The molecular evolution of pyridoxal-5′-phosphate-dependent enzymes

Advances in Enzymology and Related Areas of Molecular Biology

Volumn 74, Issue , 2000, Pages 129-184

  Mehta, Perdeep K ^a   Christen, Philipp ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE AMINOTRANSFERASE; ALANINE RACEMASE; AMINO ACID; ASPARTATE AMINOTRANSFERASE; DEXTRO AMINO ACID AMINOTRANSFERASE; ENZYME; PYRIDOXAL 5 PHOSPHATE; TRYPTOPHAN SYNTHASE;

METABOLISM; MOLECULAR EVOLUTION; MULTIGENE FAMILY; REVIEW;

ALANINE RACEMASE; ALANINE TRANSAMINASE; AMINO ACIDS; ASPARTATE AMINOTRANSFERASES; D-ALANINE TRANSAMINASE; ENZYMES; EVOLUTION, MOLECULAR; MULTIGENE FAMILY; PYRIDOXAL PHOSPHATE; TRYPTOPHAN SYNTHASE;

EID: 0033649909     PISSN: 0065258X     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (154)

1. Alexander FW, Sandmeier E, Mehta PK, Christen P (1994): Eur J Biochem 219: 953-960.
2. Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L (1998): J Mol Biol 284: 401-419.
3. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ (1997): Nucl Acids Res 25: 3389-3402.
4. Antson AA, Strokopytov BV, Murshudov GN, Isupov MN, Harutyunyan EH, Demidkina TV, Vassyiyer DG, Dauter Z, Terry H, Wilson KS (1992): FEBS Lett 302: 256-260.
5. Antson AA, Demidkina TV, Gollnick P, Dauter Z, von Tersch RL, Long J, Berezhnoy SN, Phillips RS, Harutyunyan EH, Wilson KS (1993): Biochemistry 32: 4195-4206.
6. 6 and PQQ." Basel: Birkhäuser, pp. 187-191.
7. Babbitt PC, Gerlt JA (1997): J Biol Chem 272: 30591-30594.
8. Bairoch A, Boeckmann B (1991): Nucl Acids Res 19: 2247-2249.
9. Bernstein FC, Koetzle TF, Williams GJB, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977): J Mol Biol 112: 535-542.
10. Bogorad L (1975): Science 188: 891-898.
11. Bränden CI (1991): Curr Opinion Struct Biol 1: 978-983.
12. Bruntner C, Bormann C (1998): Eur J Biochem 254: 347-355.
13. Burkhard P, Jagannatha Rao GS, Hohenester E, Schnackerz KD, Cook PF, Jansonius JN (1998): J Mol Biol 283: 121-133.
14. Capitani G, Hohenester E, Feng L, Storici P, Kirsch JF, Jansonius JN, (1999) J Mol Biol 294: 745-756.
15. Christen P, Metzler DE (eds) (1985): "Transaminases." New York: Wiley-Interscience.
16. Christen P, Riordan JF (1968): Biochemistry 7: 1531-1538.
17. Christen P, Kasper P, Gehring H, Sterk M (1996): FEBS Lett 389: 12-14.
18. Clausen T, Huber R, Laber B, Pohlenz H-D, Messerschmidt A (1996): J Mol Biol 262: 202-224.
19. Clausen T, Huber R, Prade L, Wahl MC, Messerschmidt A (1998): EMBO J 17: 6827-6838.
20. Cronin CN, Kirsch JF (1988): Biochemistry 27: 4572-4579.
21. Devereux J, Haeberli P, Smithies O (1984): Nucl Acids Res 12: 387-395.
22. 6 Pyridoxal Phosphate, Parts A and B." NewYork: Wiley.
23. Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996): Science 271: 470-477.
