Chapter 24

Where to Start

Brewin, N. J. 2013. Legume root nodule symbiosis. The Biochemist 35:14–18.

Christen, P., Jaussi, R., Juretic, N., Mehta, P. K., Hale, T. I., and Ziak, M. 1990. Evolutionary and biosynthetic aspects of aspartate aminotransferase isoenzymes and other aminotransferases. Ann. N. Y. Acad. Sci. 585:331–338.

Schneider, G., Kack, H., and Lindqvist, Y. 2000. The manifold of vitamin B6 dependent enzymes. Structure Fold Des. 8:R1–R6.

Rhee, S. G., Chock, P. B., and Stadtman, E. R. 1989. Regulation of Escherichia coli glutamine synthetase. Adv. Enzymol. Mol. Biol. 62:37–92.

Shemin, D. 1989. An illustration of the use of isotopes: The biosynthesis of porphyrins. Bioessays 10:30–35.

Books

Wu, G. 2013. Amino Acids: Biochemistry and Nutrition. CRC Press.

Bender, D. A. 2012. Amino Acid Metabolism (3rd ed.). Wiley-Blackwell.

Jordan, P. M. (Ed.). 1991. Biosynthesis of Tetrapyrroles. Elsevier.

Scriver, C. R. (Ed.), Sly, W. S. (Ed.), Childs, B., Beaudet, A. L., Valle, D., Kinzler, K. W., and Vogelstein, B. 2001. The Metabolic Basis of Inherited Disease (8th ed.). McGraw-Hill.

McMurry, J. E., and Begley, T. P. 2005. The Organic Chemistry of Biological Pathways. Roberts and Company.

Blakley, R. L., and Benkovic, S. J. 1989. Folates and Pterins (vol. 2). Wiley.

Walsh, C. 1979. Enzymatic Reaction Mechanisms. W. H. Freeman and Company.

Nitrogen Fixation

Spatzal, T., Aksoyoglu, M., Zhang, L., Andrade, S. L. A., Schleicher, E., Weber, S., Rees, D. C., Einsle, O. 2011. Evidence for interstitial carbon in nitrogenase FeMo Cofactor. Science 334:940.

Lancaster, K. M., Roemelt, M., Ettenhuber, P., Hu, Y., Ribbe, M. W., Neese, F., Bergmann, U., DeBeer, S. 2011. X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor. Science 334:974–977.

Seefeldt, L. C., Hoffman, B. M., and Dean, D. R. 2009. Mechanism of Mo-dependent nitrogenase. Annu. Rev. Biochem. 79:701–722.

Halbleib, C. M., and Ludden, P. W. 2000. Regulation of biological nitrogen fixation. J. Nutr. 130:1081–1084.

Einsle, O., Tezcan, F. A., Andrade, S. L., Schmid, B., Yoshida, M., Howard, J. B., and Rees, D. C. 2002. Nitrogenase MoFe-protein at 1.16 Å resolution: A central ligand in the FeMo-cofactor. Science 297:1696–1700.

Benton, P. M., Laryukhin, M., Mayer, S. M., Hoffman, B. M., Dean, D. R., and Seefeldt, L. C. 2003. Localization of a substrate binding site on the FeMo-cofactor in nitrogenase: Trapping propargyl alcohol with an α-70-substituted MoFe protein. Biochemistry 42:9102–9109.

Regulation of Amino Acid Biosynthesis

Li, Y., Zhang, H., Jiang, C., Xu, M., Pang, Y., Feng, J., Xiang, X., Kong, W., Xu, G., Li, Y., et al. 2013. Hyperhomocysteinemia promotes insulin resistance by inducing endoplasmic reticulum stress in adipose tissue. J. Biol. Chem. 288:9583–9592.

Eisenberg, D., Gill, H. S., Pfluegl, G. M., and Rotstein, S. H. 2000. Structure-function relationships of glutamine synthetases. Biochim. Biophys. Acta 1477:122–145.

Purich, D. L. 1998. Advances in the enzymology of glutamine synthesis. Adv. Enzymol. Relat. Areas Mol. Biol. 72:9–42.

Yamashita, M. M., Almassy, R. J., Janson, C. A., Cascio, D., and Eisenberg, D. 1989. Refined atomic model of glutamine synthetase at 3.5 Å resolution. J. Biol. Chem. 264:17681–17690.

Schuller, D. J., Grant, G. A., and Banaszak, L. J. 1995. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nat. Struct. Biol. 2:69–76.

Rhee, S. G., Park, R., Chock, P. B., and Stadtman, E. R. 1978. Allosteric regulation of monocyclic interconvertible enzyme cascade systems: Use of Escherichia coli glutamine synthetase as an experimental model. Proc. Natl. Acad. Sci. U.S.A. 75:3138–3142.

Wessel, P. M., Graciet, E., Douce, R., and Dumas, R. 2000. Evidence for two distinct effector-binding sites in threonine deaminase by site-directed mutagenesis, kinetic, and binding experiments. Biochemistry 39:15136–15143.

B27

James, C. L., and Viola, R. E. 2002. Production and characterization of bifunctional enzymes: Domain swapping to produce new bifunctional enzymes in the aspartate pathway. Biochemistry 41:3720–3725.

