Chapter 25

Where to Start

Sutherland, J. D. 2010. Ribonucleotides. Cold Spring Harb. Perspect. Biol. 2:a005439.

Ipata, P. L. 2011. Origin, utilization, and recycling of nucleosides in the central nervous system. Adv. Physiol. Educ. 35:342–346.

Ordi, J., Alonso, P. L., de Zulueta, J., Esteban, J., Velasco, M., Mas, E., Campo, E., and Fernández, P. L. 2006. The severe gout of Holy Roman Emperor Charles V. New Eng. J. Med. 355:516–520.

Kappock, T. J., Ealick, S. E., and Stubbe, J. 2000. Modular evolution of the purine biosynthetic pathway. Curr. Opin. Chem. Biol. 4:567–572.

Jordan, A., and Reichard, P. 1998. Ribonucleotide reductases. Annu. Rev. Biochem. 67:71–98.

Pyrimidine Biosynthesis

Raushel, F. M., Thoden, J. B., Reinhart, G. D., and Holden, H. M. 1998. Carbamoyl phosphate synthetase: A crooked path from substrates to products. Curr. Opin. Chem. Biol. 2:624–632.

Huang, X., Holden, H. M., and Raushel, F. M. 2001. Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu. Rev. Biochem. 70:149–180.

Begley, T. P., Appleby, T. C., and Ealick, S. E. 2000. The structural basis for the remarkable proficiency of orotidine 5′-monophosphate decarboxylase. Curr. Opin. Struct. Biol. 10:711–718.

Traut, T. W., and Temple, B. R. 2000. The chemistry of the reaction determines the invariant amino acids during the evolution and divergence of orotidine 5′-monophosphate decarboxylase. J. Biol. Chem. 275:28675–28681.

Purine Biosynthesis

Zhao, H., French, J. B., Fang, Y., and Benkovic, S. J. 2013. The purinosome, a multi-protein complex involved in the de novo biosynthesis of purines in humans. Chem. Commun. 49:4444–4452.

Verrier, F., An, S., Ferrie, A. M., Sun, H., Kyoung, M., Deng, H., Fang, Y., and Benkovic, S. J. 2011. GPCRs regulate the assembly of a multienzyme complex for purine biosynthesis. Nat. Chem. Biol. 7:909–915.

Mastrangelo, L., Kim, J.-E., Miyanohara, A., Kang, T. H., and Friedmann, T. 2012. Purinergic signaling in human pluripotent stem cells is regulated by the housekeeping gene encoding hypoxanthine guanine phosphoribosyltransferase. Proc. Natl. Acad. Sci. U.S.A. 109:3377–3382.

B28

An, S., Kyoung, M., Allen, J. J., Shokat, K. M., and Benkovic, S. J. 2010. Dynamic regulation of a metabolic multienzyme complex by protein kinase CK2. J. Biol. Chem. 285:11093–11099.

Thoden, J. B., Firestine, S., Nixon, A., Benkovic, S. J., and Holden, H. M. 2000. Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase. Biochemistry 39:8791–8802.

McMillan, F. M., Cahoon, M., White, A., Hedstrom, L., Petsko, G. A., and Ringe, D. 2000. Crystal structure at 2.4 Å resolution of Borrelia burgdorferi inosine 5′-monophosphate dehydrogenase: Evidence of a substrate-induced hinged-lid motion by loop 6. Biochemistry 39:4533–4542.

Levdikov, V. M., Barynin, V. V., Grebenko, A. I., Melik-Adamyan, W. R., Lamzin, V. S., and Wilson, K. S. 1998. The structure of SAICAR synthase: An enzyme in the de novo pathway of purine nucleotide biosynthesis. Structure 6:363–376.

Ribonucleotide Reductases

Ahmad, M. F., and Dealwis, C. G. 2013. The structural basis for the allosteric regulation of ribonucleotide reductase. Prog. Mol. Biol. Transl. Sci. 117:389–410.

Minnihan, E. C., Nocera, D. G., and Stubbe, J. 2013. Reversible, long-range radical transfer in E. coli class Ia ribonucleotide reductase. Acc. Chem. Res. 46:2524−2535.

Reichard, P. 2010. Ribonucleotide reductases: Substrate specificity by allostery. Biochem. Biophys. Res. Commun. 396:19–23

Avval, F. Z., and Holmgren, A. 2009. Molecular mechanisms of thioredoxin and glutaredoxin as hydrogen donors for mammalian S phase ribonucleotide reductase. J. Biol. Chem. 284:8233–8240.

Rofougaran, R., Crona M., Vodnala, M., Sjöberg, B. M., and Hofer, A. 2008. Oligomerization status directs overall activity regulation of the Escherichia coli class Ia ribonucleotide reductase. J. Biol. Chem. 283:35310–35318.

Nordlund, P., and Reichard, P. 2006. Ribonucleotide reductases. Annu. Rev. Biochem. 75:681–706.

