Molecular evolution of B6 enzymes: Binding of pyridoxal-5′-phosphate and Lys41Arg substitution turn ribonuclease A into a model B6 protoenzyme

BMC Biochemistry

Volumn 9, Issue 1, 2008, Pages

  Vacca, Rosa A ^a   Giannattasio, Sergio ^a   Capitani, Guido ^b,c   Marra, Ersilia ^a   Christen, Philipp ^b  

^a CNR   (Italy)

^b UNIVERSITY OF ZURICH   (Switzerland)

^c PAUL SCHERRER INSTITUTE   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; ASPARTIC ACID; GLUTAMIC ACID; LYSINE; PHENYLALANINE; PYRIDOXAL 5 PHOSPHATE; PYRIDOXINE; RIBONUCLEASE E; PANCREATIC RIBONUCLEASE; RECOMBINANT PROTEIN;

AMINO ACID METABOLISM; AMINO ACID SUBSTITUTION; ARTICLE; CATTLE; DECARBOXYLATION; DISSOCIATION CONSTANT; ENZYME ACTIVITY; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; EQUILIBRIUM CONSTANT; MOLECULAR EVOLUTION; MOLECULAR STABILITY; NONHUMAN; PROTEIN FAMILY; RACEMIZATION; SITE DIRECTED MUTAGENESIS; BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; KINETICS; METABOLISM;

AMINO ACID SUBSTITUTION; ARGININE; BINDING SITES; CATALYSIS; EVOLUTION, MOLECULAR; KINETICS; LYSINE; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PYRIDOXAL PHOSPHATE; RECOMBINANT PROTEINS; RIBONUCLEASE, PANCREATIC; VITAMIN B 6;

EID: 46649116753     PISSN: None     EISSN: 14712091     Source Type: Journal    
DOI: 10.1186/1471-2091-9-17     Document Type: Article

References (45)

