Biological Assembly 1  

 3D View: Structure

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly 2  

 3D View: Structure

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.39 kDa 
• Atom Count: 5881 
• Residue Count: 746 
• Unique protein chains: 1

1KZ1

Mutant enzyme W27G Lumazine Synthase from S.pombe

• DOI: 10.2210/pdb1KZ1/pdb

• Classification: TRANSFERASE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-02-06 Released: 2002-07-24 
• Deposition Author(s): Gerhardt, S., Haase, I., Steinbacher, S., Kaiser, J.T., Cushman, M., Bacher, A., Huber, R., Fischer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Literature

The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.

Gerhardt, S., Haase, I., Steinbacher, S., Kaiser, J.T., Cushman, M., Bacher, A., Huber, R., Fischer, M.

(2002) J Mol Biol 318: 1317-1329

• PubMed: 12083520 
• DOI: 10.1016/s0022-2836(02)00116-x
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
6,7-Dimethyl-8-ribityllumazine Synthase	A, B, C, D, E	159	Schizosaccharomyces pombe	Mutation(s): 1  EC: 2.5.1.78
Find proteins for Q9UUB1 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UUB1  Go to UniProtKB:  Q9UUB1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.568	α = 90
b = 144.017	β = 90
c = 126.355	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-06 
• Released Date: 2002-07-24 
Deposition Author(s): Gerhardt, S., Haase, I., Steinbacher, S., Kaiser, J.T., Cushman, M., Bacher, A., Huber, R., Fischer, M.

Revision History 

• Version 1.0: 2002-07-24
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-01-23
  Changes: Structure summary