24. Dowhan W, Snell EE (1970): J Biol Chem 245: 4618-4628.
25. Dunathan HC (1966): Proc Natl Acad Sci U S A 55: 712-716.
26. Dunathan HC (1971): Adv Enzymol 35: 79-134.
27. Dunathan HC, Voet JG (1974): Proc Natl Acad Sci U S A 71: 3888-3891.
28. Farber GK, Petsko GA (1990): TIBS 15: 228-234.
29. Fitch WM (1970): Syst Zool 19: 99-113.
30. Ford GC, Eichele G, Jansonius JN (1980): Proc Natl Acad Sci U S A 77: 2559-2563.
31. Futaki SF, Ueno H, Martinez del Pozo A, Pospischil MA, Manning JM, Ringe D, Stoddard B, Tanizawa K, Yoshimura T, Soda K (1990): J Biol Chem 265: 22306-22312.
32. Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, Chinchilla D, Eisenstein E (1998): Structure 6: 465-475.
33. Gallagher T, Snell EE, Hackert ML (1989): J Biol Chem 264: 12737-12743.
34. Gallo KA, Knowles JR (1993); Biochemistry 32: 3981-3990.
35. Gehring H, Christen P (1978): J Biol Chem 253: 3158-3163.
36. Gehring H, Wilson KJ, Christen P (1975): Biochem Biophys Res Commun 67: 73-78.
37. Gilbert W, Marchionni M, McKnight G (1986): Cell 46: 151-153.
38. Graber R, Kasper P, Malashkevich VN, Sandmeier E, Berger P, Gehring H, Jansonius JN, Christen P (1995): Eur J Biochem 232: 686-690.
39. Graber R, Kasper P, Malashkevich VN, Strop P, Gehring H, Jansonius JN, Christen P (1999): J Biol Chem 274: 31203-31208.
40. Grabowski R, Hofmeister AE, Buckel W (1993); Trends Biochem Sci 18: 297-300.
41. Graf-Hausner U, Wilson KJ, Christen P (1983): J Biol Chem 258: 8813-8826.
42. Gramatikova S, Christen P (1996): J Biol Chem 271: 30583-30586.
43. Gramatikova S, Christen P (1997): J Biol Chem 272: 9779-9784.
44. Gribskov M (1992): Gene 119: 107-111.
45. Gribskov M, Lüthy R, Eisenberg D (1990): Meth Enzymol 183: 146-159.
46. Grishin NV, Phillips MA, Goldsmith EJ (1995): Prot Sci 4: 1291-1304.
47. Hartl FU, Neupert W (1990): Science 247: 930-938.
48. Hartmann C, Christen P, Jaussi R (1991a): Nature 352: 762-763.
49. Hartmann C, Lindenmann J-M, Christen P, Jaussi R (1991b): Biochem Biophys Res Commun 174: 1232-1238.
50. Hayashi H, Wada H, Yoshimura T, Esaki N, Soda K (1990): Annu Rev Biochem 59: 87-110.
51. Healy MJ, Christen P (1972): J Am Chem Soc 94: 7911-7916.
52. Hedstrom L (1994): Curr Opin Struct Biol 4: 608-611.
53. Hennig M, Grimm B, Contestabile R, John RA, Jansonius JN (1997): Proc Natl Acad Sci U S A 94: 4866-4871.
54. Hester G, Stark W, Moser M, Rallen J, Markovic-Housley Z, Jansonius JN (1999): J Mol Biol 286: 829-850.
55. Hill RE, Himmeldirk K, Kennedy IA, Pauloski RM, Sayer BG, Wolf E, Spenser ID (1996): J Biol Chem 271: 30426-30435.
56. Hofmeister AE, Berger S, Buckel W (1992): Eur J Biochem 205: 743-749.
57. Horecker BL, Pontremoli S, Ricci C, Cheng T (1961): Proc Natl Acad Sci U S A 47: 1949-1955.
58. Huber B (1995): Diploma Thesis, University of Zurich, Zurich.
59. Hyde CC, Ahmed SA, Padlan EA, Miles EW, Davies DR (1988): J Biol Chem 263: 17857-17871.
60. Isupov MN, Antson AA, Dodson EJ, Dodson GG, Dementieva IS, Zakomirdina LN, Wilson KS, Dauter Z, Lebedev AA, Harutyunyan EH (1998): J Mol Biol 276: 603-623.
