Probing the domain structure and ligand-induced conformational changes by limited proteolysis of tyrocidine synthetase 1

Journal of Molecular Biology

Volumn 288, Issue 1, 1999, Pages 129-140

  Dieckmann, Ralf ^a   Pavela Vrancic, Maja ^b   Von Döhren, Hans ^a   Kleinkauf, Horst ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF SPLIT   (Croatia)

Author keywords

Conformational changes; Domain organization; Linkers; Multifunctional enzymes; Peptide synthetases

Indexed keywords

ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE DERIVATIVE; ALANINE; ARGININE; GLUTAMIC ACID; LUCIFERASE; PEPTIDE SYNTHASE; PROLINE; TYROCIDINE;

ADENYLATION; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; DELETION MUTANT; ENZYME KINETICS; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; X RAY CRYSTALLOGRAPHY;

EID: 0033597285     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2671     Document Type: Article

References (50)

1. Altmann M., von Döhren H., El-Samaraie A., Kittelberger R., Pore M. S., Kleinkauf H. Limited proteolysis: studies on the multienzyme GS2 of gramicidin S synthetase. Kleinkauf H., von Döhren H. Peptide Antibiotics - Biosynthesis and Functions. 1982;243-252 De Gruyter, Berlin.
2. Aparicio J. F., Caffrey P., Marsden A. F. A., Staunton J., Leadlay P. F. Limited proteolysis and active-site studies of the first multienzyme component of the erythromycin-producing polyketide synthase. J. Biol. Chem. 269:1994;8524-8528.
3. Argos P. An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J. Mol. Biol. 211:1990;943-958.
4. Arnone M. I., Birolo L., Giamberini M., Cubellis M. V., Nitti G., Sannia G., Marino G. Limited proteolysis as a probe of conformational changes in aspartate aminotransferase from Sulfolobus solfataricus. Eur. J. Biochem. 204:1992;1183-1189.
5. Babbitt D. J., Kenyon G. L., Martin B. M., Charest H., Slyvestre M., Scholten J. D., Chang K.-H., Liang P.-H., Dunaway-Mariano D. Ancestry of the 4-chlorobenzoate dehalogenase: analysis of amino acid sequence identities among families of acyl:adenyl ligases, enoyl-CoA hydratases/isomerases, and acyl-CoA thioesterases. Biochemistry. 31:1992;5594-5604.
6. 4A synthesis by seryl-tRNA synthetase. Structure. 3:1995;341-352.
7. Bevitt D. J., Cortes J., Haydock S. F., Leadlay P. F. 6-Deoxyerythronolide-B synthase 2 from Saccharopolyspora erythraea. Cloning of the structural gene, sequence analysis and inferred domain structure of the multifunctional enzyme. Eur. J. Biochem. 204:1992;39-49.
8. Cavarelli J., Eriani G., Rees B., Ruff M., Boeglin M., Mitschler A., Martin F., Gangloff J., Thierry J.-C., Moras D. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J. 13:1994;327-337.
9. Conti E., Franks N. P., Brick P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure. 4:1996;287-298.
10. Conti E., Stachelhaus T., Marahiel M. A., Brick P. Structural basis for the activation of phenylalanine and the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16:1997;4174-4183.
11. Cui J., Somerville R. The TyrR protein of Escherichia coli analysis by limited proteolysis of domain structure and ligand-mediated conformational changes. J. Biol. Chem. 268:1993;5040-5047.
12. De Crécy-Lagard V., Marlière P., Saurin W. Multienzymatic non-ribosomal peptide biosynthesis: identification of the functional domains catalysing peptide elongation and epimerisation. C. R. Acad. Sci. Paris, Life Sci. 318:1995;927-936.
13. Dieckmann R., von Döhren H. Structural model of acyl carrier domains in integrated biosynthetic systems forming peptides, polyketides and fatty acids based on analogy to the E. coli acyl carrier protein. Baltz R., Hegeman G., Skatrud P. Industrial Microorganisms: Genetics and Molecular Biology. 1997;79-87 Am. Soc. Microbiol, Fairfax.
14. Dieckmann R., Lee Y. O., van Liempt H., von Döhren H., Kleinkauf H. Expression of an active adenylate-forming domain of peptide synthetases corresponding to acyl-CoA-synthetases. FEBS Letters. 357:1995;212-216.
15. Dieckmann R., Pavela-Vrancic M., Pfeifer E., von Döhren H., Kleinkauf H. The adenylation domain of tyrocidine synthetase1: structural and functional role of the interdomain linker region and the (S/T)GT(T/S)GXPKG core sequence. Eur. J. Biochem. 247:1997;1074-1082.
16. Diez B., Gutierrez S., Barredo J. L., van Solingen P., van der Voort L. H., Martin J. F. The cluster of penicillin biosynthetic genes. Identification and characterization of the pcbAB gene encoding the α-aminoadipyl-cysteinyl-valine synthetase and linkage to the pcbC and penDE genes. J. Biol. Chem. 265:1990;16358-16365.
