1KZL

Riboflavin Synthase from S.pombe bound to Carboxyethyllumazine

Summary for 1KZL

• Entry DOI: 10.2210/pdb1kzl/pdb
• Descriptor: Riboflavin Synthase, MERCURY (II) ION, 3-[8-((2S,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL)-2,4,7-TRIOXO-1,3,8-TRIHYDROPTERIDIN-6-YL]PROPANOIC ACID, ... (4 entities in total)
• Functional Keywords: biosynthesis of riboflavin, riboflavin synthase, schizosaccharomyces pombe, ligand binding, transferase
• Biological source: Schizosaccharomyces pombe (fission yeast)
• Total number of polymer chains: 1
• Total formula weight: 23860.33

Authors

Gerhardt, S.,Schott, A.K.,Kairies, N.,Cushman, M.,Illarionov, B.,Eisenreich, W.,Bacher, A.,Huber, R.,Steinbacher, S.,Fischer, M. (deposition date: 2002-02-07, release date: 2002-11-06, Last modification date: 2024-03-13)

Primary citation

Gerhardt, S.,Schott, A.K.,Kairies, N.,Cushman, M.,Illarionov, B.,Eisenreich, W.,Bacher, A.,Huber, R.,Steinbacher, S.,Fischer, M.
Studies on the Reaction Mechanism of Riboflavin Synthase; X-Ray Crystal Structure of a Complex with 6-Carboxyethyl-7-Oxo-8-Ribityllumazine
STRUCTURE, 10:1371-1381, 2002

PubMed Abstract: Riboflavin synthase catalyzes the disproportionation of 6,7-dimethyl-8-ribityllumazine affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. We have determined the structure of riboflavin synthase from Schizosaccharomyces pombe in complex with the substrate analog, 6-carboxyethyl-7-oxo-8-ribityllumazine at 2.1 A resolution. In contrast to the homotrimeric solution state of native riboflavin synthase, we found the enzyme to be monomeric in the crystal structure. Structural comparison of the riboflavin synthases of S. pombe and Escherichia coli suggests oligomer contact sites and delineates the catalytic site for dimerization of the substrate and subsequent fragmentation of the pentacyclic intermediate. The pentacyclic substrate dimer was modeled into the proposed active site, and its stereochemical features were determined. The model suggests that the substrate molecule at the C-terminal domain donates a four-carbon unit to the substrate molecule bound at the N-terminal domain of an adjacent subunit in the oligomer.

PubMed: 12377123
DOI: 10.1016/S0969-2126(02)00864-X

Experimental method

X-RAY DIFFRACTION (2.1 Å)