8XTC

Crystal structure of a novel PU plastic degradation urethanase UMG-SP2 mutant from uncultured bacterium in complex with ligand

This is a non-PDB format compatible entry.

Summary for 8XTC

• Entry DOI: 10.2210/pdb8xtc/pdb
• Descriptor: umgsp2-mut, 4-oxidanylbutyl ~{N}-(4-aminophenyl)carbamate, GLYCEROL, ... (4 entities in total)
• Functional Keywords: pu, degradation, mutant, hydrolase
• Biological source: metagenome
• Total number of polymer chains: 2
• Total formula weight: 94913.14

Authors

Cong, L.,Li, Z.S.,Zheng, Z.R.,Han, X.,Gert, W.,Wei, R.,Liu, W.D.,Bornscheuer, U.T. (deposition date: 2024-01-10, release date: 2025-01-15, Last modification date: 2025-04-30)

Primary citation

Li, Z.,Han, X.,Cong, L.,Singh, P.,Paiva, P.,Branson, Y.,Li, W.,Chen, Y.,Jaradat, D.M.M.,Lennartz, F.,Bayer, T.,Schmidt, L.,Garscha, U.,You, S.,Fernandes, P.A.,Ramos, M.J.,Bornscheuer, U.T.,Weber, G.,Wei, R.,Liu, W.
Structure-Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity.
Adv Sci, 12:e2416019-e2416019, 2025

PubMed Abstract: Polyurethane (PUR), the fifth most prevalent synthetic polymer, substantially contributes to the global plastic waste problem. Biotechnology-based recycling methods have recently emerged as innovative solutions to plastic waste disposal and sparked interest among scientific communities and industrial stakeholders in discovering and designing highly active plastic-degrading enzymes. Here, the ligand-free crystal structure of UMG-SP2, a metagenome-derived urethanase with depolymerization activities, at 2.59 Å resolution, as well as its (co-)structures bound to a suicide hydrolase inhibitor and a short-chain carbamate substrate at 2.16 and 2.40 Å resolutions, respectively, is reported. Structural analysis and molecular dynamics simulations reveal that the flexible loop L3 consisting of residues 219-226 is crucial for regulating the hydrolytic activity of UMG-SP2. The semi-rational redesign of UMG-SP2 reveals superior variants, A141G and Q399A, exhibiting over 30.7- and 7.4-fold increased activities on polyester-PUR and a methylene diamine derivative of PUR, respectively, compared to the wild-type enzyme. These findings advance the understanding of the structure-function relationship of PUR-hydrolyzing enzymes, which hold great promise for developing effective industrial PUR recycling processes and mitigating the environmental footprint of plastic waste.

PubMed: 39921299
DOI: 10.1002/advs.202416019

Experimental method

X-RAY DIFFRACTION (2.4 Å)