ReviewModular evolution of the purine biosynthetic pathway
Introduction
The purine biosynthetic pathway is nearly ubiquitous and results in the conversion of phosphoribosyl pyrophosphate (PRPP) to inosine monophosphate (IMP). The seminal experiments in the 1950s and 1960s of Buchanan and his co-workers 1, 2, 3 established, in pigeon liver extracts, that 10 enzymatic activities are required for the interconversion of PRPP to IMP. In contrast, in most microorganisms, 12 enzymatic activities are involved in effecting the same interconversion (Figure 1). Structures of all of the enzymes in the bacterial pathway except PurL are now available, with seven of these structures from the same organism, Escherichia coli (PurF, PurD, PurN, PurM, PurK, PurT and PurE). The availability of this structural information in conjunction with the information from the genome sequencing projects has provided some provocative observations leading to insight into the factors that could govern the evolution of a biosynthetic pathway.
In general, biosynthetic pathways are built by patchwork. The proteins in pathways are composed of domains with defined catalytic activities that are fused to generate new activities. The purine pathway is no exception. In this review, we will present evidence for three different factors that should be considered in the evolution of the purine biosynthetic enzymes. First, we consider the importance of chemistry in this process. Of the twelve enzymes in procaryotes, six utilize ATP, two utilize glutamine, and two utilize N10-formyl tetrahydrofolate (THF). The question can be raised as to which of these proteins share structural homology. Second, in contrast with most biosynthetic pathways, all of the substrates in this pathway share a ribose 5-phosphate (R5P) moiety upon which the purine base is built sequentially (Figure 1). The question can be raised as to whether there is a common R5P-binding motif amongst the 12 enzymes. Finally, many of the intermediates in the purine biosynthetic pathway are chemically unstable. The question can be raised as to whether the surfaces of proteins provide a mechanism for direct transfer of these chemically unstable intermediates between successive enzymes in the pathway. In this review, each of these factors will be described in turn, focusing on recent information obtained from structural, sequence, and biochemical analyses.
The nomenclature of the enzymes and the intermediates in the purine pathway are cumbersome. To limit this complexity, we will call each protein by its gene name in E. coli, as indicated in Figure 1. In addition, each of the intermediates will be described using the acronyms in Figure 1. Initially we will focus on the importance of chemistry and the binding of R5P in the evolution of this pathway.
Section snippets
Chemistry and ribose 5-phosphate binding: importance in pathway evolution?
Four of the six ATP-requiring enzymes (PurD, PurK, PurT, and PurC) utilize ATP to phosphorylate a carboxylate, activating it for nucleophilic attack (Figure 2a). In the case of PurD, PurK and PurT, the nucleophiles are nucleotides, whereas in the case of PurC, the nucleophile is aspartate (Figure 2a). We have recently solved the structures of PurD and PurK from E. coli 4••, 5•. The high degree of sequence homology between PurK and PurT guarantees that all three of these enzymes are structurally
Protein surfaces: importance in pathway evolution?
The third factor that may be of importance in the evolution of a pathway involves the surfaces of the proteins that catalyze the formation of chemically unstable intermediates. The model is that the product–protein complex of one enzyme would present a surface recognized by the subsequent enzyme in the pathway. A transient interaction between the two proteins would result in the direct transfer (channeling) of the metabolite between the two proteins. In the purine pathway, we have postulated
Conclusions
The structural revolution, sequence information, and biochemical methods in vitro and in vivo have now allowed us unprecedented insight into the evolution of a biosynthetic pathway. The importance of chemistry, substrate binding, and the surfaces of proteins have been suggested by recent advances. Future studies should allow more rigorous analysis of the importance of these factors in the purine biosynthetic pathway and in other pathways.
Acknowledgements
Work on purine biosynthesis in the authors’ laboratories is supported by a National Institutes of Health grant to J Stubbe (GM32191). Research conducted at the Cornell High Energy Synchrotron Source (CHESS) is supported by the National Science Foundation under award DMR-9311772, and the Macromolecular Diffraction at CHESS (MacCHESS) facility, is supported by award RR-01646 from the National Institutes of Health. SE Ealick is indebted to the WM Keck Foundation and the Lucille P Markey Charitable
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
References (27)
- et al.
Biosynthesis of the purines: the identification of the formyl donors of the transformylation reaction
J Biol Chem
(1959) - et al.
The enzymatic synthesis of 5-amino-1-ribosyl-4-imidazolecarboxylic acid 5′-phosphate from 5-amino-1-ribosylimidazole 5′-phospahte and carbon dioxide
J Biol Chem
(1959) - et al.
The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis
Structure Fold Des
(1998) Phosphatidylinositol phosphate kinase: a link between protein kinase and glutathione synthase folds
J Mol Biol
(1999)- et al.
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 Å resolution
Structure Fold Des
(1999) - et al.
Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway
Structure Fold Des
(1999) - et al.
The structure of adenylosuccinate lyase, an enzyme with dual activity in the de novo purine biosynthetic pathway
Structure Fold Des
(2000) - et al.
Interdomain signaling in glutamine phosphoribosylpyrophosphate amidotransferase
J Biol Chem
(1999) - et al.
Formylglycinamidine ribotide and 5-aminoimidazole ribotide — intermediates in the biosynthesis of inosinic acid de novo
J Am Chem Soc
(1956) - et al.
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli
Biochemistry
(1998)
Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily
Biochemistry
Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase
Biochemistry
A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity
Protein Sci
Cited by (83)
A Caenorhabditis elegans model of adenylosuccinate lyase deficiency reveals neuromuscular and reproductive phenotypes of distinct etiology
2023, Molecular Genetics and MetabolismTranscriptome analysis revealing the mechanism of soybean protein isolates and soybean peptides on Lacticaseibacillus rhamnosus Lra05
2022, Food BioscienceCitation Excerpt :The expression of a series of genes involved in purine biosynthesis were significantly upregulated in dPEP group compared with MRS group. These induced genes almost covered all the crucial steps of IMP synthesis from phosphoribosylamine-glycine ligase (purD, LGG_RS08685) responsible for the first step to IMP cyclohydrolase (purH, LGG_RS08690) responsible for the ninth step (Kappock et al., 2000). Within the process, the expression of phosphoribosylformylglycinamidine cyclo-ligase (purM, LGG_RS08700) catalyzing N-formylglycinamidine ribonucleotide (FGAM) to aminoimidazole ribonucleotide (AIR) increased most by 6.72 folds.
Microbial production of riboflavin: Biotechnological advances and perspectives
2021, Metabolic EngineeringCellulose-based biocomposites
2021, Green Biocomposites for Biomedical Engineering: Design, Properties, and ApplicationsMetabolomics study on revealing the inhibition and metabolic dysregulation in Pseudomonas fluorescens induced by 3-carene
2020, Food ChemistryCitation Excerpt :As shown in Fig. 3B, we observed the upregulation of xanthine, hypoxanthine and uracil in response to 3-carene treatment, suggesting a significant difference in xanthine-related metabolism. Purine metabolism is a crucial part in cell physiology and involved in various respects of cell metabolism, while xanthine and hypoxanthine are significant components of the cellular nucleotide pool in purine metabolism (Kappock, Ealick, & Stubbe, 2000). Six of the twelve enzymes in the purine pathway are related to ATP, which also confirms the reduction in intracellular ATP.
Primitive purine biosynthesis connects ancient geochemistry to modern metabolism
2024, Nature Ecology and Evolution
- 1
Present address: Department of Chemistry, Washington University, One Brookings Drive, Campus Box 1134, St Louis, MO 63130, USA