1KYY

Lumazine Synthase from S.pombe bound to nitropyrimidinedione

Summary for 1KYY

• Entry DOI: 10.2210/pdb1kyy/pdb
• Related: 1KYV 1KYX 1KZ1 1KZ4 1KZ6 1KZ9
• Descriptor: 6,7-Dimethyl-8-ribityllumazine Synthase, PHOSPHATE ION, 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE, ... (4 entities in total)
• Functional Keywords: riboflavin biosynthesis, lumazine synthase, schizosaccharomyces pombe, ligand binding, transferase
• Biological source: Schizosaccharomyces pombe (fission yeast)
• Total number of polymer chains: 5
• Total formula weight: 88039.96

Authors

Gerhardt, S.,Haase, I.,Steinbacher, S.,Kaiser, J.T.,Cushman, M.,Bacher, A.,Huber, R.,Fischer, M. (deposition date: 2002-02-06, release date: 2002-07-24, Last modification date: 2024-03-13)

Primary citation

Gerhardt, S.,Haase, I.,Steinbacher, S.,Kaiser, J.T.,Cushman, M.,Bacher, A.,Huber, R.,Fischer, M.
The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.
J.Mol.Biol., 318:1317-1329, 2002

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.

PubMed: 12083520
DOI: 10.1016/S0022-2836(02)00116-X

Experimental method

X-RAY DIFFRACTION (2.4 Å)