PDBsum entry 1a8r

Hydrolase

PDB id: 1a8r

Contents

Protein chains

(+ 9 more) 221 a.a. *

Ligands

GTP ×15

Waters ×975

* Residue conservation analysis

PDB id:

1a8r

Name:

Hydrolase

Title:

Gtp cyclohydrolase i (h112s mutant) in complex with gtp

Structure:

Gtp cyclohydrolase i. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Organ: brain. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: homologous expression

Biol. unit:

Homo-Decamer (from PDB file)

Resolution:

2.10Å R-factor: 0.200 R-free: 0.246

Authors:

G.Auerbach,H.Nar,A.Bracher,A.Bacher,R.Huber

Key ref:

J.Rebelo et al. (2003). Biosynthesis of pteridines. Reaction mechanism of GTP cyclohydrolase I. J Mol Biol, 326, 503-516. PubMed id: 12559918 DOI: 10.1016/S0022-2836(02)01303-7

Date:

27-Mar-98 Release date: 11-May-99

Protein chains

P0A6T5  (GCH1_ECOLI) -  GTP cyclohydrolase 1 from Escherichia coli (strain K12)

Seq: 222 a.a.

Struc: 221 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.4.16 - Gtp cyclohydrolase i.
• Pathway: Folate Biosynthesis (early stages)
• Reaction: GTP + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H⁺

GTP (Bound ligand (Het Group name = GTP) corresponds exactly) + H2O = 7,8-dihydroneopterin 3'-triphosphate + formate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S0022-2836(02)01303-7

J Mol Biol 326:503-516 (2003)

PubMed id: 12559918

Biosynthesis of pteridines. Reaction mechanism of GTP cyclohydrolase I.

J.Rebelo, G.Auerbach, G.Bader, A.Bracher, H.Nar, C.Hösl, N.Schramek, J.Kaiser, A.Bacher, R.Huber, M.Fischer.

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.

Selected figure(s)

Figure 1.
Figure 1. Hypothetical mechanism of the reaction catalysed by GTP cyclohydrolase I.[8.]

Figure 4.
Figure 4. Stereo diagram from the active site of the E. coli GTP cyclohydrolase I His113Ser mutant in complex with the substrate GTP. The GTP molecule (shown as a transparent wire model representation) is embedded in a large hydrogen bond network (broken lines) within the active site. Amino acid residues are shown as ball-and-stick models coloured according to the subunit to which they belong: A, red; B, blue; and D, green. The Figure was created using MOLSCRIPT[39.] and Raster3D. [40.]

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 503-516) copyright 2003.

Figures were selected by an automated process.