6RV8 | pdb_00006rv8

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

• PDB DOI: https://doi.org/10.2210/pdb6RV8/pdb

• Classification: HYDROLASE
• Organism(s): Cerrena unicolor
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-05-31 Released: 2020-03-18 
• Deposition Author(s): Ernst, H.A., Mosbech, C., Langkilde, A., Westh, P., Meyer, A., Agger, J.W., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

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

• PubMed: 32094331 
• DOI: https://doi.org/10.1038/s41467-020-14833-9
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kongens Lyngby, Denmark.
Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark.
Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, 2800, Kongens Lyngby, Denmark. [e-mail].
Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104 kDa 
• Atom Count: 6,485 
• Modeled Residue Count: 762 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-O-methyl-glucuronoyl methylesterase	A, B	481	Cerrena unicolor	Mutation(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
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-Xylitol	C	4		N/A
Glycosylation Resources
GlyTouCan: G73163UB GlyCosmos: G73163UB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan: G87728WL GlyCosmos: G87728WL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	G [auth A], H [auth A], J [auth B], K [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	D	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.75	α = 90
b = 84.75	β = 90
c = 261.062	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Ernst, H.A., Mosbech, C., Langkilde, A., Westh, P., Meyer, A., Agger, J.W., Larsen, S.

Revision History  

• 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
• Version 2.2: 2024-11-13
  Changes: Structure summary