Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase 1 1Edited by K. Nagai

Ploom, Tarmo; Thöny, Beat; Yim, Jeongbin; Lee, Soo Jin; Nar, Herbert; Leimbacher, Walter; Richardson, Jeffrey Ralph James; Huber, Robert; Auerbach, Günter

doi:10.1006/jmbi.1998.2511

Cited by 51 publications

(62 citation statements)

References 31 publications

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“…The structures of Escherichia coli GTP cyclohydrolase I (eGTP-CH-I) (7), rat liver 6-pyruvoyl tetrahydropterin synthase (8,9), and mouse sepiapterin reductase (10) have been determined by x-ray crystallography; eGTP-CH-I is a toroid-shaped, D5-symmetric homodecamer (11). The 10 equivalent active sites are located at the periphery of the toroid, and each catalytic site is located at the interface of three adjacent subunits.…”

mentioning

confidence: 99%

Zinc plays a key role in human and bacterial GTP cyclohydrolase I

Auerbach

Herrmann

Bracher

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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127

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The crystal structure of recombinant human GTP cyclohydrolase I was solved by Patterson search methods by using the coordinates of the Escherichia coli enzyme as a model. The human as well as bacterial enzyme were shown to contain an essential zinc ion coordinated to a His side chain and two thiol groups in each active site of the homodecameric enzymes that had escaped detection during earlier studies of the E. coli enzyme. The zinc ion is proposed to generate a hydroxyl nucleophile for attack of imidazole ring carbon atom eight of the substrate, GTP. It may also be involved in the hydrolytic release of formate from the intermediate, 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5-triphosphate, and in the consecutive Amadori rearrangement of the ribosyl moiety.

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mentioning

confidence: 99%

Zinc plays a key role in human and bacterial GTP cyclohydrolase I

Auerbach

Herrmann

Bracher

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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131

127

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“…The catalytic zinc ions (shown as green spheres) are positioned near the equator and toward the outside of the assembly, near the confluence of three protein chains. As with mPTPS, the zinc divalent cation is coordinated by the imidazole side chains of three histidine residues (His (29,35). Interestingly, a second unique dyad, His 25 -Asp 54 , is also present in QueD, which we hypothesize is responsible for promoting the novel retroaldol cleavage to form CPH 4 by additional interactions with Cys 27 .…”

Section: Resultsmentioning

confidence: 93%

“…Enzymatic Preparation and Purification of H 2 NTP-H 2 NTP was produced as reported previously (29). The lyophilized material was dissolved in deoxygenated water in the anaerobic chamber and aliquots were frozen at Ϫ80°C.…”

Section: Methodsmentioning

confidence: 99%

“…The substrate in each active site is bound to a conserved zinc divalent cation via the C1Ј and C2Ј hydroxyl groups and the proteins retain similar binding interactions with the substrate (35). Each active site houses an essential cysteine residue whose activation with a conserved Asp/His dyad is proposed to initiate catalysis (29). The most conspicuous structural difference between the two active sites is the presence of an additional His/Asp dyad in the bacterial enzyme on the opposite face of the Cys 27 residue relative to the conserved dyad.…”

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confidence: 99%

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Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily

Miles

Roberts

McCarty

et al. 2014

Journal of Biological Chemistry

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Background:The bacterial homolog, 6-carboxy-5,6,7,8-tetrahydropterin synthase, of the eukaryotic 6-pyruvoyltetrahydropterin synthase enzyme acts on the same substrate but produces different products. Results: Structural and biochemical studies trace the differential reactivity to four residues. Conclusion: Differential reactivity between the enzyme homologs is a result of small changes in the enzyme active site. Significance: This work furthers our understanding of how novel activities may arise from common protein-folds.

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“…The T-fold superfamily has two structural subfamilies, a unimodular subfamily, with proteins formed by subunits containing a single T-fold domain repeat and a bimodular subfamily composed of proteins formed by subunits with tandem T-fold domains ( Figure 2). 26 To date, the T-fold superfamily has 6 known members: Guanosine cyclohydrolase 1A/B (GCYH-1A/B), 29,30 QueD (previously ykvK) 31 , 7-cyano-7-deazaguanine reductase (QueF), 27,32 7,8-dihydroneopterin triphosphate epimerase 33 , 6-pyruvoyl tetrahydropterin synthase (PTPS) 34 , Urate oxidase (UOX) 35 and Dihydroneopterin aldolase (DHNA) 36 . GTP cyclohydrolase (GCYH-I) catalyzes the first step of the de novo tetrahydrofolate biosynthetic pathway in bacteria and plants, the 7-deazapurine (Queuosine and Archaeosine) biosynthetic pathways in Bacteria and Archaea, 37 and the biopterin biosynthetic pathway in Eukarya.…”

Section: The T-fold Superfamilymentioning

confidence: 99%

QueF and QueF-like: Diverse Chemistries in a Common Fold

Ramos¹

2000

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The tunneling fold (T-Fold) superfamily is a small superfamily of enzymes found in organisms encompassing all kingdoms of life. Seven members have been identified thus far. Despite sharing a common three-dimensional structure these enzymes perform very diverse chemistries.QueF is a bacterial NADPH-dependent oxidoreductase that catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ0) to a primary amine (preQ1) in the queuosine biosynthetic pathway. Previous work on this enzyme has revealed the mechanism of reaction but the cofactor binding Based on bond angles and energies, the disulfide bond between Cys55 and Cys99 was characterized as non-structural. Enzyme oxidation assays were consistent with the bond serving to protect QueF against irreversible oxidation of ii Cys55, which would render the enzyme inactive. This is the only known example of a stress protective mechanism in the Tunneling-fold superfamily.QueF-like is an amidinotransferase found in some species of Crenarchaeota and involved in the biosynthesis of archaeosine-tRNA. The work presented here is focused on the preliminary characterization of this enzyme, including the elucidation of the natural substrate as well as the source of ammonia. The structure of the enzyme was solved and is also discussed.Substrate analysis for QueF-like indicated this enzyme is capable of binding both preQ0 and preQ0-tRNA and reacting to form a thioimide intermediate analogous to QueF but only the latter serves as a substrate for the reaction. This makes QueF-like the first example of a nucleic acid binding enzyme in the Tunnelingfold superfamily. Ammonia, glutamine and asparagine were tested as nitrogen sources and unlike most known amidotransferases, QueF-like can only use free ammonia to produce the archaeosine-tRNA product. The crystal structure of P.calidifontis QueF-like indicates the functional enzyme is a dimer of pentamers pinned together by a large number of salt bridges. The structure presents a high degree of similarity to that of QueF albeit the higher twist of the QueF-like pentamers with respect to QueF results in a more compact structure.iii DedicationThis dissertation is dedicated to my husband Aaron, who's belief in my strength and capabilities has always surpassed my own.

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Crystallographic and kinetic investigations on the mechanism of 6-pyruvoyl tetrahydropterin synthase 1 1Edited by K. Nagai

Cited by 51 publications

References 31 publications

Zinc plays a key role in human and bacterial GTP cyclohydrolase I

Zinc plays a key role in human and bacterial GTP cyclohydrolase I

Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily

QueF and QueF-like: Diverse Chemistries in a Common Fold

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