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Unexpected Sequence Similarity Between Nucleosidases and Phosphoribosyltransferases of Different Specificity

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Unexpected Sequence Similarity Between Nucleosidases and Phosphoribosyltransferases of Different Specificity Protein Science (1994), 3:1081-1088. Cambridge University Press. Printed in the USA. Copyright 0 1994 The Protein Society Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity ARCADY R. MUSHEGIAN' AND EUGENE V. KOONIN' Department of Plant Pathology, University of Kentucky, Lexington, Kentucky 40546-0091 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 (RECEIVEDFebruary 17, 1994; ACCEPTEDApril 29, 1994) Abstract Amino acid sequences of enzymes that catalyze hydrolysis or phosphorolysis of the N-glycosidic bond in nucleo- sides and nucleotides (nucleosidases and phosphoribosyltransferases) were explored using computer methods for database similarity search and multiple alignment. Two new families, each including bacterial and eukaryotic en- zymes, were identified. Family I consists of Escherichia coli AMP hydrolase (Amn), uridine phosphorylase (Udp), purine phosphorylase (DeoD), uncharacterized proteins from E. coli and Bacteroides uniformis, and, unexpectedly, a group of plant stress-inducible proteins. It is hypothesized that these plant proteins have evolved from nucleo- sidases and may possess nucleosidase activity. The proteins in this new family contain 3 conserved motifs, one of which was found also in eukaryotic purine nucleosidases, where it corresponds to thenucleoside-binding site. Family I1 is comprised of bacterial and eukaryotic thymidine phosphorylases and anthranilate phosphoribosyl- transferases, the relationship between which has not been suspected previously. Based on the known tertiary struc- ture of E. coli thymidine phosphorylase, structural interpretation was given to thesequence conservation in this family. The highest conservation is observed in the N-terminal a-helical domain, whose exactfunction is not known. Parts of the conserved active site of thymidine phosphorylasesand anthranilatephosphoribosyltransferases were delineated. A motif in the putative phosphate-binding site is conserved in family I1 and in other phosphoribosyl- transferases. Our analysis suggests that certain enzymes of very similar specificity, e.g., uridine and thymidine phosphorylases, could have evolved independently. In contrast, enzymes catalyzing such different reactions as AMP hydrolysis and uridine phosphorolysis or thymidine phosphorolysis and phosphoribosyl anthranilate syn- thesis are likely to have evolved from common ancestors. Keywords: nucleosidases; phosphoribosyltransferases; sequence similarity Enzymes that catalyze hydrolysis or phosphorolysis of the platelet-derived endothelial cell growth factor is identical to thy- N-glycosidic bond in nucleotides, nucleosides, and related com- midine phosphorylase (Barton et al., 1992; Ishizawa & Yamada, pounds are central to salvage pathways of nucleotide metabolism 1992). Phosphoribosyltransferases also have attracted consid- and arealso important in de novo synthesis of nucleotides and erable attention because deficiencyin these enzymes leadsto var- certain amino acids (Table 1; reviewed by Lin, 1987; Neuhard ious metabolic disorders in humans, e.g., Lesch-Nyhan disease & Nygaard, 1987). Nucleosidases are involved in the regulation (Stout & Caskey, 1985). of the intracellular concentration of nucleotides and allow utiliza- A single organism, i.e., Escherichia coli, which has been stud- tion of ribose and deoxyribose as a source of carbon and energy. ied in the most detail, encodes numerous nucleosidases and Phosphoribosyltransferases provide, via 5-phosphoribosyl- phosphoribosyltransferases, including enzymes that catalyze es- 1-pyrophosphate (PRPP), a crucial link between nucleotide and sentially identical reactions but differin their specificity toward amino acid metabolism. The substrates of these enzymesare very the nucleotide base (e.g., thymidine phosphorylase, uridine diverse, but the reacting groups always involve phosphate and phosphorylase, and purine phosphorylase; see Table 1). A num- ribose or deoxyribose (Table 1). The interest to the nucleosid- ber of nucleotide sequences of genes encoding these enzymes ases has been enhanced by the recent observation that human from all types of organisms have been reported (Table 1). The 3-dimensional (3D) structure has been determined for human purine nucleoside phosphorylase (PNP; Ealick et al., 1990) and Reprint requests to: EugeneV. Koonin, National Centerfor Biotech- nology Information, National Library of Medicine, National Institutes E. coli thymidine phosphorylase (DeoA; Walter et al., 1990), of Health, Bethesda, Maryland 20894; e-mail: [email protected]. leading to detailed characterization of