1. Biochemistry. DE Metzler, Burlington, MA, Harcourt/Academic Press 2 2001
2. Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes. Regio-specific alpha, beta and gamma families. FW Alexander E Sandmeier PK Mehta P Christen, Eur J Biochem 1994 219 953 960 8112347
3. 6-dependent enzymes. JN Jansonius, Curr Opin Struct Biol 1998 8 759 769 9914259
4. The molecular evolution of pyridoxal-5′-phosphate-dependent enzymes. PK Mehta P Christen, Adv Enzymol Relat Areas Mol Biol 2000 74 129 184 10800595
5. From cofactor to enzymes. The molecular evolution of pyridoxal-5′- phosphate-dependent enzymes. P Christen PK Mehta, Chem Rec 2001 1 6 436 447 11933250
6. Pyridoxal 5′-phosphate-dependent catalytic antibody. SI Gramatikova P Christen, J Biol Chem 1996 271 30583 30586 8940030
7. α-(5′- phosphopyridoxyl)-L-lysine. SI Gramatikova P Christen, J Biol Chem 1997 272 9779 9784 9092511
8. Structural basis for D-amino acid transamination by the pyridoxal-5′-phosphate-dependent catalytic antibody 15A9. B Golinelli-Pimpaneau C Lüthi P Christen, J Biol Chem 2006 281 23969 23977 16790434
9. Chemical approaches to the properties of active sites of enzymes. BL Vallee JF Riordan, Annu Rev Biochem 1969 38 733 794 4896248
10. Chemical modification of proteins. GE Means RE Feeney, San Francisco: Holden-Day 1971
11. Structure of ribonuclease A: results of joint neutron and X-ray refinement at 2.0-A resolution. A Wlodawer L Sjölin, Biochemistry 1983 22 2720 2728 6871157
12. Bovine pancreatic ribonuclease. FM Richards HW Wyckoff, The Enzymes New York: Academic Press, Boyer PD, 1971 IV 647 806
13. Pancreatic ribonuclease. P Blockburn S Moore, The Enzymes New York: Academic Press, Boyer PD, 3 1982 XV 317 443
14. Pancreatic ribonuclease A: the most studied endoribonuclease. M Eftink RL Biltonen, Hydrolytic Enzymes Amsterdam: Elsevier, Neuberger A, Brocklehurst K, 1987 333 376
15. The role of non-catalytic binding subsites in endonuclease activity of bovine pancreatic ribonuclease A. M Moussaoui A Guasch E Boix CM Cucillo, J Biochem 1996 271 4687 4692
16. Affinity labelling of pancreatic ribonuclease. GE Means RE Feeney, J Biol Chem 1971 246 5532 5533 5106444
17. Schiff bases of pyridoxal phosphate with active center lysines of ribonuclease A. CRH Raetz DS Auld, Biochemistry 1972 11 2229 2236 5028492
18. Modification of ribonuclease A with pyridoxal-5′-phosphate. SN Borisova VI Matrosov SV Shlyapnikov MY Karpeiskii, Mol Biol 1974 8 228 236 4610348
19. Modification of bovine pancreatic ribonuclease A with pyridoxal 5′-phosphate. Isolation and identification of derivatives. P Riquelme WE Brown F Marcus, Int J Pept Protein Res 1975 7 5 379 387 1237472
20. Preparation of crystalline phosphorylated derivatives of vitamin B6. E Peterson NA Sober, J Amer Chem Soc 1954 76 169 173
21. Chemical modification by pyridoxal 5′-phosphate and cyclohexane-1,2-dione indicates that Lys-7 and Arg-10 are involved in the p2 phosphate-binding subsite of bovine pancreatic ribonuclease A. RM Richardson X Pares CM Cuchillo, Biochem J 1990 267 593 599 2111131
22. Site-directed mutagenesis of bovine pancreatic ribonuclease: lysine 41 and aspartate 121. K Trautwein P Halliger J Stackhouse SA Benner, FEBS Lett 1991 281 275 277 1901803
23. 1.6 A structure of semisynthetic ribonuclease crystallized from aqueous ethanol. Comparison with crystals from salt solutions and with ribonuclease A from aqueous alcohol solutions. SJ de Mel MS Doscher PD Martin F Rodier BF Edwards, Acta Crystallogr D Biol Crystallogr 1995 51 1003 1012 15299768
24. Structure of three ribonuclease-A covalent derivatives with pyridoxal 5′-phosphate. L Boqué MG Coll M Ribó CM Cuchillo I Fita M Vilanova, Protein Peptide Lett 1998 5 101 108
25. 7(41)-ribonuclease A. SM Dudkin LV Karabachyan SN Borisova SV Shlyapnikov MY Karpeisky TG Geidarov, Biochim Biophys Acta 1975 386 275 282 236023
26. The role of pyridoxal 5′-phosphate in glycogen phosphorylase catalysis. D Palm HW Klein R Schinzel M Buehner EJM Helmreich, Biochemistry 1990 29 1099 1107 2182117
27. Determination of D-amino acids. II. Use of a bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene. P Marfey, Carlsberg Res Commun 1984 49 591 596
28. The enantiomeric error frequency of aspartate aminotransferase. S Kochhar P Christen, Eur J Biochem 1988 175 433 438 2900141
29. Active-site Arg → Lys substitution alter reaction and substrate specificity of aspartate aminotransferase. RA Vacca S Giannattasio R Graber E Sandmeier E Marra P Christen, J Biol Chem 1997 272 21932 21937 9268327
30. Conversion of tyrosine phenol-lyase to dicarboxylic amino acid β-lyase, an enzyme not found in nature. B Mouratou P Kasper H Gehring P Christen, J Biol Chem 1999 274 1320 1325 9880502
31. Conversion of aspartate aminotransferase into an L-aspartate β-decarboxylase by a triple active-site mutation. R Graber P Kasper VN Malashkevich P Strop H Gehring JN Jansonius P Christen, J Biol Chem 1999 274 31203 31208 10531314
32. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. AC Eliot JF Kirsch, Annu Rev Biochem 2004 73 383 415 15189147
33. Conversion of a PLP-dependent racemase into an aldolase by single active site mutation. FP Seebeck D Hilvert, J Am Chem Soc 2003 125 34 10158 10159 12926923
34. Conformation and reaction specificity in pyridoxal phosphate enzymes. HC Dunathan, Proc Natl Acad Sci USA 1966 55 712 716 5219675
35. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. S Oue A Okamoto T Yano H Kagamiyama, J Biol Chem 1999 274 2344 2349 9891001
36. How does an enzyme evolved in vitro compare to naturally occurring homologs possessing the targeted function? Tyrosine aminotransferase from aspartate aminotransferase. SC Rothman JF Kirsch, J Mol Biol 2003 327 593 608 12634055
37. Recognizing very distant sequence relationships among proteins by family profile analysis. PK Mehta P Argos AD Barbour P Christen, Proteins 1999 35 387 400 10382666
38. The determinants of the dimeric structure of seminal ribonuclease are located in its N-terminal region. A Di Donato V Cafaro M de Nigris M Rizzo G D'Alessio, Biochem Biophys Res Commun 1993 194 1440 1445 8352802
39. Rapid and efficient site-specific mutagenesis without phenotypic selection. TA Kunkel, Proc Natl Acad Sci USA 1985 82 488 492 3881765
40. New muteins of RNase A with enhanced antitumor action. V Cafaro A Bracale A Di Maro S Sorrentino G D'Alessio A Di Donato, FEBS Lett 1998 437 149 152 9804190
41. Crystalline desoxyribonuclease; isolation and general properties; spectrophotometric method for the measurement of desoxyribonuclease activity. M Kunitz, J Gen Physiol 1950 33 349 362 15406373
42. Some spectrophotometric and polarimetric experiments with ribonuclease. M Sela CB Anfinsen, Biochim Biophys Acta 1957 24 229 235 13436418
43. Model-Building Tools for Molecular Graphics. P Emsley C Cowtan, Acta Cryst 2004 D60 2126 2132
44. PHENIX: building new software for automated crystallographic structure determination. PD Adams RW Grosse-Kunstleve LW Hung TR Ioerger AJ McCoy NW Moriarty RJ Read JC Sacchettini NK Sauter TC Terwilliger, Acta Crystallogr D Biol Crystallogr 2002 58 Pt 11 1948 1954 12393927
45. The sequence of amino acid residues in bovine pancreatic ribonuclease: revisions and confirmations. DG Smyth WH Stein S Moore, J Biol Chem 1963 238 227 234