8X65 | pdb_00008x65

Crystal structure of X11P(P71T) xylanase from a metagenome derived gene from sugarcane bagasse collection site

• PDB DOI: https://doi.org/10.2210/pdb8X65/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-11-20 Released: 2024-11-27 
• Deposition Author(s): Chitnumsub, P., Jaruwat, A., Boonyapakron, K., Prabmark, K.
• Funding Organization(s): National Center for Genetic Engineering and Biotechnology (Thailand)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.166 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Starting Model: experimental

Literature

Hyperthermophilic xylanase and thermophilicity analysis by molecular dynamic simulation with quantum mechanics.

Boonyapakron, K., Keiser, B., Prabmark, K., Aiewviriyasakul, K., Arunrattanamook, N., Jaruwat, A., Chitnumsub, P., Li, J.Y., Wong, T.S., Zhao, X.Q., Liu, C.G., Wei, D.Q., Champreda, V.

(2024) Appl Microbiol Biotechnol 108: 526-526

• PubMed: 39630239 
• DOI: https://doi.org/10.1007/s00253-024-13356-3
• Primary Citation of Related Structures:  
  8X65


• PubMed Abstract: 
  

  Thermophilic xylanases catalyzing the cleavage of β-1,4-glycosidic bonds in xylan have applications in food, feed, biorefinery, and pulp industries. In this study, a hyperthermophilic endo-xylanase was obtained by further enhancement of thermal tolerance of a thermophilic GH11 xylanase originated from metagenome of bagasse pile based on rational design. Introducing N13F and Q34L to the previously reported X11P enzyme shifted the optimal working temperature to 85 °C and led to 20.7-fold improvement in thermostability at 90 °C along with a marked increase in T _m to 93.3 °C. X11PNQ enzyme converted xylan to prebiotic xylooligosaccharides with high specificity on xylobiose to xylohexaose and high operational stability at 85 °C, resulting in 10.3-folds yield improvement compared to the parental enzyme. Molecular dynamic simulation and quantum mechanical analysis revealed improved H-bonding networks within GH11 xylanase principal domains and greater dynamic cross-correlations. A novel thermostabilization mechanism by π-amide interaction with slightly lower interaction energy than the native H-bond, but compensated by increased occurrence frequency was firstly demonstrated for thermophilic enzymes. The enzyme represents one of the most thermostable xylanases ever reported with biotechnological potential. KEY POINTS: • Hyperthemophilic xylanase X11PNQ was obtained by rational design engineering. • X11PNQ showed specificity to prebiotic xylooligosaccharides (XOS) at 85 °C with improved t _1/2 at 90 °C. • Novel thermostabilization by π-amide interaction was demonstrated by MD/QM.

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Organizational Affiliation: 
• Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, 12120, Patumthani, Thailand.
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
Biomolecular Analysis and Application Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Patumthani, 12120, Thailand.
School of Chemical, Materials and Biological Engineering, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK.
State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China. [e-mail].
Qihe Laboratory, Qishui Guang East, Qibin District, Hebi, Henan, 458030, China. [e-mail].
Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, 12120, Patumthani, Thailand. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.91 kDa 
• Atom Count: 1,850 
• Modeled Residue Count: 202 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase	A	207	uncultured bacterium	Mutation(s): 1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.166 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.466	α = 90
b = 68.547	β = 90
c = 74.4	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Chitnumsub, P., Jaruwat, A., Boonyapakron, K., Prabmark, K.

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Funding Organization	Location	Grant Number
National Center for Genetic Engineering and Biotechnology (Thailand)	Thailand	--

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Database references