1RYI

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-function correlation in glycine oxidase from Bacillus subtilis

Moertl, M.Diederichs, K.Welte, W.Molla, G.Motteran, L.Andriolo, G.Pilone, M.S.Pollegioni, L.

(2004) J.Biol.Chem. 279: 29718-29727

  • DOI: 10.1074/jbc.M401224200

  • PubMed Abstract: 
  • Structure-function relationships of the flavoprotein glycine oxidase (GO), which was recently proposed as the first enzyme in the biosynthesis of thiamine in Bacillus subtilis, has been investigated by a combination of structural and functional studi ...

    Structure-function relationships of the flavoprotein glycine oxidase (GO), which was recently proposed as the first enzyme in the biosynthesis of thiamine in Bacillus subtilis, has been investigated by a combination of structural and functional studies. The structure of the GO-glycolate complex was determined at 1.8 A, a resolution at which a sketch of the residues involved in FAD binding and in substrate interaction can be depicted. GO can be considered a member of the "amine oxidase" class of flavoproteins, such as d-amino acid oxidase and monomeric sarcosine oxidase. With the obtained model of GO the monomer-monomer interactions can be analyzed in detail, thus explaining the structural basis of the stable tetrameric oligomerization state of GO, which is unique for the GR(2) subfamily of flavooxidases. On the other hand, the three-dimensional structure of GO and the functional experiments do not provide the functional significance of such an oligomerization state; GO does not show an allosteric behavior. The results do not clarify the metabolic role of this enzyme in B. subtilis; the broad substrate specificity of GO cannot be correlated with the inferred function in thiamine biosynthesis, and the structure does not show how GO could interact with ThiS, the following enzyme in thiamine biosynthesis. However, they do let a general catabolic role of this enzyme on primary or secondary amines to be excluded because the expression of GO is not inducible by glycine, sarcosine, or d-alanine as carbon or nitrogen sources.


    Organizational Affiliation

    Section of Biology, University of Konstanz, P O Box 5560-M656, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCINE OXIDASE
A, B, C, D
382Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: thiO (goxB, yjbR)
EC: 1.4.3.19
Find proteins for O31616 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31616
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOA
Query on GOA

Download SDF File 
Download CCD File 
A, B, C, D
GLYCOLIC ACID
HYDROXYACETIC ACID; HYDROXYETHANOIC ACID
C2 H4 O3
AEMRFAOFKBGASW-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.713α = 90.00
b = 218.765β = 90.00
c = 217.800γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
MAR345data collection
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description