The Crystal Structure of the Orotate Phosphoribosyltransferase Complexed with Orotate and .alpha.-D-5-Phosphoribosyl-1-Pyrophosphate

Scapin, Giovanna; Ozturk, Derya H.; Grubmeyer, Charles; Sacchettini, James C.

doi:10.1021/bi00034a006

Cited by 101 publications

(169 citation statements)

References 33 publications

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“…Orotate phospho-ribosyltransferase, a typical type I phosphoribosyltransferase, contains the "usual" structural elements, a five-stranded ␤-sheet surrounded by a number of helices, usually four, a hood structure involved in the binding of the substrate orotate, and a flexible catalytic loop, which closes the active site on catalysis. The structures of orotate phosphoribosyltransferase from a variety of sources, including S. enterica (223), E. coli (224), S. mutans (225), Plasmodium falciparum (226), and L. donovani (227) have been published.…”

Section: Reactions At the Anomeric Carbon Of Prppmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

169

187

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SUMMARY Phosphoribosyl diphosphate (PRPP) is an important intermediate in cellular metabolism. PRPP is synthesized by PRPP synthase, as follows: ribose 5-phosphate + ATP → PRPP + AMP. PRPP is ubiquitously found in living organisms and is used in substitution reactions with the formation of glycosidic bonds. PRPP is utilized in the biosynthesis of purine and pyrimidine nucleotides, the amino acids histidine and tryptophan, the cofactors NAD and tetrahydromethanopterin, arabinosyl monophosphodecaprenol, and certain aminoglycoside antibiotics. The participation of PRPP in each of these metabolic pathways is reviewed. Central to the metabolism of PRPP is PRPP synthase, which has been studied from all kingdoms of life by classical mechanistic procedures. The results of these analyses are unified with recent progress in molecular enzymology and the elucidation of the three-dimensional structures of PRPP synthases from eubacteria, archaea, and humans. The structures and mechanisms of catalysis of the five diphosphoryltransferases are compared, as are those of selected enzymes of diphosphoryl transfer, phosphoryl transfer, and nucleotidyl transfer reactions. PRPP is used as a substrate by a large number phosphoribosyltransferases. The protein structures and reaction mechanisms of these phosphoribosyltransferases vary and demonstrate the versatility of PRPP as an intermediate in cellular physiology. PRPP synthases appear to have originated from a phosphoribosyltransferase during evolution, as demonstrated by phylogenetic analysis. PRPP, furthermore, is an effector molecule of purine and pyrimidine nucleotide biosynthesis, either by binding to PurR or PyrR regulatory proteins or as an allosteric activator of carbamoylphosphate synthetase. Genetic analyses have disclosed a number of mutants altered in the PRPP synthase-specifying genes in humans as well as bacterial species.

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Section: Reactions At the Anomeric Carbon Of Prppmentioning

confidence: 99%

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Hove‐Jensen

Andersen

Kilstrup

et al. 2017

Microbiol Mol Biol Rev

169

187

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“…Several lines of evidence support this idea. First, the structure of OPRT co-crystallized with orotate and PRPP reveals that Lys 100 and Lys 103 within the flexible loop of OPRT are translocated to within 6 Å of the active site of the enzymesubstrate complex (36) and may form contacts with the PP i moiety of PRPP (39). The crystal structures of the T. gondii HGXPRT apoenzyme and product-bound form also reveal a shift of this loop toward the active site (9).…”

Section: -Fold (28)mentioning

confidence: 99%

The Conserved Serine-Tyrosine Dipeptide in Leishmania donovani Hypoxanthine-guanine Phosphoribosyltransferase Is Essential for Catalytic Activity

