1RYI

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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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
  • Primary Citation of Related Structures:  
    1RYI

  • 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 studies. The structure of the GO-glycolate complex was determined at 1 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCINE OXIDASEA, B, C, D382Bacillus subtilisMutation(s): 0 
Gene Names: goxB, BSU11670
EC: 1.4.3.19
UniProt
Find proteins for O31616 (Bacillus subtilis (strain 168))
Explore O31616 
Go to UniProtKB:  O31616
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31616
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.713α = 90
b = 218.765β = 90
c = 217.8γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata reduction
SOLVEphasing
REFMACrefinement
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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