6A0M

Mandelate oxidase mutant-Y128F with 2-Phenylacetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1107/S2059798319009574
  • Primary Citation of Related Structures:  
  • Also Cited By: 6A19, 6A13, 6A0V, 6A08, 5ZZP, 5ZZR

  • 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 cry ...

    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.,Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxymandelate oxidase
A
377Amycolatopsis orientalisMutation(s): 1 
Gene Names: hmo
EC: 1.1.3.46
Find proteins for O52792 (Amycolatopsis orientalis)
Go to UniProtKB:  O52792
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PAC
Query on PAC

Download SDF File 
Download CCD File 
A
2-PHENYLACETIC ACID
C8 H8 O2
WLJVXDMOQOGPHL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 138.150α = 90.00
b = 138.150β = 90.00
c = 111.217γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-06-05 
  • 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
    Type: Data collection, Database references