Structural basis for the activity of two muconate cycloisomerase variants toward substituted muconates

Proteins: Structure, Function and Genetics

Volumn 34, Issue 1, 1999, Pages 125-136

  Schell, Ursula ^a   Helin, Sari ^b,c   Kajander, Tommi ^b   Schlömann, Michael ^a   Goldman, Adrian ^b  

^a UNIVERSITY OF STUTTGART   (Germany)

^b UNIVERSITY OF TURKU   (Finland)

^c ÅBO AKADEMI UNIVERSITY   (Finland)

Author keywords

ketoadipate pathway; ( barrel; Muconate cycloisomerase; Muconate lactonizing enzyme; Protein structure; X ray crystallography

Indexed keywords

ADIPIC ACID; ISOMERASE; MUCONATE CYCLOISOMERASE; MUCONIC ACID; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME PURIFICATION; PRIORITY JOURNAL; PROTON TRANSPORT; STEREOCHEMISTRY; X RAY CRYSTALLOGRAPHY;

BINDING SITES; INTRAMOLECULAR LYASES; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MUTATION; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0032964802     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990101)34:1<125::AID-PROT10>3.0.CO;2-Y     Document Type: Article

References (54)

1. Häggblom MM. Microbial breakdown of halogenated aromatic pesticides and related compounds. FEMS Microbiol Rev 1992;103: 29-72.
2. Reineke W. Degradation of chlorinated aromatic compounds by bacteria: strain development. Biological degradation and bioremediation of toxic chemicals. Chaudhry GR, editor. Portland, OR: Dioscorides Press; 1994. p 416-454.
3. Schmidt E, Knackmuss H-J. Conversion of chlorinated muconic acids into maleoylacetic acid. Biochem J 1980;192:339-347.
4. Blasco R, Wittich R-M, Mallavarapu M, Timmis KN, Pieper DH. From xenobiotic to antibiotic, formation of protoanemonin from 4-chlorocatechol by enzymes of the 3-oxoadipate pathway. J Biol Chem 1995;270:29229-29235.
5. Vollmer MD, Schlömann M. Conversion of 2-chloro-cis,cis-muconate and its metabolites 2-chloro-and 5-chloromuconolactone by chloromuconate cycloisomerases of pJP4 and pAC27. J Bacteriol 1995;177:2938-2941.
6. Sistrom WR, Stanier RY. The mechanism of formation of β-ketoadipic acid by bacteria. J Biol Chem 1954;210:821-836.
7. Avigad G, Englard S, Olsen BR, Wolfenstein-Todel C, Wiggins R. Molecular properties of cis,cis-muconate cycloisomerase from Pseudomonas putida. J Mol Biol 1974;89:651-662.
8. Vollmer MD, Fischer P, Knackmuss H-J, Schlömann M. Inability of muconate cycloisomerases to cause dehalogenation during conversion of 2-chloro-cis,cis-muconate. J Bacteriol 1994;176:4366-4375.
9. Houghton JE, Brown TM, Appel AJ, Hughes EJ, Ornston LN. Discontinuities in the evolution of Pseudomonas putida cat genes. J Bacteriol 1995;177:401-412.
10. Perkins EJ, Gordon MP, Caceres O, Lurquin PF. Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol 1990;172:2351-2359.
11. Aldrich TL, Frantz B, Gill JF, Kilbane JJ, Chakrabarty AM. Cloning and complete nucleotide sequence determination of the catB gene encoding cis,cis-muconate lactonizing enzyme. Gene 1987;52:185-195.
12. Eulberg D, Kourbatova EM, Golovleva LA, Schlömann M. Evolutionary relationship between chlorocatechol catabolic enzymes from Rhodococcus opacus 1CP and their counterparts in proteobacteria: sequence divergence and functional convergence. J Bacteriol 1998;180:1082-1094.
13. Frantz B, Chakrabarty AM. Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc Natl Acad Sci USA 1987;84:4460-4464.
14. van der Meer JR, Eggen RIL, Zehnder AJB, de Vos WM. Sequence analysis of the Pseudomonas sp strain P51 tcb gene cluster, which encodes metabolism of chlorinated catechols: evidence for specialization of catechol 1,2-dioxygenases for chlorinated substrates. J Bacteriol 1991;173:2425-2434.
15. Shanley MS, Harrison A, Parales RE, Kowalchuk G, Mitchell DJ, Ornston LN. Unusual G + C content and codon usage in catIJF, a segment of the ben-cat supraoperonic cluster in the Acinetobacter calcoaceticus chromosome. Gene 1994;138:59-65.
16. Eulberg D, Golovleva LA, Schlömann M. Characterization of catechol catabolic genes from Rhodococcus erythropolis 1CP. J Bacteriol 1997;179:370-381.
17. Goldman A, Ollis DL, Steitz TA. Crystal structure of muconate lactonizing enzyme at 3 Å resolution. J Mol Biol 1987;194:143-153.
18. Helin S, Kahn PC, Guha BL, Mallows DJ, Goldman A. The refined X-ray structure of muconate lactonizing enzyme from Pseudomonas putida prs2000 at 1.85 Å resolution. J Mol Biol 1995;254:918-941.
19. Hoier H, Schlömann M, Hammer A, et al. Crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus JMP134 (pJP4) at 3 Å resolution. Acta Crystallogr 1994;D50: 75-84.
20. Kleywegt GJ, Hoier H, Jones TA. A re-evaluation of the crystal structure of chloromuconate cycloisomerase. Acta Crystallogr 1996;D52:858-863.
21. Neidhart DJ, Kenyon GL, Gerlt JA, Petsko GA. Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous. Nature 1990;347:692-694.