61. Jäger J, Moser M, Sauder U, Jansonius JN (1994): J Mol Biol 239: 285-305.
62. Jansonius JN (1998): Curr Opinion Struct Biol 8: 759-769.
63. Jaussi R (1995): Eur J Biochem 228: 551-561.
64. Jencks WP (1969): "Catalysis in Chemistry and Enzymology." New York: McGraw-Hill, pp. 133-146.
65. Jhee K-H, Yang L, Ahmed SA, McPhie R Rowlett R, Miles EW (1998): J Biol Chem 273: 11417-11422.
66. John RA (1995): Biochim Biophys Acta 1248: 81-96.
67. Juretic J, Jaussi R, Mattes U, Christen P (1987): Nucl Acids Res 15: 10083-10087.
68. Juretic N, Mattes U, Ziak M, Christen P, Jaussi R (1990): Eur J Biochem 192: 119-126.
69. Kern AD, Oliveira MA, Coffino P, Hackert ML (1999): Structure 7: 567-581.
70. 6," Korpela T, Christen P (eds). Basel: Birkhäuser, pp. 59-67.
71. Kirsch JF, Eichele G, Ford CC, Vincent MG, Jansonius JN, Gehring H, Christen P (1984): J Mol Biol 174: 497-525.
72. Kochhar S, Hunziker PE, Leong-Morgenthaler P, Hottinger H (1992): J Biol Chem 267: 8499-8513.
73. Lam HM, Winkler ME (1990): J Bacteriol 172: 6518-6528.
74. Lamont HC, Staudenbauer WL, Strominger JL (1972): J Biol Chem 247: 5103-5106.
75. Liao D-I, Breddam K, Sweet RM, Bullock T, Remington SJ (1992): Biochemistry 31: 9796-9812.
76. Liu J-Q, Dairi T, Itoh N, Kataoka M, Shimizu S, Yamada H (1998): J Biol Chem 273: 16678-16685.
77. Mahon MM, Gramatikova SI, Christen P, Fitzpatrick TB, Malthouse JPG (1998): FEBS Lett 427: 74-78.
78. Malashkevich VN, Onuffer JJ, Kirsch JF, Jansonius JN (1995): Nat Struct Biol 2: 548-553.
79. Malcolm BA, Kirsch JF (1985): Biochem Biophys Res Commun 132: 915-921.
80. McPhalen CA, Vincent MG, Jansonius JN (1992): J Mol Biol 225: 495-517.
81. Mehta PK, Christen P (1994): Biochem Biophys Res Commun 198: 138-143.
82. Mehta PK, Hale TI, Christen P (1989): Eur J Biochem 186: 249-253.
83. Mehta PK, Hale TI, Christen P (1993): Eur J Biochem 214: 549-561.
84. Mehta PK, Argos P, Barbour AD, Christen P (1999): Proteins 35: 387-400.
85. Metzler DE (1977): "Biochemistry." New York: Academic Press, pp. 444-461.
86. Momany C, Emst S, Ghosh R, Chang N, Hackert ML (1995a): J Mol Biol 252: 643-655.
87. Momany C, Ghosh R, Hackert ML (1995b): Prot Sci 4: 849-854.
88. Morino Y, Osman AM, Okamoto M (1974): J Biol Chem 249: 6684-6692.
89. Mouratou B, Kasper P, Gehring H, Christen P (1999): J Biol Chem 274: 1320-1325.
90. Nakai T, Okada K, Akutsu S, Miyahara I, Kawaguchi S-I, Kato R, Kuramitsu S, Hirotsu K (1999): Biochemistry 38: 2413-2424.
