Flexible Enantioselectivity of Tryptophanase Attributable to Benzene Ring in Heterocyclic Moiety of D-tryptophan

Overview

Journal Life (Basel)

Specialty Biology

Date 2014 Nov 11

PMID 25382167

Citations 1

Authors

Akihiko Shimada

Haruka Ozaki

Affiliations

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Abstract

The invariance principle of enzyme enantioselectivity must be absolute because it is absolutely essential to the homochiral biological world. Most enzymes are strictly enantioselective, and tryptophanase is one of the enzymes with extreme absolute enantioselectivity for L-tryptophan. Contrary to conventional knowledge about the principle, tryptophanase becomes flexible to catalyze D-tryptophan in the presence of diammonium hydrogenphosphate. Since D-amino acids are ordinarily inert or function as inhibitors even though they are bound to the active site, the inhibition behavior of D-tryptophan and several inhibitors involved in this process was examined in terms of kinetics to explain the reason for this flexible enantioselectivity in the presence of diammonium hydrogenphosphate. Diammonium hydrogenphosphate gave tryptophanase a small conformational change so that D-tryptophan could work as a substrate. As opposed to other D-amino acids, D-tryptophan is a very bulky amino acid with a benzene ring in its heterocyclic moiety, and so we suggest that this structural feature makes the catalysis of D-tryptophan degradation possible, consequently leading to the flexible enantioselectivity. The present results not only help to understand the mechanism of enzyme enantioselectivity, but also shed light on the origin of homochirality.

Citing Articles

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Ashiuchi M, Yamamoto T, Kamei T Life (Basel). 2014; 3(1):181-8.

PMID: 25371338 PMC: 4187202. DOI: 10.3390/life3010181.

References

Lazcano A, Miller S . How long did it take for life to begin and evolve to cyanobacteria?. J Mol Evol. 1994; 39(6):546-54. DOI: 10.1007/BF00160399. View

Chen H, Phillips R . Binding of phenol and analogues to alanine complexes of tyrosine phenol-lyase from Citrobacter freundii: implications for the mechanisms of alpha,beta-elimination and alanine racemization. Biochemistry. 1993; 32(43):11591-9. DOI: 10.1021/bi00094a016. View

Shimada A, Ozaki H, Saito T, Noriko F . Tryptophanase-catalyzed L-tryptophan synthesis from D-serine in the presence of diammonium hydrogen phosphate. Int J Mol Sci. 2009; 10(6):2578-2590. PMC: 2705506. DOI: 10.3390/ijms10062578. View

Polgar L . The catalytic triad of serine peptidases. Cell Mol Life Sci. 2005; 62(19-20):2161-72. PMC: 11139141. DOI: 10.1007/s00018-005-5160-x. View

Bada J, Miller S . Racemization and the origin of optically active organic compounds in living organisms. Biosystems. 1987; 20:21-6. View

Hanson K . Phenylalanine ammonia-lyase: a model for the cooperativity kinetics induced by D- and L-phenylalanine. Arch Biochem Biophys. 1981; 211(2):564-74. DOI: 10.1016/0003-9861(81)90491-4. View

Kulikova V, Zakomirdina L, Bazhulina N, Dementieva I, Faleev N, Gollnick P . Role of arginine 226 in the mechanism of tryptophan indole-lyase from Proteus vulgaris. Biochemistry (Mosc). 2003; 68(11):1181-8. DOI: 10.1023/b:biry.0000009131.78603.8b. View

Yamada T, Komoto J, Takata Y, Ogawa H, Pitot H, Takusagawa F . Crystal structure of serine dehydratase from rat liver. Biochemistry. 2003; 42(44):12854-65. DOI: 10.1021/bi035324p. View

Sundararaju B, Antson A, Phillips R, Demidkina T, Barbolina M, Gollnick P . The crystal structure of Citrobacter freundii tyrosine phenol-lyase complexed with 3-(4'-hydroxyphenyl)propionic acid, together with site-directed mutagenesis and kinetic analysis, demonstrates that arginine 381 is required for substrate specificity. Biochemistry. 1997; 36(21):6502-10. DOI: 10.1021/bi962917+. View

10.

Urusova D, Isupov M, Antonyuk S, Kachalova G, Obmolova G, Vagin A . Crystal structure of D-serine dehydratase from Escherichia coli. Biochim Biophys Acta. 2011; 1824(3):422-32. PMC: 7380123. DOI: 10.1016/j.bbapap.2011.10.017. View

11.

Shimada A, Ozaki H, Saito T, Fujii N . Reaction pathway of tryptophanase-catalyzed L-tryptophan synthesis from D-serine. J Chromatogr B Analyt Technol Biomed Life Sci. 2011; 879(29):3289-95. DOI: 10.1016/j.jchromb.2011.04.028. View

12.

Lahav M . Question 4: basic questions about the origin of life: on chirobiogenesis. Orig Life Evol Biosph. 2007; 37(4-5):371-7. DOI: 10.1007/s11084-007-9101-6. View

13.

Bentley R . Diastereoisomerism, contact points, and chiral selectivity: a four-site saga. Arch Biochem Biophys. 2003; 414(1):1-12. DOI: 10.1016/s0003-9861(03)00169-3. View

14.

Bonner W . The origin and amplification of biomolecular chirality. Orig Life Evol Biosph. 1991; 21(2):59-111. DOI: 10.1007/BF01809580. View

15.

Demidkina T, Anston A, Faleev N, Phillips R, Zakomyrdina L . [Spatial structure and mechanism of tyrosine phenol-lyase and tryptophan indole-lyase]. Mol Biol (Mosk). 2009; 43(2):295-308. View

16.

Snell E . Tryptophanase: structure, catalytic activities, and mechanism of action. Adv Enzymol Relat Areas Mol Biol. 1975; 42:287-333. DOI: 10.1002/9780470122877.ch6. View

17.

Bonner W . Chirality and life. Orig Life Evol Biosph. 1995; 25(1-3):175-90. DOI: 10.1007/BF01581581. View

18.

NEWTON W, Snell E . CATALYTIC PROPERTIES OF TRYPTOPHANASE, A MULTIFUNCTIONAL PYRIDOXAL PHOSPHATE ENZYME. Proc Natl Acad Sci U S A. 1964; 51:382-9. PMC: 300082. DOI: 10.1073/pnas.51.3.382. View

19.

Pizzarello S, Weber A . Prebiotic amino acids as asymmetric catalysts. Science. 2004; 303(5661):1151. DOI: 10.1126/science.1093057. View

20.

Reist M, Carrupt P, Francotte E, Testa B . Chiral inversion and hydrolysis of thalidomide: mechanisms and catalysis by bases and serum albumin, and chiral stability of teratogenic metabolites. Chem Res Toxicol. 1998; 11(12):1521-8. DOI: 10.1021/tx9801817. View