PDBsum entry 1a8r

Hydrolase

PDB id: 1a8r

Contents

Protein chains

(+ 9 more) 221 a.a. *

Ligands

GTP ×15

Waters ×975

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Biosynthesis of pteridines. Reaction mechanism of gtp cyclohydrolase i.

Authors

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

Ref.

J Mol Biol, 2003, 326, 503-516. [DOI no: 10.1016/S0022-2836(02)01303-7]

PubMed id

12559918

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.

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.

Secondary reference #1

Title

The pathway from gtp to tetrahydrobiopterin: three-Dimensional structures of gtp cyclohydrolase i and 6-Pyruvoyl tetrahydropterin synthase

Authors

G.Auerbach, H.Nar.

Ref.

biol chem, 1997, 378, 185.

Secondary reference #2

Title

The 1.25 a crystal structure of sepiapterin reductase reveals its binding mode to pterins and brain neurotransmitters.

Authors

G.Auerbach, A.Herrmann, M.Gütlich, M.Fischer, U.Jacob, A.Bacher, R.Huber.

Ref.

EMBO J, 1997, 16, 7219-7230. [DOI no: 10.1093/emboj/16.24.7219]

PubMed id

9405351

Figure 1.
Figure 1 The complete pathway of the de novo biosynthesis of BH[4]. The cofactor BH[4] is synthesized by only three enzymes, namely CYH, PTPS and SR. The crystal structure of E.coli CYH was recently solved by single isomorphous replacement and averaging techniques. The enzyme complex, a decamer consisting of a pentamer of tightly associated dimers, has perfect D[5] symmetry and is doughnut-shaped with dimensions of 65 100 Å. The MIR-solved crystal structure of rat PTPS shows a hexameric enzyme composed of a dimer of trimers with D[3] symmetry. Each trimer forms a 12 -stranded antiparallel -barrel, enclosing a basic pore with 6 -12 Å diameter. The crystal structure of mSR completes the structural analysis of all three enzymes involved in BH[4] biosynthesis, providing the essential information for the interpretation of the complex biochemical regulation of this pathway.

Figure 5.
Figure 5 Catalysed reaction of SR: reductase and isomerase. SR catalyses the sequential diketo reduction of PH[4] (6-pyruvoyl tetrahydropterin) conducive to the formation of BH[4] via an essential isomerization step of the mono-keto intermediates (reactions 1 -3). For C2'-reduction of the 2' -mono keto intermediate (reaction 4), an essential reorientation of the substrate's side chain toward Tyr171 and NADPH can be proposed. The reduction of the 2'-oxo function of PH[4] (reaction 5) is presumably not catalysed by SR.

The above figures are reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd

Secondary reference #3

Title

Active site topology and reaction mechanism of gtp cyclohydrolase i.

Authors

H.Nar, R.Huber, G.Auerbach, M.Fischer, C.Hösl, H.Ritz, A.Bracher, W.Meining, S.Eberhardt, A.Bacher.

Ref.

Proc Natl Acad Sci U S A, 1995, 92, 12120-12125. [DOI no: 10.1073/pnas.92.26.12120]

PubMed id

8618856

Secondary reference #4

Title

Atomic structure of gtp cyclohydrolase i.

Authors

H.Nar, R.Huber, W.Meining, C.Schmid, S.Weinkauf, A.Bacher.

Ref.

Structure, 1995, 3, 459-466. [DOI no: 10.1016/S0969-2126(01)00179-4]

PubMed id

7663943

Figure 1.
Figure 1. Biosynthesis of tetrahydrobiopterin. The reaction catalyzed by GTP cyclohydrolase I involves release of the C8 atom of GTP as formate, an Amadori rearrangement of the sugar moiety, and ring closure via a Schiff base reaction. Figure 1. Biosynthesis of tetrahydrobiopterin. The reaction catalyzed by GTP cyclohydrolase I involves release of the C8 atom of GTP as formate, an Amadori rearrangement of the sugar moiety, and ring closure via a Schiff base reaction.

Figure 4.
Figure 4. Side view of the GTP-CH-I decamer showing the pentamer surfaces in different colours. Tight contacts are made by pairs of subunits between pentamers by intercalation of their helical domains. Figure 4. Side view of the GTP-CH-I decamer showing the pentamer surfaces in different colours. Tight contacts are made by pairs of subunits between pentamers by intercalation of their helical domains.

The above figures are reproduced from the cited reference with permission from Cell Press