6A1P

Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.1 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, 6A23, 6A1H, 6A1M, 6A1L, 6A3T

  • 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 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 ...

    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.


    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
UniProt
Find proteins for O52792 (Amycolatopsis orientalis)
Explore O52792 
Go to UniProtKB:  O52792
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9O9 (Subject of Investigation/LOI)
Query on 9O9

Download Ideal Coordinates CCD File 
B [auth A]1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol
C18 H22 N3 O9 P
LAWFKZVKVIYTAR-ZNMIVQPWSA-N
 Ligand Interaction
PPY (Subject of Investigation/LOI)
Query on PPY

Download Ideal Coordinates CCD File 
D [auth A]3-PHENYLPYRUVIC ACID
C9 H8 O3
BTNMPGBKDVTSJY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.975α = 90
b = 137.975β = 90
c = 111.068γ = 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

  • Deposited Date: 2018-06-07 
  • Released Date: 2019-06-19 
  • Deposition Author(s): Li, T.L., Lin, K.H.

Revision History  (Full details and data files)

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