1N3S

Biosynthesis of pteridins. Reaction mechanism of GTP cyclohydrolase I

Summary for 1N3S

• Entry DOI: 10.2210/pdb1n3s/pdb
• Related: 1N3R 1N3T
• Descriptor: GTP cyclohydrolase I, GUANOSINE-5'-TRIPHOSPHATE (3 entities in total)
• Functional Keywords: biosynthesis, folic acid, gtp cyclohydrolase i, tetrahydropterin, pteridines, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 10
• Total formula weight: 252055.61

Authors

Rebelo, J.,Auerbach, G.,Bader, G.,Bracher, A.,Nar, H.,Hoesl, C.,Schramek, N.,Kaiser, J.,Bacher, A.,Huber, R.,Fischer, M. (deposition date: 2002-10-29, release date: 2004-03-02, Last modification date: 2024-10-30)

Primary citation

Rebelo, J.,Auerbach, G.,Bader, G.,Bracher, A.,Nar, H.,Hoesl, C.,Schramek, N.,Kaiser, J.,Bacher, A.,Huber, R.,Fischer, M.
Biosynthesis of Pteridines. Reaction Mechanism of GTP Cyclohydrolase I
J.MOL.BIOL., 326:503-516, 2003

PubMed Abstract: GTP cyclohydrolase I catalyses the hydrolytic release of formate from GTP followed by cyclization to dihydroneopterin triphosphate. The enzymes from bacteria and animals are homodecamers containing one zinc ion per subunit. Replacement of Cys110, Cys181, His112 or His113 of the enzyme from Escherichia coli by serine affords catalytically inactive mutant proteins with reduced capacity to bind zinc. These mutant proteins are unable to convert GTP or the committed reaction intermediate, 2-amino-5-formylamino-6-(beta-ribosylamino)-4(3H)-pyrimidinone 5'-triphosphate, to dihydroneopterin triphosphate. The crystal structures of GTP complexes of the His113Ser, His112Ser and Cys181Ser mutant proteins determined at resolutions of 2.5A, 2.8A and 3.2A, respectively, revealed the conformation of substrate GTP in the active site cavity. The carboxylic group of the highly conserved residue Glu152 anchors the substrate GTP, by hydrogen bonding to N-3 and to the position 2 amino group. Several basic amino acid residues interact with the triphosphate moiety of the substrate. The structure of the His112Ser mutant in complex with an undefined mixture of nucleotides determined at a resolution of 2.1A afforded additional details of the peptide folding. Comparison between the wild-type and mutant enzyme structures indicates that the catalytically active zinc ion is directly coordinated to Cys110, Cys181 and His113. Moreover, the zinc ion is complexed to a water molecule, which is in close hydrogen bond contact to His112. In close analogy to zinc proteases, the zinc-coordinated water molecule is suggested to attack C-8 of the substrate affording a zinc-bound 8R hydrate of GTP. Opening of the hydrated imidazole ring affords a formamide derivative, which remains coordinated to zinc. The subsequent hydrolysis of the formamide motif has an absolute requirement for zinc ion catalysis. The hydrolysis of the formamide bond shows close mechanistic similarity with peptide hydrolysis by zinc proteases.

PubMed: 12559918
DOI: 10.1016/S0022-2836(02)01303-7

Experimental method

X-RAY DIFFRACTION (2.55 Å)