9DYS | pdb_00009dys

X-ray Crystallographic Structure of the Poly(Hexamethylene Adipamide) (Nylon66) Hydrolase Nyl50 at Room Temperature bound to tetraethylene glycol

• PDB DOI: https://doi.org/10.2210/pdb9DYS/pdb

• Classification: HYDROLASE
• Organism(s): Alphaproteobacteria bacterium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-14 Released: 2025-01-29 
• Deposition Author(s): Capra, N., Meilleur, F.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Identification and characterization of substrate- and product-selective nylon hydrolases.

Drufva, E.E., Cahill, J.F., Saint-Vincent, P.M.B., Williams, A.N., Bocharova, V., Capra, N., Meilleur, F., Carper, D.L., Bourgery, C., Miyazaki, K., Yonemura, M., Shiraishi, Y., Parks, J.M., Zhou, M., Dishner, I.T., Foster, J.C., Koehler, S.J., Valentino, H.R., Sedova, A., Kertesz, V., Vasileva, D.P., Hochanadel, L.H., Figg, C.A., Negoro, S., Kato, D.I., Chen, S.H., Michener, J.K.

(2024) bioRxiv 

• PubMed: 39605696 
• DOI: https://doi.org/10.1101/2024.11.14.623603
• Primary Citation Related Structures: 
  9CXR, 9DYS


• PubMed Abstract: 
  

  Enzymes have evolved to rapidly and selectively hydrolyze diverse natural and anthropogenic polymers, but only a limited group of related enzymes have been shown to hydrolyze synthetic polyamides. In this work, we synthesized and characterized a panel of 95 diverse enzymes from the N-terminal nucleophile hydrolase superfamily with 30-50% pairwise amino acid identity. We found that nearly 40% of the enzymes had substantial nylon hydrolase activity, in many cases comparable to that of the best-characterized nylon hydrolase, NylC. There was no relationship between phylogeny and activity, nor any evidence of prior selection for nylon hydrolase activity. Several newly-identified hydrolases showed significant substrate selectivity, generating up to 20-fold higher product titers with Nylon 6,6 versus Nylon 6. Finally, we determined the crystal structure and oligomerization state of a Nylon 6,6-selective hydrolase to elucidate structural factors that could affect activity and selectivity. These new enzymes provide insights into the widespread potential for nylon hydrolase evolution and opportunities for analysis and engineering of improved hydrolases.

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Organizational Affiliation: 
• Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA 37830.
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA 37830.
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA 37830.
Neutron Scattering Division, and Oak Ridge National Laboratory, Oak Ridge, TN, USA 37830.
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA 27695.
Department of Science, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, 890-0065, Japan.
Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia 24061, United States.
Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA 37830.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 63.12 kDa 
• Atom Count: 4,609 
• Modeled Residue Count: 605 
• Deposited Residue Count: 610 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(hexamethylene adipamide) hydrolase	A, B	305	Alphaproteobacteria bacterium	Mutation(s): 0  Gene Names: EPN97_01225
UniProt
Find proteins for A0ACD6BAK9 (Alphaproteobacteria bacterium) Explore A0ACD6BAK9  Go to UniProtKB:  A0ACD6BAK9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.879	α = 90
b = 96.511	β = 90
c = 105.188	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
CrysalisPro	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Capra, N., Meilleur, F.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC05-00OR22725

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release