Jardim

Ullman

1997

Journal of Biological Chemistry

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Protozoan parasites constitute a devastating public health and socioeconomic burden in the tropical and subtropical regions of the world. In the absence of effective vaccines, empirically derived drugs are the only means available to treat parasitic infections. However, the current arsenal of antiparasitic drugs is far from ideal, as these agents are moderately to highly toxic, possibly mutagenic and/or carcinogenic, and require protracted treatment regimens. The control of parasitic diseases has also been complicated by the emergence of drugresistant strains (1), further underscoring the need for novel antiparasitic agents. Rational development of new drugs that selectively target protozoan pathogens requires the exploitation of biochemical or metabolic differences between parasite and host. As protozoan parasites, unlike mammalian cells, are auxotrophic for purines and consequently rely on purine appropriation from the host for survival and proliferation (2), the purine salvage pathway has stimulated considerable interest as a paradigm for antiparasitic drug development. One enzyme that is central to purine acquisition in many parasites (2) is hypoxanthine-guanine phosphoribosyltransferase (HGPRT) 1 which catalyzes the phosphoribosylpyrophosphate (PRPP)-dependent phosphoribosylation of hypoxanthine and guanine to the nucleotide level. In some parasites, HGPRT also recognizes xanthine as a substrate (3) and is, therefore, termed a hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGX-PRT). Genes and cDNAs encoding HG(X)PRT (HG(X)PRT) from a number of protozoan parasites have now been cloned, sequenced, and overexpressed in Escherichia coli, and the recombinant HG(X)PRT enzymes have been purified and characterized kinetically (3). Multisequence alignments demonstrate several short regions of amino acid homology among HG(X)-PRT family members that are flanked by much longer regions without significant sequence similarity. The crystal structures for the product-bound form of the human HGPRT (4) and the Tritrichomonas foetus HGXPRT (5) have revealed, however, a common core framework within the tertiary structure that is conserved among other members of the phosphoribosyltransferase (PRT) family (6 -8). These structures have established functional roles for all of the conserved regions in HG(X)PRT proteins, except one motif that is located on a flexible loop distal to the active site. This flexible loop encompasses a SerTyr dipeptide that is found in all HG(X)PRTs for which sequence is available. The recently determined crystal structures of the HGXPRT from Toxoplasma gondii in the absence of ligand and in the presence of product have demonstrated that this flexible loop in the apoenzyme is shifted toward the active

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“…Features of this transition state require a ribooxocarbenium ion structure. The X-ray crystal structure of the enzyme has been solved with orotidine 5 -monophosphate or 5-phosphoribosyl-1-pyrophosphate at the catalytic site (101,102). Although the structure is not in a transition state conformation, Arg156 is shown to interact with the 4-carbonyl group of orotic acid and can be proposed to activate the orotic acid leaving group.…”

mentioning

confidence: 99%

Enzymatic Transition States and Transition State Analog Design

Schramm

1998

Annu. Rev. Biochem.

273

264

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All chemical transformations pass through an unstable structure called the transition state, which is poised between the chemical structures of the substrates and products. The transition states for chemical reactions are proposed to have lifetimes near 10 −13 sec, the time for a single bond vibration. No physical or spectroscopic method is available to directly observe the structure of the transition state for enzymatic reactions. Yet transition state structure is central to understanding catalysis, because enzymes function by lowering activation energy. An accepted view of enzymatic catalysis is tight binding to the unstable transition state structure. Transition state mimics bind tightly to enzymes by capturing a fraction of the binding energy for the transition state species. The identification of numerous transition state inhibitors supports the transition state stabilization hypothesis for enzymatic catalysis. Advances in methods for measuring and interpreting kinetic isotope effects and advances in computational chemistry have provided an experimental route to understand transition state structure. Systematic analysis of intrinsic kinetic isotope effects provides geometric and electronic structure for enzyme-bound transition states. This information has been used to compare transition states for chemical and enzymatic reactions; determine whether enzymatic activators alter transition state structure; design transition state inhibitors; and provide the basis for predicting the affinity of enzymatic inhibitors. Enzymatic transition states provide an understanding of catalysis and permit the design of transition state inhibitors. This article reviews transition state theory for enzymatic reactions. Selected examples of enzymatic transition states are compared to the respective transition state inhibitors.

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The Crystal Structure of the Orotate Phosphoribosyltransferase Complexed with Orotate and .alpha.-D-5-Phosphoribosyl-1-Pyrophosphate

Cited by 101 publications

References 33 publications

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

Phosphoribosyl Diphosphate (PRPP): Biosynthesis, Enzymology, Utilization, and Metabolic Significance

The Conserved Serine-Tyrosine Dipeptide in Leishmania donovani Hypoxanthine-guanine Phosphoribosyltransferase Is Essential for Catalytic Activity

Enzymatic Transition States and Transition State Analog Design

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