6A3D

The crystal structure of Mandelate oxidase Y128F with 4-Br-2-hydroxy-methylphenylacetate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

    Department of Food Science, National Taiwan Ocean University, Keelung, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxymandelate oxidase377Amycolatopsis orientalisMutation(s): 1 
Gene Names: hmo
EC: 1.1.3.46
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9PX
Query on 9PX

Download Ideal Coordinates CCD File 
B [auth A]1-deoxy-1-[(4aS)-4a-[(methoxycarbonyl)peroxy]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol
C19 H25 N4 O13 P
BKTAMFVARSDVLC-LJPSSGMGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.546α = 90
b = 138.546β = 90
c = 108.501γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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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