91. Neupert W (1997): Annu Rev Biochem 66: 863-917.
92. Nomiyama H, Fukuda M, Wakasugi S, Tsuzuki T, Shimada K (1985): Nucleic Acids Res 13: 1649-1658.
93. Obaru K, Tsuzuki T, Setoyama C, Shimada K (1988): J Mol Biol 200: 13-22.
94. Okada K, Hirotsu K, Sato M, Hayashi H, Kagamiyama H (1997): J Biochem 121: 637-641.
95. Okamoto A, Higuchi T, Hirotsu K, Kuramitsu S, Kagamiyama H (1994): J Biochem 116: 95-107.
96. Okamoto A, Kato R, Masui R, Yamagishi A, Oshima T, Kuramitsu S (1996): J Biochem 119: 135-144.
97. Okamoto A, Nakai Y, Hayashi H, Kirotsu K, Kagamiyama H (1998): J Mol Biol 280: 443-461.
98. Onuffer JJ, Kirsch JF (1994): Prot Engin 7: 413-424.
99. Onuffer JJ, Kirsch JF (1995): Prot Sci 4: 1750-1757.
100. Due S, Okamoto A, Yano T, Kagamiyama H (1999): J Biol Chem 274: 2344-2349.
101. Ouzounis C, Kyrpides N (1996): FEBS Lett 390: 119-123.
102. Palm D, Klein HW, Schinzel R, Buehner M, Helmreich EJM (1990): Biochemistry 29: 1099-1107.
103. Pascarella S, Bossa F (1994): Prot Sci 3: 701-705.
104. Pascarella S, Schirch V, Bossa F (1993): FEBS Lett 331: 145-149.
105. Peisach D, Chipman DM, van Ophem PW, Manning JM, Ringe D (1998): Biochemistry 37: 4958-4967.
106. Perona JJ, Craik CS (1997): J Biol Chem 272: 29987-29990.
107. Pfister K, Sandmeier E, Berchtold W, Christen P (1985): J Biol Chem 260: 11414-11421.
108. Reardon D, Farber G (1995): FASEB J 9: 497-503.
109. Recsei PA, Snell EE (1970): Biochemistry 9: 1492-1497.
110. Renwick SB, Snell K, Baumann U (1998): Structures 6: 1105-1116.
111. Rétey J (1990): Angew Chem Int Ed Engl 29: 355-361.
112. Rhee S, Parris KD, Ahmed SA, Miles EW, Davies DR (1996): Biochemistry 35: 4211-4221.
113. Riley WO, Snell EE (1968): Biochemistry 7: 3520-3528.
114. Rosenthaler J, Guirard BM, Chang GW, Snell EE (1965): Proc Natl Acad Sci U S A 54: 152-158.
115. Rubinstein PA, Strominger JL (1974): J Biol Chem 249: 3776-3781.
116. Rutter WJ (1964): Federation Proc 23: 1248-1257.
117. Salzmann D, Christen P, Mehta PK, Sandmeier E (to be published).
118. Sandmeier E, Hale TI, Christen P (1994): Eur J Biochem 221: 997-1002.
119. Scarsdale JN, Kazanina G, Radaev S, Schirch V, Wright HT (1999): Biochemistry 38: 8347-8358.
120. Schatz G, Dobberstein B (1996): Science 271: 1519-1526.
121. Schonbeck ND, Skalski M, Shafer JA (1975): J Biol Chem 250: 5343-5351.
122. Shaw JP, Petsko GA, Ringe D (1997): Biochemistry 36: 1329-1342.
123. Shen BW, Hennig M, Hohenester E, Jansonius JN, Schirmer T (1998): J Mol Biol 277: 81-102.
124. Sonderegger P, Christen P (1978): Nature 275: 157-159.
125. Sonderegger P, Gehring H, Christen P (1977): J Biol Chem 252: 609-612.
126. Sonderegger P, Jaussi R, Christen P (1985): "Transaminases." Christen P, Metzler DE (eds) New York: Wiley, pp. 502-510.
