Crystal structure of 7,8-dihydroneopterin triphosphate epimerase

• Published in: Structure (London) 1999-05, Vol.7 (5), p.509-516
• Main Authors: Ploom, Tarmo, Haußmann, Christoph, Hof, Peter, Steinbacher, Stefan, Bacher, Adelbert, Richardson, John, Huber, Robert
• Format: Article
• Language: English
• Subjects: 6-pyruvoyl tetrahydropterin synthase; 7,8-dihydroneopterin aldolase; 8-dihydroneopterin triphosphate epimerase; Amino Acid Sequence; Binding Sites; Catalysis; crystal structure; Crystallography, X-Ray; Escherichia coli Proteins; guanosine triphosphate cyclohydrolase I; Models, Molecular; Molecular Sequence Data; Protein Structure, Secondary; Protein Structure, Tertiary; Racemases and Epimerases - chemistry; Racemases and Epimerases - metabolism; Sequence Homology, Amino Acid; uroate oxidase
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/S0969-2126(99)80067-7

Background: Dihydroneopterin triphosphate (H 2NTP) is the central substrate in the biosynthesis of folate and tetrahydrobiopterin. Folate serves as a cofactor in amino acid and purine biosynthesis and tetrahydrobiopterin is used as a cofactor in amino acid hydroxylation and nitric oxide synthesis. In bacteria, H 2NTP enters the folate biosynthetic pathway after nonenzymatic dephosphorylation; in vertebrates, H 2NTP is used to synthesize tetrahydrobiopterin. The dihydroneopterin triphosphate epimerase of Escherichia coli catalyzes the inversion of carbon 2′ of H 2NTP. Results: The crystal structure of the homo-octameric protein has been solved by a combination of multiple isomorphous replacement, Patterson search techniques and cyclic averaging and has been refined to a crystallographic R factor of 18.8% at 2.9 Å resolution. The enzyme is a torus-shaped, D 4 symmetric homo-octamer with approximate dimensions of 65 × 65 Å. Four epimerase monomers form an unusual 16-stranded antiparallel β barrel by tight association between the N- and C-terminal β strands of two adjacent subunits. Two tetramers associate in a head-to-head fashion to form the active enzyme complex. Conclusions: The folding topology, quaternary structure and amino acid sequence of epimerase is similar to that of the dihydroneopterin aldolase involved in the biosynthesis of the vitamin folic acid. The monomer fold of epimerase is also topologically similar to that of GTP cyclohydrolase I (GTP CH-1), 6-pyrovoyl tetrahydropterin synthase (PTPS) and uroate oxidase (UO). Despite a lack of significant sequence homology these proteins share a common subunit fold and oligomerize to form central β barrel structures employing different cyclic symmetry elements, D 4, D 5, D 3 and D 2, respectively. Moreover, these enzymes have a topologically equivalent acceptor site for the 2-amino-4-oxo pyrimidine (2-oxo-4-oxo pyrimidine in uroate oxidase) moiety of their respective substrates.