9FZ1

UMG-SP3 amidase from uncultured bacterium in complex with 4,4'-MDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IHKClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Characterization of an Amidase Targeting a Polyurethane for Sustainable Recycling.

Rotilio, L.Bayer, T.Meinert, H.Teixeira, L.M.C.Johansen, M.B.Sommerfeldt, A.Petersen, A.R.Sandahl, A.Keller, M.B.Holck, J.Paiva, P.Otzen, D.E.Bornscheuer, U.T.Wei, R.Fernandes, P.A.Ramos, M.J.Westh, P.Morth, J.P.

(2025) Angew Chem Int Ed Engl 64: e202419535-e202419535

  • DOI: https://doi.org/10.1002/anie.202419535
  • Primary Citation of Related Structures:  
    9FVF, 9FW1, 9FZ1

  • PubMed Abstract: 

    Global plastic production exceeded 400 million tons in 2022, urgently demanding improved waste management and recycling strategies for a circular plastic economy. While the enzymatic hydrolysis of polyethylene terephthalate (PET) has become feasible on industrial scales, efficient enzymes targeting other hydrolyzable plastic types, such as polyurethanes (PURs), are lacking. Recently, enzymes of the amidase signature (AS) family, capable of cleaving urethane bonds in a polyether-PUR analog and a linear polyester-PUR, have been identified. Herein, we present high-resolution crystal structures of the AS enzyme UMG-SP3 in three states: ligand-free, bound with a suicidal inhibitor mimicking the transition state, and bound with a monomeric PUR degradation product. Besides revealing the conserved core and catalytic triad akin to other AS family members, the UMG-SP3 structures show remarkable flexibility of loop regions. Particularly, Arg209 in loop 3 adopts two induced-fit conformations upon ligand binding. Through structure-guided kinetic studies and enzyme engineering, we mapped structural key elements that determine the enhanced hydrolysis of urethane and amide bonds in various small molecules, including a linear PUR fragment analog. Our findings contribute critical insights into urethanase activity, aiding PUR degradation campaigns and sustainable plastic recycling efforts in the future.


  • Organizational Affiliation

    EnZync Center for Enzymatic Deconstruction of Thermoset Plastics.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UMG-SP3
A, B
439uncultured bacteriumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IHK (Subject of Investigation/LOI)
Query on A1IHK

Download Ideal Coordinates CCD File 
G [auth A],
H [auth B],
L [auth B]
4-[(4-aminophenyl)methyl]aniline
C13 H14 N2
YBRVSVVVWCFQMG-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.642α = 90
b = 90.642β = 90
c = 277.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IHKClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmark--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Database references