6A11 | pdb_00006a11

Mandelate oxidase mutant-Y128F with phenylpyruvic acid

• PDB DOI: https://doi.org/10.2210/pdb6A11/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Amycolatopsis orientalis
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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

• PubMed: 31373572 
• DOI: https://doi.org/10.1107/S2059798319009574
• Primary Citation 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.

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Organizational Affiliation: 
• Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.
Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.65 kDa 
• Atom Count: 3,077 
• Modeled Residue Count: 334 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxymandelate oxidase	A	377	Amycolatopsis orientalis	Mutation(s): 1  Gene Names: hmo EC: 1.1.3.46
UniProt
Find proteins for O52792 (Amycolatopsis orientalis) Explore O52792  Go to UniProtKB:  O52792

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PPY	C [auth A]	3-PHENYLPYRUVIC ACID C9 H8 O3 BTNMPGBKDVTSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.485	α = 90
b = 138.485	β = 90
c = 111.539	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• 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: 2023-11-22
  Changes: Data collection, Database references, Refinement description