1NG4

Structure of ThiO (glycine oxidase) from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb1NG4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-16 Released: 2003-04-08 
• Deposition Author(s): Settembre, E.C., Dorrestein, P.C., Park, J., Augustine, A., Begley, T.P., Ealick, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 

Literature

Structural and Mechanistic Studies on ThiO, a Glycine Oxidase Essential for Thiamin Biosynthesis in Bacillus subtilis

Settembre, E.C., Dorrestein, P.C., Park, J., Augustine, A., Begley, T.P., Ealick, S.E.

(2003) Biochemistry 42: 2971-2981

• PubMed: 12627963 
• DOI: https://doi.org/10.1021/bi026916v
• Primary Citation of Related Structures:  
  1NG3, 1NG4


• PubMed Abstract: 
  

  The thiO gene of Bacillus subtilis encodes an FAD-dependent glycine oxidase. This enzyme is a homotetramer with a monomer molecular mass of 42 kDa. In this paper, we demonstrate that ThiO is required for the biosynthesis of the thiazole moiety of thiamin pyrophosphate and describe the structure of the enzyme with N-acetylglycine bound at the active site. The closest structural relatives of ThiO are sarcosine oxidase and d-amino acid oxidase. The ThiO structure, as well as the observation that N-cyclopropylglycine is a good substrate, supports a hydride transfer mechanism for the enzyme. A mechanistic proposal for the role of ThiO in thiazole biosynthesis is also described.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 88.83 kDa 
• Atom Count: 6,024 
• Modelled Residue Count: 728 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine oxidase	A, B	390	Bacillus subtilis	Mutation(s): 0  Gene Names: GOXB EC: 1.5.3
UniProt
Find proteins for O31616 (Bacillus subtilis (strain 168)) Explore O31616  Go to UniProtKB:  O31616

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
PEO	D [auth A], G [auth B]	HYDROGEN PEROXIDE H2 O2 MHAJPDPJQMAIIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.203 
• R-Value Observed: 0.203 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.456	α = 90
b = 139.456	β = 90
c = 210.278	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
Adxv	data processing
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-08 
Deposition Author(s): Settembre, E.C., Dorrestein, P.C., Park, J., Augustine, A., Begley, T.P., Ealick, S.E.

Revision History  

• Version 1.0: 2003-04-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations