X-ray structure of N-methyl-L-tryptophan oxidase (MTOX)

Experimental Data Snapshot

  • Resolution: 3.20 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 

Starting Model: experimental
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The X-Ray Structure of N-Methyltryptophan Oxidase Reveals the Structural Determinants of Substrate Specificity.

Ilari, A.Bonamore, A.Franceschini, S.Fiorillo, A.Boffi, A.Colotti, G.

(2008) Proteins 71: 2065

  • DOI: https://doi.org/10.1002/prot.21898
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The X-ray structure of monomeric N-methyltryptophan oxidase from Escherichia coli (MTOX) has been solved at 3.2 A resolution by molecular replacement methods using Bacillus sp. sarcosine oxidase structure (MSOX, 43% sequence identity) as search model. The analysis of the substrate binding site highlights the structural determinants that favour the accommodation of the bulky N-methyltryptophan residue in MTOX. In fact, although the nature and geometry of the catalytic residues within the first contact shell of the FAD moiety appear to be virtually superposable in MTOX and MSOX, the presence of a Thr residue in position 239 in MTOX (Met245 in MSOX) located at the entrance of the active site appears to play a key role for the recognition of the amino acid substrate side chain. Accordingly, a 15 fold increase in k(cat) and 100 fold decrease in K(m) for sarcosine as substrate has been achieved in MTOX upon T239M mutation, with a concomitant three-fold decrease in activity towards N-methyltryptophan. These data provide clear evidence for the presence of a catalytic core, common to the members of the methylaminoacid oxidase subfamily, and of a side chain recognition pocket, located at the entrance of the active site, that can be adjusted to host diverse aminoacids in the different enzyme species. The site involved in the covalent attachment of flavin has also been addressed by screening degenerate mutants in the relevant positions around Cys308-FAD linkage. Lys341 appears to be the key residue involved in flavin incorporation and covalent linkage.

  • Organizational Affiliation

    Institute of Molecular Biology and Pathology, C.N.R., Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
372Escherichia coli BL21(DE3)Mutation(s): 0 
EC: 1.5.3
Find proteins for P40874 (Escherichia coli (strain K12))
Explore P40874 
Go to UniProtKB:  P40874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40874
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.20 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.240 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.188α = 90
b = 89.809β = 104.75
c = 91.915γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Data collection, Derived calculations, Other, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description