Structure of 6-aminohexanoate-dimer hydrolase, G181D/H266N/D370Y mutant

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold.

Kawashima, Y.Ohki, T.Shibata, N.Higuchi, Y.Wakitani, Y.Matsuura, Y.Nakata, Y.Takeo, M.Kato, D.Negoro, S.

(2009) FEBS J 276: 2547-2556

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.06978.x
  • Primary Citation of Related Structures:  
    2E8I, 2ZM0, 2ZM7, 2ZMA

  • PubMed Abstract: 

    A carboxylesterase with a beta-lactamase fold from Arthrobacter possesses a low level of hydrolytic activity (0.023 mumol.min(-1).mg(-1)) when acting on a 6-aminohexanoate linear dimer byproduct of the nylon-6 industry (Ald). G181D/H266N/D370Y triple mutations in the parental esterase increased the Ald-hydrolytic activity 160-fold. Kinetic studies showed that the triple mutant possesses higher affinity for the substrate Ald (K(m) = 2.0 mm) than the wild-type Ald hydrolase from Arthrobacter (K(m) = 21 mm). In addition, the k(cat)/K(m) of the mutant (1.58 s(-1).mm(-1)) was superior to that of the wild-type enzyme (0.43 s(-1).mm(-1)), demonstrating that the mutant efficiently converts the unnatural amide compounds even at low substrate concentrations, and potentially possesses an advantage for biotechnological applications. X-ray crystallographic analyses of the G181D/H266N/D370Y enzyme and the inactive S112A-mutant-Ald complex revealed that Ald binding induces rotation of Tyr370/His375, movement of the loop region (N167-V177), and flip-flop of Tyr170, resulting in the transition from open to closed forms. From the comparison of the three-dimensional structures of various mutant enzymes and site-directed mutagenesis at positions 266 and 370, we now conclude that Asn266 makes suitable contacts with Ald and improves the electrostatic environment at the N-terminal region of Ald cooperatively with Asp181, and that Tyr370 stabilizes Ald binding by hydrogen-bonding/hydrophobic interactions at the C-terminal region of Ald.

  • Organizational Affiliation

    Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-aminohexanoate-dimer hydrolase392Flavobacterium sp.Mutation(s): 3 
Gene Names: NYLBNYLB'
Find proteins for P07062 (Paenarthrobacter ureafaciens)
Explore P07062 
Go to UniProtKB:  P07062
Find proteins for P07061 (Paenarthrobacter ureafaciens)
Explore P07061 
Go to UniProtKB:  P07061
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07061P07062
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.663α = 90
b = 96.663β = 90
c = 112.936γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-11-01
    Changes: Data collection, Refinement description