9LMT | pdb_00009lmt

Crystal structure of variant FAST-ACC-A248E

• PDB DOI: https://doi.org/10.2210/pdb9LMT/pdb

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


• Deposited: 2025-01-20 Released: 2025-07-23 
• Deposition Author(s): Li, X., Ning, Z.Y., Huang, S.Q., Zeng, C., Zeng, Z.Y., Ji, R., Huang, J.-W., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.162 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Combined approaches to enhance the Pichia pastoris-expressed PET hydrolase.

Li, X., Huang, J.W., Ning, Z., Huang, S., Zeng, C., Zeng, Z., Ji, R., Peng, R., Liu, X., Min, J., Chen, C.C., Guo, R.T.

(2025) Int J Biol Macromol 320: 145862-145862

• PubMed: 40653245 
• DOI: https://doi.org/10.1016/j.ijbiomac.2025.145862
• Primary Citation Related Structures: 
  9LMS, 9LMT, 9LMU, 9LMV, 9LMW, 9LMX


• PubMed Abstract: 
  

  Enzymatic degradation of polyethylene terephthalate (PET) provides a sustainable and promising strategy for the recycling of plastic waste. Herein, we employed site-directed mutagenesis and machine learning methods to further enhance the performance of an efficient mutant of IsPETase, FAST-PETase-N212A, and resulting in seven variants with enhanced activity. We also found that the α3-β5 loop containing the T140D mutation plays a significant role in both type I and type II cutinases. Subsequently, we determined the complex structures of two activity-elevated mutants with the PET analogue mono(2-hydroxyethyl)terephthalic acid, revealing a different binding mode. Finally, to facilitate the industrial application of PET hydrolases, we exploited the industrial strain Pichia pastoris to express the activity-enhanced mutants. Compared with E. coli-produced proteins, these mutants expressed by P. pastoris exhibited higher activity and thermal stability.

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Organizational Affiliation: 
• Zhejiang Key Laboratory of Medical Epigenetics, Hubei Hongshan Laboratory, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, China; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
Zhejiang Key Laboratory of Medical Epigenetics, Hubei Hongshan Laboratory, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, China.
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China. Electronic address: [e-mail].
Zhejiang Key Laboratory of Medical Epigenetics, Hubei Hongshan Laboratory, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, China. Electronic address: [e-mail].
Zhejiang Key Laboratory of Medical Epigenetics, Hubei Hongshan Laboratory, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, 311121 Hangzhou, China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.39 kDa 
• Atom Count: 2,254 
• Modeled Residue Count: 262 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	262	Piscinibacter sakaiensis	Mutation(s): 1  Gene Names: ISF6_4831 EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Piscinibacter sakaiensis) Explore A0A0K8P6T7  Go to UniProtKB:  A0A0K8P6T7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.162 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.134 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.026	α = 90
b = 51.61	β = 90
c = 84.496	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Li, X., Ning, Z.Y., Huang, S.Q., Zeng, C., Zeng, Z.Y., Ji, R., Huang, J.-W., Chen, C.-C., Guo, R.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release
  
• Version 1.1: 2025-07-30
  Changes: Database references