6XYC

Truncated form of carbohydrate esterase from gut microbiota

• PDB DOI: https://doi.org/10.2210/pdb6XYC/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-30 Released: 2021-01-27 
• Deposition Author(s): Penttinen, L., Hakulinen, N., Master, E.
• Funding Organization(s): European Research Council (ERC), Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans.

Hameleers, L., Penttinen, L., Ikonen, M., Jaillot, L., Faure, R., Terrapon, N., Deuss, P.J., Hakulinen, N., Master, E.R., Jurak, E.

(2021) Biotechnol Biofuels 14: 127-127

• PubMed: 34059129 
• DOI: https://doi.org/10.1186/s13068-021-01976-0
• Primary Citation of Related Structures:  
  6TKX, 6XYC


• PubMed Abstract: 
  

  Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes.

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Organizational Affiliation: 

Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: mass spectrometry, native gel electrophoresis, light scattering

Macromolecule Content

• Total Structure Weight: 31.87 kDa 
• Atom Count: 2,367 
• Modelled Residue Count: 285 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl xylan esterase	A	293	metagenome	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AES	B [auth A]	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE C8 H10 F N O2 S MGSKVZWGBWPBTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.56	α = 90
b = 107.56	β = 90
c = 44.378	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Penttinen, L., Hakulinen, N., Master, E.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	648925
Academy of Finland	Finland	292705

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-06-09
  Changes: Database references
• Version 1.2: 2021-06-16
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description