6A0O

Mandelate oxidase mutant-Y128F with benzaldehyde


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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: 733-742

  • DOI: https://doi.org/10.1107/S2059798319009574
  • Primary Citation of Related Structures:  
    5ZZQ, 5ZZS, 5ZZX, 5ZZY, 6A00, 6A0D, 6A0G, 6A0M, 6A0O, 6A0Y, 6A11, 6A1A

  • PubMed Abstract: 

    p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallography, were exploited to reach these conclusions and provide additional insights.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 115, 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.743α = 90
b = 137.743β = 90
c = 111.732γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
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: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description