Mandelate oxidase mutant-Y128F with (2R,3S)-3-fluoro-2-hydroxy-3-phenylpropanoic acid

Experimental Data Snapshot

  • Resolution: 1.42 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity.

Lin, K.H.Lyu, S.Y.Yeh, H.W.Li, Y.S.Hsu, N.S.Huang, C.M.Wang, Y.L.Shih, H.W.Wang, Z.C.Wu, C.J.Li, T.L.

(2020) Protein Sci 29: 1655-1666

  • DOI: https://doi.org/10.1002/pro.3879
  • Primary Citation of Related Structures:  
    5ZZT, 6A01, 6A0B, 6A1B, 6A1N, 6A1W, 6A24, 6A36, 6A3D, 6A4G, 6A4H, 7BSR

  • PubMed Abstract: 

    Though reactive flavin-N5/C4α-oxide intermediates can be spectroscopically profiled for some flavin-assisted enzymatic reactions, their exact chemical configurations are hardly visualized. Structural systems biology and stable isotopic labelling techniques were exploited to correct this stereotypical view. Three transition-like complexes, the α-ketoacid…N5-FMN ox complex (I), the FMN ox -N5-aloxyl-C'α - -C4α + zwitterion (II), and the FMN-N5-ethenol-N5-C4α-epoxide (III), were determined from mandelate oxidase (Hmo) or its mutant Y128F (monooxygenase) crystals soaked with monofluoropyruvate (a product mimic), establishing that N5 of FMN ox an alternative reaction center can polarize to an ylide-like mesomer in the active site. In contrast, four distinct flavin-C4α-oxide adducts (IV-VII) from Y128F crystals soaked with selected substrates materialize C4α of FMN an intrinsic reaction center, witnessing oxidation, Baeyer-Villiger/peroxide-assisted decarboxylation, and epoxidation reactions. In conjunction with stopped-flow kinetics, the multifaceted flavin-dependent reaction continuum is physically dissected at molecular level for the first time.

  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxymandelate oxidase377Amycolatopsis orientalisMutation(s): 1 
Gene Names: hmo
Find proteins for O52792 (Amycolatopsis orientalis)
Explore O52792 
Go to UniProtKB:  O52792
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO52792
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.42 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.156α = 90
b = 138.156β = 90
c = 111.838γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description