127. Storici P, Capitani G, De Biase D, Moser M, John RA, Jansonius JN, Schirmer T (1999): Biochemistry 38: 8628-8634.
128. Sugio S, Patsko GA, Manning M, Soda K, Ringe D. (1995): Biochemistry 34: 9661-9669.
129. Sundararaju B, Antson AA, Phillips RS, Demidkina TV, Barbolina MV, Gollnick P, Dodson GG, Wilson KS (1997): Biochemistry 36: 6502-6510.
130. Taguchi H, Ohta T (1991): J Biol Chem 266: 12588-12594.
131. Taoka S, West M, Banerjee R (1999): Biochemistry 38: 2738-2744.
132. Tobler HP, Gehring H, Christen P (1987): J Biol Chem 262: 8985-8989.
133. Toney MD, Kirsch JF (1991): J Biol Chem 266: 23900-23903.
134. Toney MD, Hohenester E, Cowan SW, Jansonius JN (1993): Science 261: 756-759.
135. Toney MD, Hohenester E, Keller JW, Jansonius JN (1995): J Mol Biol 245: 151-179.
136. Tormay P, Wilting R, Lottspeich F, Mehta PK, Christen P, Bock A (1998) Eur J Biochem 254: 655-661.
137. Tsai MD, Byrn SR, Chang C, Floss HG, Weintraub JR (1978): Biochemistry 17: 3177-3182.
138. Tsuzuki T, Obaru K, Setoyama C, Shimada K (1987): J Mol Biol 198: 21-31.
139. Tumanyan VG, Mamaeva DK, Bocharov AC, Ivanov VI, Karpeisky M, Yakovlev GI (1974): Eur J Biochem 50: 119-127.
140. Vacca RA, Giannattasio S, Graber R, Sandmeier E, Marra E, Christen P (1997): J Biol Chem 272: 21932-21937.
141. Vallee BL, Falchuk KH (1993): Physiol Rev 73: 79-118.
142. Vederas JC, Floss HG (1980): Ace Chem Res 13: 455-463.
143. Voet JG, Hindenlang DM, Blanck TJ, Ulevitch RJ, Kallen RG, Dunathan HC (1973): J Biol Chem 248: 841-842.
144. Watanabe N, Sakabe K, Sakabe N, Higashi T, Sasaki K, Aibara S, Morito Y, Yonaha K, Toyama S, Fukutani H (1989): J Biochem Tokyo 105: 1-3.
145. Webb EC (1992): "Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology." Orlando: Academic Press.
146. Williamson JM, Brown GM (1979): J Biol Chem 254: 8074-8082.
147. Wilmanns M, Hyde CC, Davies RD, Kirschner K, Jansonius JN (1991): Biochemistry 30: 9161-9169.
148. Wilson AC, Carlson SS, White TJ (1977): Ann Rev Biochem 46: 573-639.
149. Yamauchi T, Choi SY, Okada H, Yohda M, Kumagai H, Esaki H, Soda K (1992): J Biol Chem 267: 18361-18364.
150. Yano T, Kuramitsu S, Tanase S, Morino Y, Kagamiyama H (1992): Biochemistry 32: 1810-1815.
151. Yano T, Oue S, Kagamiyama H (1998): Proc Natl Acad Sci U S A 95: 5511-5515.
152. Yoshimura T, Nishimura K, Ito J, Esaki N, Kagamiyama H, Manning JM, Soda K (1993): J Am Chem Soc 115: 3897-3900.
153. Ziak M, Jaussi R, Gehring H, Christen P (1990): Eur J Biochem 187: 329-333.
154. Ziak M, Jäger J, Malashkevich VN, Gehring H, Jaussi R, Jansonius JN, Christen P (1993): Eur J Biochem 211: 475-484.