Eklund, H., Uhlin, U., Farnegardh, M., Logan, D. T., and Nordlund, P. 2001. Structure and function of the radical enzyme ribonucleotide reductase. Prog. Biophys. Mol. Biol. 77:177–268.

Reichard, P. 1997. The evolution of ribonucleotide reduction. Trends Biochem. Sci. 22:81–85.

Stubbe, J. 2000. Ribonucleotide reductases: The link between an RNA and a DNA world? Curr. Opin. Struct. Biol. 10:731–736.

Logan, D. T., Andersson, J., Sjöberg, B. M., and Nordlund, P. 1999. A glycyl radical site in the crystal structure of a class III ribonucleotide reductase. Science 283:1499–1504.

Tauer, A., and Benner, S. A. 1997. The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: An evolutionary solution to the ribonucleotide reductase conundrum. Proc. Natl. Acad. Sci. U.S.A. 94:53–58.

Stubbe, J., Nocera, D. G., Yee, C. S. and Chang, M. C. 2003. Radical initiation in the class I ribonucleotide reductase: Long-range proton-coupled electron transfer? Chem. Rev. 103:2167–2201.

Stubbe, J., and Riggs-Gelasco, P. 1998. Harnessing free radicals: Formation and function of the tyrosyl radical in ribonucleotide reductase. Trends Biochem. Sci. 23:438–443.

Thymidylate Synthase and Dihydrofolate Reductase

Liu, C. T., Hanoian, P., French, J. B., Pringle, T. H., Hammes-Schiffer, S., and Benkovic, S. J. 2013. Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans. Proc. Natl. Acad. Sci. U.S.A. 110: 10159–10164.

Abali, E. E., Skacel, N. E., Celikkaya, H., and Hsieh, Y.-C. 2008. Regulation of human dihydrofolate reductase activity and expression. Vitam. Horm. 79:267–292.

Schnell, J. R., Dyson, H. J., and Wright, P. E. 2004. Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu. Rev. Biophys. Biomol. Struct. 33:119–140.

Li, R., Sirawaraporn, R., Chitnumsub, P., Sirawaraporn, W., Wooden, J., Athappilly, F., Turley, S., and Hol, W. G. 2000. Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs. J. Mol. Biol. 295:307–323.

Liang, P. H., and Anderson, K. S. 1998. Substrate channeling and domain-domain interactions in bifunctional thymidylate synthase-dihydrofolate reductase. Biochemistry 37:12195–12205.

Miller, G. P., and Benkovic, S. J. 1998. Stretching exercises: Flexibility in dihydrofolate reductase catalysis. Chem. Biol. 5:R105–R113.

Carreras, C. W., and Santi, D. V. 1995. The catalytic mechanism and structure of thymidylate synthase. Annu. Rev. Biochem. 64:721–762.

Defects in Nucleotide Biosynthesis

Grunebaum, E., Cohen, A., and Roifman, C. M. 2013. Recent advances in understanding and managing adenosine deaminase and purine nucleoside phosphorylase deficiencies. Curr. Opin. Allergy Clin. Immunol. 13:630–638.

Fu, R., and Jinnah, H. A. 2012. Genotype-phenotype correlations in Lesch-Nyhan Disease: Moving beyond the gene. J. Biol. Chem. 287:2997−3008.

Richette, P. and Bardin, T. 2010. Gout. Lancet 375:318–328.

Aiuti, A., Cattaneo, F., Galimberti, S., Benninghoff, U., Cassani, B., Callegaro, L., Scaramuzza, S., Andolfi, G., Mirolo, M., Brigida, I., et al. 2009. Gene therapy for immunodeficiency due to adenosine deaminase deficiency. New Engl. J. Med. 360:447–458.

Jurecka, A. 2009. Inborn errors of purine and pyrimidine metabolism. J. Inherit. Metab. Dis. 32:247–263.

Nyhan, W. L., Barshop, B. A., and Ozand, P. T. 2005. Atlas of Metabolic Diseases. (2d ed., pp. 429–462). Hodder Arnold.

Scriver, C. R., Sly, W. S., Childs, B., Beaudet, A. L., Valle, D., Kinzler, K. W., and Vogelstein, B. (Eds.). 2001. The Metabolic and Molecular Bases of Inherited Diseases (8th ed., pp. 2513–2704). McGraw-Hill.

Nyhan, W. L. 1997. The recognition of Lesch-Nyhan syndrome as an inborn error of purine metabolism. J. Inherited Metab. Dis. 20:171–178.

Wong, D. F., Harris, J. C., Naidu, S., Yokoi, F., Marenco, S., Dannals, R. F., Ravert, H. T., Yaster, M., Evans, A., Rousset, O., et al. 1996. Dopamine transporters are markedly reduced in Lesch-Nyhan disease in vivo. Proc. Natl. Acad. Sci. U.S.A. 93:5539–5543.

Neychev, V. K., and Mitev, V. I. 2004. The biochemical basis of the neurobehavioral abnormalities in the Lesch-Nyhan syndrome: A hypothesis. Med. Hypotheses 63:131–134.