1NG3

Complex of ThiO (glycine oxidase) with acetyl-glycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1021/bi026916v
  • Primary Citation of Related Structures:  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 thi ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine oxidase
A, B
390Bacillus subtilis (strain 168)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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
AAC
Query on AAC

Download SDF File 
Download CCD File 
A, B
ACETYLAMINO-ACETIC ACID
C4 H7 N O3
OKJIRPAQVSHGFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.378α = 90.00
b = 139.378β = 90.00
c = 208.155γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
CCP4data scaling
Adxvdata processing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description