the respective active cen- gov. ters. Except for the obvious similarity between human TYPH 1081 1082 A.R. Mushegian and E. K Koonin Table 1. Nucleosidases, phosphoribosyltransferases, and related enzymesa -__ Protein/ Enzymatic MJquaternary Metabolic geneb Organism(s) activity Reaction structure' pathway References Udp/udp E. coli Uridine Uridine + Pi = 8 x 22 Pyrimidine Neuhard & phosphorylase ribose-I-P + salvage Nygaard, 1987 uracil DeoD/deoD E. coli Purine nucleoside Purine (deoxy)- 6 x 23.7 Purine salvage Neuhard & phosphorylase ribonucleoside + Nygaard, 1987 Pi = (deoxy)- ribose-I-P + purine Amdamn E. coli AMP glycosylase AMP + Hz0 = 6 x 52 Purine salvage Leung & Schramm, adenine + ribose- 1980; Leung 5-P et al., 1989; Neuhard & Nygaard, 1987 PNP Mammals, Purine nucleoside Purine (deoxy)- 3(2) x 32 Purine salvage Neuhard & B. subtilis, phosphorylase ribonucleoside + Nygaard, 1987; M. leprae Pi = (deoxy)- Lin, 1987; Ealick ribose-I-P + et al., 1990 purine DeoA/deoA E. coli Thymidine Thymidine + Pi = 2 x 45 Thymidine Neuhard & phosphorylase ribose- 1-P + salvage Nygaard, 1987; thymine Lin, 1987; Walter et al., 1990 TYPH Human Thymidine Thymidine + Pi = 2 x 45 Thymidine Yoshimura et al., phosphorylase ribose- 1 -P + salvage 1990; Bartonet (=PD-ECGF) thymine al., 1992 TrpD/trpD Eubacteria, Anthranilate Anthranilate + 2(?) x 36 Second step in Crawford, 1989; (Eubacteria) archaea, yeast, phosphoribosyl. PRPP = N- tryptophan Kim et al., 1993 plants transferase phosphoribosyl- biosynthesis anthranilate + PPi TrpG/trpG E. coli and sev- Anthranilate Anthranilate + 2 x 58.3 First and second Pittard, 1987; eral other bac- phosphoribosyl- PRPP = N- step in trypto- Crawford, 1989 terial species transferase (with phosphoribosyl- phan biosyn- N-terminal gluta- anthranilate + thesis mine aminotrans- PP,; chorismate + ferase domain) L-glutamine = anthranilate + pyruvate + L-glutamine Apt/apt (E. coli) Eubacteria, Adenine phospho- Adenine + PRPP = 2 x 20 Purine salvage Neuhard & eukaryotes ribosyltransferase AMP + PPi Nygaard, 1987 Gpt/gpt (E. coli) Eubacteria, Guanine phospho- Guanine + PRPP = 3 x 16.9 Purine salvage Neuhard & eukaryotes ribosyltransferase GMP + PP,; Nygaard, 1987 xanthine + PRPP = XMP + PPI; hypoxan- thine + PRPP = HXMP + PPi Hpt/hpt Eubacteria, Hypoxanthine Hypoxanthine + ? x 20 Purine salvage Neuhard & (L. lactis) eukaryotes phosphoribosyl- PRPP = IMP + Nygaard, 1987 transferase pp, UPP/UPP Eubacteria, Uracil phospho- Uracil + PRPP = 3 x 23.5 Pyrimidine Neuhard & (E. coli) eukaryotes ribosyltransferase UMP + PP; salvage Nygaard, 1987 PyrE/pyrE Eubacteria, Orotate phospho- Orotate + PRPP = 2 x 23.4 Fifthstep in Neuhard & (E. coli) eukaryotes ribosyltransferase OMP + PPi pyrimidine Nygaard, 1987 biosynthesis (continued) Sequence similarity between nucleosidases and phosphoribosyltransferases 1083 Table 1. Continued Protein/ Enzymatic M,/quaternary Metabolic geneb Organism(s) geneb activity Reaction structureC pathway References PurF/purF Eubacteria, Glutamine phospho- L-glutamine + 4(3) X 53 First step in de Neuhard & (E. coli) eukaryotes ribosyltransferase PRPP = novo purine Nygaard, 1987 L-glutamate + biosynthesis PPI + 5-ph0~- phoribosylamine HisG/hisC Eubacteria, ATP phosphoribo- ATP + PRPP = 6 x 33 First step in Winkler, 1987 (E. coli) eukaryotes syltransferase 1-(5-phospho-D- histidine ribosyl)-ATP + biosynthesis PPI PncB/pncB E. coli Nicotinate phospho- Quinolinate + ? x 44 NAD White, 1982; (E. coli) ribosyltransferase PRPP = biosynthesis Tritz, 1987 NaMN + PPI + co2 NadC/nadC S. typhimurium Quinolinate phos- Nicotinate + 2x31 NAD White, 1982; phoribosyltrans- PRPP + ATP = biosynthesis Tritz, 1987 ferase NaMN + PPI + ADP + Pi PrsA/prsA Eubacteria,PrsA/prsA Ribose-phosphate ATP + ribose- 5(?) X 31 PRPP synthesis Neuhard & (E. coli) eukaryotes pyrophosphokinase 5-phosphate = for de novo Nygaard, 1987 (PRPP synthetase) AMP + PRPP and salvage pathways of nucleotide metabolism a Only enzymes for which sequence information is available were included. Where sequences are available for several organisms, the proteidgene name is for the organism(s) indicated in parentheses. The first number is the number of identical subunits and the second number is the Mr. (endothelial growth factor) and E. coli thymidine phosphory- base translated in 6 reading frames for similarity to an amino lase encoded by the deoA gene (Barton et al., 1992), and the acid sequence), and multiple alignment using the MACAW pro- somewhat lower similarity between human PNP and partial nu- gram (Schuler et al., 1991) showed that these pairs of relatively cleosidase sequence from Bacillussubtilis (Wu et al., 1992), no strongly similar proteins belonged to 2 distinct families of en- significant relationships have been derived from analysis of zymes that have not been described previously. amino acid sequences
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