29PZ

Putative Polyurethane Degrading Esterase Bound to Fragment VT00162

Summary for 29PZ

• Entry DOI: 10.2210/pdb29pz/pdb
• Descriptor: Carboxylic ester hydrolase, ASN-LEU-TYR-PHE, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: esterase, hydrolase
• Biological source: Alloalcanivorax xenomutans; More
• Total number of polymer chains: 2
• Total formula weight: 59891.76

Authors

Bicer, D.,Otzen, D.E.,Morth, J.P.,Thirup, S.S. (deposition date: 2026-03-29, release date: 2026-11-04, Last modification date: 2026-11-11)

Primary citation

Bicer, D.,Kochubei, D.,Graham, R.,Pena-Diaz, S.,Rotilio, L.,Villadsen, N.L.,Sommerfeldt, A.,Johansen, M.B.,Sandahl, A.,Thirup, S.S.,Morth, J.P.,Otzen, D.E.
Fragment-based active-site exploration of urethane hydrolases reveals a diversity of urethane binding modes.
Acta Crystallogr D Struct Biol, 82:1298-1317, 2026

PubMed Abstract: Recent advances in the discovery, characterization and engineering of urethanases provide new opportunities for the sustainable biocatalytic degradation of polyurethane waste. A mechanistic understanding of enzyme-plastic interactions is essential for structure-based engineering to enhance urethanase activity. However, the extremely complex and hydrophobic nature of polyurethane makes it challenging to elucidate the structural basis of enzyme-plastic interactions. Here, we used a fragment-based approach to characterize the active sites of two novel urethanases called amidase U11 and esterase AX with different catalytic scaffolds, employing a crystallographic fragment-screening campaign to map subpockets in the active site and validate these subpockets as plastic binding sites by using soluble plastic fragment analogues that mimic the substrate, transition state or product. We resolved 42 high-resolution structures for both esterase AX and amidase U11. The fragment-based approach identified new substrate-binding subpockets, while interactions of plastic mimetics in the active site provided a mechanistic understanding of the recognition and binding of polyurethane fragments by these subpockets. These results highlight a diversity of binding modes among urethanases towards different polyurethane fragments.

PubMed: 42929454
DOI: 10.1107/S2059798326010624

Experimental method

X-RAY DIFFRACTION (1.59 Å)