4CNJ | pdb_00004cnj

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 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
    • *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly.

Macromolecule Content 

  • Total Structure Weight: 174.08 kDa 
  • Atom Count: 12,264 
  • Modeled Residue Count: 1,564 
  • Deposited Residue Count: 1,564 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-AMINO ACID OXIDASE
A, B, C, D
391Streptococcus cristatusMutation(s): 0 
EC: 1.1.3.2 (PDB Primary Data), 1 (UniProt)
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.239 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.149α = 90
b = 130.346β = 90
c = 224.199γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description