L-Aminoacetone oxidase from Streptococcus oligofermentans belongs to a new 3-domain family of bacterial flavoproteins

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

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Aminoacetone Oxidase from Streptococcus Oligofermentas Belongs to a New Three-Domain Family of Bacterial Flavoproteins.

Molla, G.Nardini, M.Motta, P.D'Arrigo, P.Panzeri, W.Pollegioni, L.

(2014) Biochem J 464: 387

  • DOI: https://doi.org/10.1042/BJ20140972
  • Primary Citation of Related Structures:  
    4CNJ, 4CNK

  • PubMed Abstract: 

    The aaoSo gene from Streptococcus oligofermentans encodes a 43 kDa flavoprotein, aminoacetone oxidase (SoAAO), which was reported to possess a low catalytic activity against several different L-amino acids; accordingly, it was classified as an L-amino acid oxidase. Subsequently, SoAAO was demonstrated to oxidize aminoacetone (a pro-oxidant metabolite), with an activity ~25-fold higher than the activity displayed on L-lysine, thus lending support to the assumption of aminoacetone as the preferred substrate. In the present study, we have characterized the SoAAO structure-function relationship. SoAAO is an FAD-containing enzyme that does not possess the classical properties of the oxidase/dehydrogenase class of flavoproteins (i.e. no flavin semiquinone formation is observed during anaerobic photoreduction as well as no reaction with sulfite) and does not show a true L-amino acid oxidase activity. From a structural point of view, SoAAO belongs to a novel protein family composed of three domains: an α/β domain corresponding to the FAD-binding domain, a β-domain partially modulating accessibility to the coenzyme, and an additional α-domain. Analysis of the reaction products of SoAAO on aminoacetone showed 2,5-dimethylpyrazine as the main product; we propose that condensation of two aminoacetone molecules yields 3,6-dimethyl-2,5-dihydropyrazine that is subsequently oxidized to 2,5-dimethylpyrazine. The ability of SoAAO to bind two molecules of the substrate analogue O-methylglycine ligand is thought to facilitate the condensation reaction. A specialized role for SoAAO in the microbial defence mechanism related to aminoacetone catabolism through a pathway yielding dimethylpyrazine derivatives instead of methylglyoxal can be proposed.

  • Organizational Affiliation

    †The Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM CNR Milano, and Università degli Studi deII'Insubria, Varese, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
391Streptococcus cristatusMutation(s): 0 
Gene Names: SOL01_18080
Find proteins for B1PUC6 (Streptococcus cristatus)
Explore B1PUC6 
Go to UniProtKB:  B1PUC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1PUC6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
C27 H33 N9 O15 P2
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
V [auth B]
W [auth B]
K [auth A],
L [auth A],
M [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
C3 H8 O3
Query on MEU

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
P [auth B]
C3 H7 N O2
Binding Affinity Annotations 
IDSourceBinding Affinity
MEU Binding MOAD:  4CNK Kd: 2.80e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.8α = 90
b = 231.075β = 90
c = 124.93γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references