8YTV | pdb_00008ytv

The M19 variant of Mipa-Petase from Micromonospora pattaloongensis

• PDB DOI: https://doi.org/10.2210/pdb8YTV/pdb

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


• Deposited: 2024-03-26 Released: 2025-01-15 
• Deposition Author(s): Hong, H., Seo, H., Park, J., Kim, K.-J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Landscape profiling of PET depolymerases using a natural sequence cluster framework.

Seo, H., Hong, H., Park, J., Lee, S.H., Ki, D., Ryu, A., Sagong, H.Y., Kim, K.J.

(2025) Science 387: eadp5637-eadp5637

• PubMed: 39745946 
• DOI: https://doi.org/10.1126/science.adp5637
• Primary Citation Related Structures: 
  8YTU, 8YTV, 8YTW, 8YTY, 8YTZ


• PubMed Abstract: 
  

  Enzymes capable of breaking down polymers have been identified from natural sources and developed for industrial use in plastic recycling. However, there are many potential starting points for enzyme optimization that remain unexplored. We generated a landscape of 170 lineages of 1894 polyethylene terephthalate depolymerase (PETase) candidates and performed profiling using sampling approaches with features associated with PET-degrading capabilities. We identified three promising yet unexplored PETase lineages and two potent PETases, Mipa-P and Kubu-P. An engineered variant of Kubu-P outperformed benchmarks in terms of PET depolymerization in harsh environments, such as those with high substrate load and ethylene glycol as the solvent.

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Organizational Affiliation: 
• KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea.
Zyen Co., Daegu, Republic of Korea.
Institute of Biotechnology, CJ CheilJedang Co., Suwon-si, Republic of Korea.
School of Life Sciences and Biotechnology, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.53 kDa 
• Atom Count: 3,984 
• Modeled Residue Count: 502 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cutinase	A, B	265	Micromonospora pattaloongensis	Mutation(s): 19  Gene Names: SAMN05444365_106119 EC: 3.1.1.74
UniProt
Find proteins for A0A1H3QT72 (Micromonospora pattaloongensis) Explore A0A1H3QT72  Go to UniProtKB:  A0A1H3QT72

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.619	α = 90
b = 51.359	β = 94.33
c = 107.654	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Hong, H., Seo, H., Park, J., Kim, K.-J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020M3A9I5037635

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release