Crystal structure of aminocaproic acid cyclase in complex with NAD (+)

Experimental Data Snapshot

  • Resolution: 2.28 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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This is version 1.2 of the entry. See complete history


A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts

Yeom, S.J.Kim, M.Kwon, K.K.Fu, Y.Rha, E.Park, S.H.Lee, H.Kim, H.Lee, D.H.Kim, D.M.Lee, S.G.

(2018) Nat Commun 9: 5053-5053

  • DOI: https://doi.org/10.1038/s41467-018-07488-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Biocatalytic cyclization is highly desirable for efficient synthesis of biologically derived chemical substances, such as the commodity chemicals ε-caprolactam and δ-valerolactam. To identify biocatalysts in lactam biosynthesis, we develop a caprolactam-detecting genetic enzyme screening system (CL-GESS). The Alcaligenes faecalis regulatory protein NitR is adopted for the highly specific detection of lactam compounds against lactam biosynthetic intermediates. We further systematically optimize the genetic components of the CL-GESS to enhance sensitivity, achieving 10-fold improvement. Using this highly sensitive GESS, we screen marine metagenomes and find an enzyme that cyclizes ω-amino fatty acids to lactam. Moreover, we determine the X-ray crystal structure and catalytic residues based on mutational analysis of the cyclase. The cyclase is also used as a helper enzyme to sense intracellular ω-amino fatty acids. We expect this simple and accurate biosensor to have wide-ranging applications in rapid screening of new lactam-synthesizing enzymes and metabolic engineering for lactam bio-production.

  • Organizational Affiliation

    Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxybutyrate dehydrogenase
A, B, C, D
256Citrobacter freundiiMutation(s): 0 
Gene Names: AZ002_004124BED45_07125CES93_13130HMPREF3212_01462TO64_00155
Find proteins for A0A0D7LY80 (Citrobacter freundii)
Explore A0A0D7LY80 
Go to UniProtKB:  A0A0D7LY80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D7LY80
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
C21 H27 N7 O14 P2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.28 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.47α = 90
b = 148.259β = 101.47
c = 62.382γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2018R1A2B3004755

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description