Structure of L-lysine oxidase

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

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Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, l-lysine alpha-oxidase from Trichoderma viride.

Amano, M.Mizuguchi, H.Sano, T.Kondo, H.Shinyashiki, K.Inagaki, J.Tamura, T.Kawaguchi, T.Kusakabe, H.Imada, K.Inagaki, K.

(2015) J Biochem 157: 549-559

  • DOI: https://doi.org/10.1093/jb/mvv012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    L-Lysine α-oxidase (LysOX) from Trichoderma viride is a homodimeric 112 kDa flavoenzyme that catalyzes the oxidative deamination of L-lysine to form α-keto-ε-aminocaproate. LysOX severely inhibited growth of cancer cells but showed relatively low cytotoxicity for normal cells. We have determined the cDNA nucleotide sequence encoding LysOX from T. viride. The full-length cDNA consists of 2,119 bp and encodes a possible signal peptide (Met1-Arg77) and the mature protein (Ala78-Ile617). The LysOX gene have been cloned and heterologously expressed in Streptomyces lividans TK24 with the enzyme activity up to 9.8 U/ml. The enzymatic properties of the purified recombinant LysOX, such as substrate specificity and thermal stability, are same as those of native LysOX. The crystal structure of LysOX at 1.9 Å resolution revealed that the overall structure is similar to that of snake venom L-amino acid oxidase (LAAO), and the residues involved in the interaction with the amino or carboxy group of the substrate are structurally conserved. However, the entrance and the inner surface structures of the funnel to the active site, as well as the residues involved in the substrate side-chain recognition, are distinct from LAAOs. These structural differences well explain the unique substrate specificity of LysOX.

  • Organizational Affiliation

    Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan; Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan; and Enzyme Sensor Co., Ltd., Tsukuba, Ibaraki 305-0047, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lysine oxidase
A, B
541Trichoderma virideMutation(s): 0 
Find proteins for A0A0J9X1X3 (Hypocrea rufa)
Explore A0A0J9X1X3 
Go to UniProtKB:  A0A0J9X1X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X1X3
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.975α = 90
b = 170.012β = 132.01
c = 81.046γ = 90
Software Package:
Software NamePurpose
SPring-8data collection
PHENIXmodel building
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description