuronoyl Esterase from Cerrena unicolor covalent complex with the aldouronic acid UXXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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
481Cerrena unicolorMutation(s): 0 
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: 3
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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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)-Xylitol
C
4N/A
Glycosylation Resources
GlyTouCan:  G73163UB
GlyCosmos:  G73163UB
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
D
2N/A
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth B],
K [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.75α = 90
b = 84.75β = 90
c = 261.062γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

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: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary