1N06

Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold

Summary for 1N06

• Entry DOI: 10.2210/pdb1n06/pdb
• Related: 1N05 1N07 1N08
• Descriptor: PUTATIVE riboflavin kinase, ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: kinase, phosphoryl transferases, flavin cofactors, metal binding, transferase
• Biological source: Schizosaccharomyces pombe (fission yeast)
• Total number of polymer chains: 2
• Total formula weight: 38731.90

Authors

Bauer, S.,Kemter, K.,Bacher, A.,Huber, R.,Fischer, M.,Steinbacher, S. (deposition date: 2002-10-11, release date: 2003-02-25, Last modification date: 2024-02-14)

Primary citation

Bauer, S.,Kemter, K.,Bacher, A.,Huber, R.,Fischer, M.,Steinbacher, S.
Crystal Structure of Schizosaccharomyces pombe Riboflavin Kinase Reveals a Novel ATP and Riboflavin Binding Fold
J.Mol.Biol., 326:1463-1473, 2003

PubMed Abstract: The essential redox cofactors riboflavin monophosphate (FMN) and flavin adenine dinucleotide (FAD) are synthesised from their precursor, riboflavin, in sequential reactions by the metal-dependent riboflavin kinase and FAD synthetase. Here, we describe the 1.6A crystal structure of the Schizosaccharomyces pombe riboflavin kinase. The enzyme represents a novel family of phosphoryl transferring enzymes. It is a monomer comprising a central beta-barrel clasped on one side by two C-terminal helices that display an L-like shape. The opposite side of the beta-barrel serves as a platform for substrate binding as demonstrated by complexes with ADP and FMN. Formation of the ATP-binding site requires significant rearrangements in a short alpha-helix as compared to the substrate free form. The diphosphate moiety of ADP is covered by the glycine-rich flap I formed from parts of this alpha-helix. In contrast, no significant changes are observed upon binding of riboflavin. The ribityl side-chain might be covered by a rather flexible flap II. The unusual metal-binding site involves, in addition to the ADP phosphates, only the strictly conserved Thr45. This may explain the preference for zinc observed in vitro.

PubMed: 12595258
DOI: 10.1016/S0022-2836(03)00059-7

Experimental method

X-RAY DIFFRACTION (2 Å)