22. Petsko GA, Kenyon GL, Gerlt JA, Ringe D, Kozarich JW. On the origin of enzymatic species. Trends Biochem Sci 1993;18:372-376.
23. 1H NMR "ricochet" analysis. J Am Chem Soc 1987;109:5520-5521.
24. Gerlt JA, Kenyon GL, Kozarich JW, Neidhart DJ, Petsko GA, Powers VM. Mandelate racemase and class-related enzymes. Curr Opin Struct Biol 1992;2:736-742.
25. Gerlt JA, Gassman PG. Understanding enzyme-catalyzed proton abstraction from carbon acids: details of stepwise mechanisms for β-elimination reactions. J Am Chem Soc 1992:114:5928-5934.
26. Gerlt JA, Gassman PG. Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. Biochemistry 1993;32:11943-11952.
27. Kallarakal AT, Mitra B, Kozarich JW, et al. Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant. Biochemistry 1995;34:2788-2797.
28. Landro JA, Gerlt JA, Kozarich JW, et al. The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-α-phenylglycidate. Biochemistry 1994;33:635-643.
29. Mitra B, Kallarakal AT, Kozarich JW, et al. Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317. Biochemistry 1995;34:2777-2787.
30. Solyanikova IP, Maltseva OV, Vollmer MD, Golovleva LA, Schlömann M. Characterization of muconate and chloromuconate cycloisomerase from Rhodococcus erythropolis 1CP: indications for functionally convergent evolution among bacterial cycloisomerases. J Bacteriol 1995;177:2821-2826.
31. Vollmer MD, Hoier H, Hecht H-J, Gröning J, Goldman A, Schlömann M. Substrate specificity of and product formation by muconate cycloisomerases: an analysis of wild-type enzymes and engineered variants. Appl Environ Microbiol 1998;64:3290-3299.
32. Cantor CR, Schimmel PR. Biophysical chemistry. Part II: Techniques for the study of biological structure and function. New York: WH Freeman, 1980, p 380.
33. Goldman A. The crystal structure of muconate lactonising enzyme at 3 Å resclution. Ph.D. Thesis, Yale University, 1985.
34. Goldman A, Ollis DL, Ngai K-L, Steitz TA. Crystal structure of muconate lactonizing enzyme at 6.5 Å resolution. J Mol Biol 1985;182:353-355.
35. Sato M, Yimamoto M, Imada K, Katsube Y. A high-speed data-collection system for large unit-cell crystals using an imaging plate as a detector. J Appl Crystallogr 1992;25:348-357.
36. Otwinowski Z. DENZO: an oscillation data processing program for protein crystallography. New Haven, CT: Yale University, 1993.
37. McRee DE. A visual protein crystallographic software system for X11/XView. J Mol Graphics 1992;10:44-47.
38. Brünger AT. X-PLOR version 3.1. A system for X-Ray crystallography and NMR. New Haven, CT: Yale University Press; 1992.
39. Powell MJD. Restart procedures for the conjugate gradient method. Math Program 1977;12:241-254.
40. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr 1991;A47:110-119.
41. Jones TA, Kjeldgaard MO. O - the manual. Uppsala, 1992.
42. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993;26:283-291.
43. Ngai K-L, Kallen RG. Enzymes of the β-ketoadipate pathway in Pseudomonas putida: primary and secondary kinetic and equilibrium deuterium isotope effects upon the interconversion of (+)-muconolactone to cis,cis-muconate catalyzed by cis,cis-muconate cycloisomerase. Biochemistry 1983;22:5231-5236.
44. Ramachandran GN, Ramakhrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J Mol Biol 1963;7: 955-959.
45. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein structure coordinates. Proteins Struct Funct Genet 1992;12:345-364.
46. Luzzati V. Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Crystallogr 1952;A5:802-810.
47. Ngai K-L, Ornston LN, Kallen RG. Enzymes of the β-ketoaclipate pathway in Pseudomonas putida: kinetic and magnetic resonance studies of the cis,cis-muconate cycloisomerase catalyzed reaction. Biochemistry 1983;22:5223-5230.
48. Knackmuss H-J, Hellwig M, Lackner H, Otting W. Cometabolism of 3-methylbenzoate and methylcatechols by a 3-chlorobenzoate utilizing Pseudomonas: accumulation of (+)-2,5-dihydro-4-methyland (+)-2,5-dihydro-2-methyl-5-oxo-furan-2-acetic acid. Eur J Appl Microbiol 1976-2:267-276.
49. Kenyon GL, Gerlt JA, Petsko GA, Kozarich JW. Mandelate racemace: structure-function studies of a pseudosymmetric enzyme. Acc Chem Res 1995;28:178-186.
50. Brünger AT. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 1992;355:472-475.
51. Arnez JG. MINIMAGE: a program for plotting electron-density maps. J Appl Crystallogr 1994;27:649-653.
52. Kraulis PJ. MolScript: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.
53. Nicholls A, Sharp KA, Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct Funct Genet 1991;11:281-296.
54. Hasson MS, Schlichting I, Moulai J, et al. Evolution of an enzyme active site: The structure of a new crystal form of muconate lactonizing enzyme compare with mandelate racemase and enolase. Proc Natl Acad Sci USA 1998;95:10396-10401.