6A0V

Mandelate oxidase mutant-Y128F with (S)-mandelic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level.

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

(2019) Acta Crystallogr D Struct Biol 75: 918-929

  • DOI: 10.1107/S2059798319011938
  • Primary Citation of Related Structures:  
    5ZZP, 5ZZR, 5ZZZ, 6A08, 6A0V, 6A19, 6A13, 6A1P, 6A21, 6A1R

  • PubMed Abstract: 
  • The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen perox ...

    The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen peroxide (an oxidant) were used as substrates the reaction did not proceed, suggesting that free hydrogen peroxide is not the committed oxidant in the second two-electron oxidation. How the flavin mononucleotide (FMN)-dependent four-electron oxidation reaction takes place remains elusive. Structural and biochemical explorations have shed new light on this issue. 15 high-resolution crystal structures of Hmo and its mutants liganded with or without a substrate reveal that oxidized FMN (FMN ox ) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMN ox to a nucleophilic ylide, which is in a position to act on an α-ketoacid, forming an N5-acyl-FMN red dead-end adduct. In four-electron oxidation, an intramolecular disproportionation reaction via an N5-alkanol-FMN red C'α carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMN ox cofactor in combination with an α-hydroxyamide or α-ketoamide biochemically and structurally supports the proposed mechanism.


    Related Citations: 
    • Biochemical and structural explorations of alpha-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction.
      Yeh, H.W., Lin, K.H., Lyu, S.Y., Li, Y.S., Huang, C.M., Wang, Y.L., Shih, H.W., Hsu, N.S., Wu, C.J., Li, T.L.
      (2019) Acta Crystallogr D Struct Biol 75: 733

    Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxymandelate oxidaseA377Amycolatopsis orientalisMutation(s): 1 
Gene Names: hmo
EC: 1.1.3.46
Find proteins for O52792 (Amycolatopsis orientalis)
Explore O52792 
Go to UniProtKB:  O52792
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SMN
Query on SMN

Download CCD File 
A
(S)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-ZETCQYMHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.845α = 90
b = 137.845β = 90
c = 111.833γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-06-06 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Li, T.L., Lin, K.H.

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references