Xu, Y., Carr, P. D., Huber, T., Vasudevan, S. G., and Ollis, D. L. 2001. The structure of the PII-ATP complex. Eur. J. Biochem. 268:2028–2037.

Krappmann, S., Lipscomb, W. N., and Braus, G. H. 2000. Coevolution of transcriptional and allosteric regulation at the chorismate metabolic branch point of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 97:13585–13590.

Aromatic Amino Acid Biosynthesis

Brown, K. A., Carpenter, E. P., Watson, K. A., Coggins, J. R., Hawkins, A. R., Koch, M. H., and Svergun, D. I. 2003. Twists and turns: A tale of two shikimate-pathway enzymes. Biochem. Soc. Trans. 31:543–547.

Pan, P., Woehl, E., and Dunn, M. F. 1997. Protein architecture, dynamics and allostery in tryptophan synthase channeling. Trends Biochem. Sci. 22:22–27.

Sachpatzidis, A., Dealwis, C., Lubetsky, J. B., Liang, P. H., Anderson, K. S., and Lolis, E. 1999. Crystallographic studies of phosphonate-based α-reaction transition-state analogues complexed to tryptophan synthase. Biochemistry 38:12665–12674.

Weyand, M., and Schlichting, I. 1999. Crystal structure of wild-type tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate. Biochemistry 38:16469–16480.

Crawford, I. P. 1989. Evolution of a biosynthetic pathway: The tryptophan paradigm. Annu. Rev. Microbiol. 43:567–600.

Carpenter, E. P., Hawkins, A. R., Frost, J. W., and Brown, K. A. 1998. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature 394:299–302.

Schlichting, I., Yang, X. J., Miles, E. W., Kim, A. Y., and Anderson, K. S. 1994. Structural and kinetic analysis of a channel-impaired mutant of tryptophan synthase. J. Biol. Chem. 269:26591–26593.

Glutathione

Edwards, R., Dixon, D. P., and Walbot, V. 2000. Plant glutathione S-transferases: Enzymes with multiple functions in sickness and in health. Trends Plant Sci. 5:193–198.

Lu, S. C. 2000. Regulation of glutathione synthesis. Curr. Top. Cell Regul. 36:95–116.

Schulz, J. B., Lindenau, J., Seyfried, J., and Dichgans, J. 2000. Glutathione, oxidative stress and neurodegeneration. Eur. J. Biochem. 267:4904–4911.

Lu, S. C. 1999. Regulation of hepatic glutathione synthesis: Current concepts and controversies. FASEB J. 13:1169–1183.

Ethylene and Nitric Oxide

Hill, B. G., Dranka, B. P., Baily, S. M., Lancaster, Jr., J. R., and Darley-Usmar, V. M. 2010. What part of NO don’t you understand? Some answers to the cardinal questions in nitric oxide biology. J. Biol. Chem. 285:19699–19704.

Nisoli, E., Falcone, S., Tonello, C., Cozzi, V., Palomba, L., Fiorani, M., Pisconti, A., Brunelli, S., Cardile, A., Francolini, M., et al. 2004. Mitochondrial biogenesis by NO yields functionally active mitochondria in mammals. Proc. Natl. Acad. Sci U.S.A. 101: 16507–16512.

Bretscher, L. E., Li, H., Poulos, T. L. and Griffith, O. W. 2003. Structural characterization and kinetics of nitric oxide synthase inhibition by novel N5-(iminoalkyl)- and N5-(iminoalkenyl)-ornithines. J. Biol. Chem. 278:46789–46797.

Haendeler, J., Zeiher, A. M., and Dimmeler, S. 1999. Nitric oxide and apoptosis. Vitam. Horm. 57:49–77.

Capitani, G., Hohenester, E., Feng, L., Storici, P., Kirsch, J. F., and Jansonius, J. N. 1999. Structure of 1-aminocyclopropane-1-carboxylate synthase, a key enzyme in the biosynthesis of the plant hormone ethylene. J. Mol. Biol. 294:745–756.

Hobbs, A. J., Higgs, A., and Moncada, S. 1999. Inhibition of nitric oxide synthase as a potential therapeutic target. Annu. Rev. Pharmacol. Toxicol. 39:191–220.

Stuehr, D. J. 1999. Mammalian nitric oxide synthases. Biochim. Biophys. Acta 1411:217–230.

Chang, C., and Shockey, J. A. 1999. The ethylene-response pathway: Signal perception to gene regulation. Curr. Opin. Plant Biol. 2:352–358.

Theologis, A. 1992. One rotten apple spoils the whole bushel: The role of ethylene in fruit ripening. Cell 70:181–184.

Biosynthesis of Porphyrins

Kaasik, K., and Lee, C. C. 2004. Reciprocal regulation of haem biosynthesis and the circadian clock in mammals. Nature 430:467–471.

Leeper, F. J. 1989. The biosynthesis of porphyrins, chlorophylls, and vitamin B12. Nat. Prod. Rep. 6:171–199.

Porra, R. J., and Meisch, H.-U. 1984. The biosynthesis of chlorophyll. Trends Biochem. Sci. 9:99–104.