6GU8

Glucuronoyl Esterase from Solibacter usitatus

• PDB DOI: https://doi.org/10.2210/pdb6GU8/pdb

• Classification: HYDROLASE
• Organism(s): Candidatus Solibacter usitatus Ellin6076
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-19 Released: 2018-08-15 
• Deposition Author(s): Lo Leggio, L., Larsbrink, J., Meland Knudsen, R., Mazurkewich, S., Navarro Poulsen, J.C.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.249 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Biochemical and structural features of diverse bacterial glucuronoyl esterases facilitating recalcitrant biomass conversion.

Arnling Baath, J., Mazurkewich, S., Knudsen, R.M., Poulsen, J.N., Olsson, L., Lo Leggio, L., Larsbrink, J.

(2018) Biotechnol Biofuels 11: 213-213

• PubMed: 30083226 
• DOI: https://doi.org/10.1186/s13068-018-1213-x
• Primary Citation of Related Structures:  
  6GRW, 6GRY, 6GS0, 6GU8


• PubMed Abstract: 
  

  Lignocellulose is highly recalcitrant to enzymatic deconstruction, where the recalcitrance primarily results from chemical linkages between lignin and carbohydrates. Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. However, only a limited number of GEs have been biochemically characterized and structurally determined to date, limiting our understanding of these enzymes and their potential exploration.

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Organizational Affiliation: 

1Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.03 kDa 
• Atom Count: 3,448 
• Modelled Residue Count: 392 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyl xylan esterase	A	397	Candidatus Solibacter usitatus Ellin6076	Mutation(s): 0  Gene Names: Acid_4275
UniProt
Find proteins for Q01YM8 (Solibacter usitatus (strain Ellin6076)) Explore Q01YM8  Go to UniProtKB:  Q01YM8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth A], K [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.249 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.579	α = 90
b = 54.579	β = 90
c = 284.112	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Lo Leggio, L., Larsbrink, J., Meland Knudsen, R., Mazurkewich, S., Navarro Poulsen, J.C.

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Funding Organization	Location	Grant Number
	Denmark	Novo Nordisk Foundation NNF17OC0027698
European Union	Denmark	Interreg-programmet for Oresund-Kattegat-Skagerrak

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release