17. Fontana A., Fassina G., Vita C., Dalzoppo D., Zamai M., Zambonin M. Correlation between sites of limited proteolysis and segmental mobility in thermolysin. Biochemistry. 25:1986;1847-1851.
18. Fulda M., Heinz E., Wolter F. P. The fadD gene of Escherichia coli K12 is located close to rnd at 39.6 min of the chromosomal map and is a new member of the AMP-binding protein family. Mol. Gen. Genet. 242:1994;241-249.
19. Gocht M., Marahiel M. A. Analysis of the core sequences in the D -Phe activating domain of the multifunctional peptide synthetase tycA by site-directed mutagenesis. J. Bacteriol. 176:1994;2654-2662.
20. Green J. D. F., Perham R. N., Ullrich S. J., Appella E. Conformational studies of the interdomain linker peptides in the dihydrolipoyl acetyltransferase component of the pyruvate dehydrogenase multienzyme complex of Escherichia coli. J. Biol. Chem. 267:1992;23484-23488.
21. Hamoen L. W., Eshuis H., Jongbloed J., Venema G., Sinderen D. A small gene, designated comS, located within the coding region of the fourth amino acid activation domain ofsrfA , is required for competence development in Bacillus brevis. Mol. Microbiol. 15:1995;55-63.
22. Hubbard S. J. The structural aspects of limited proteolysis of native proteins. Biochim. Biophys. Acta. 1382:1998;191-206.
23. Kleinkauf H., Koischwitz H. Gramicidin S synthetase. Bisswanger H., Schmincke-Ott E. Multifunctional Proteins. 1980;217-233 Wiley, New York.
24. Kleinkauf H., von Döhren H. A nonribosomal system of peptide biosynthesis. Eur. J. Biochem. 236:1996;335-351.
25. 2+complex and mechanism of its pyrophosphohydrolase action. Biochemistry. 36:1997;1199-1211.
26. MacCabe A. P., van Liempt H., Palissa H., Unkles S. E., Riach M. B. R., Pfeifer E., von Döhren H., Kinghorn J. R. δ-(L -α-Aminoadipyl)- L -cysteinyl- D -valine synthetase from Aspergillus nidulans. J. Biol. Chem. 266:1991;12646-12654.
27. Marahiel M. A., Stachelhaus T., Mootz H. D. Modular peptide synthetases involved in nonribosomal peptide synthesis. Chem. Rev. 97:1997;2651-2673.
28. Negishi M., Sugimoto Y., Hayashi Y., Namba T., Honda A., Watabe A., Narumiya S., Ichikawa A. Functional interaction of prostaglandin E receptor EP3 subtype with guanine nucleotide-binding proteins, showing low-affinity ligand binding. Biochim. Biophys. Acta. 1175:1993;343-350.
29. Packman L. C., Perham R. N. Limited proteolysis and sequence analysis of the 2-oxo acid dehydrogenase complexes from Escherichia coli. Biochem. J. 242:1987;531-538.
30. Pavela-Vrancic M., van Liempt H., Pfeifer E., Freist W., von Döhren H. Nucleotide binding by multienzyme peptide synthetases. Eur. J. Biochem. 220:1994a;535-542.
31. Pavela-Vrancic M., Pfeifer E., Schröder W., von Döhren H., Kleinkauf H. Identification of the ATP binding site in tyrocidine synthetase 1 by selective modification with fluorescein 5′-isothiocyanate. J. Biol. Chem. 269:1994b;14962-14966.
32. Pavela-Vrancic M., Pfeifer E., van Liempt H., Schäfer H. J., von Döhren H., Kleinkauf H. ATP binding in peptide synthetases: determination of contact sites of the adenine moiety by photoaffinity labeling of tyrocidine synthetase 1 with 2-azidoadenosine triphosphate. Biochemistry. 33:1994c;6276-6283.
33. Perham R. N. Domains, motifs, and linkers in 2-oxo acid dehydrogenase multienzyme complexes: a paradigm in the design of a multifunctional protein. Biochemistry. 30:1991;8501-8511.
34. Pfeifer E., Pavela-Vrancic M., von Döhren H., Kleinkauf H. Characterization of tyrocidine synthetase 1 (TY1): requirement of posttranslational modification for peptide biosynthesis. Biochemistry. 34:1995;7450-7459.
35. Pieper R., Haese A., Schröder W., Zocher R. Arrangement of catalytic sites in the multifunctional enzyme enniatin synthetase. Eur. J. Biochem. 230:1995;119-126.
36. Radford S. E., Laue E. D., Perham R. N., Martin S. R., Appella E. Conformational flexibility and folding of synthetic peptides representing an interdomain segment of polypeptide chain in the pyruvate dehydrogenase multienzyme complex of Escherichia coli. J. Biol. Chem. 264:1989;767-775.
37. Russel G. C., Guest J. R. Sequences similarities within the family of dihydrolipoamide acyltransferases and discovery of a previously unidentified fungal enzyme. Biochim. Biophys. Acta. 1076:1991;225-232.
38. Schägger H., von Jagow G. Tricine-sodium-dodecyl-sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range of 1 to 100 kDa. Anal. Biochem. 166:1987;368-370.
39. Skarpeid H. J., Zimmer T. L., von Döhren H. On the domain construction of the multienzyme gramicidin S synthetase 2. Isolation of domains activating valine and leucine. Eur. J. Biochem. 189:1990a;517-522.
40. Skarpeid H. J., Zimmer T. L., Shen B., von Döhren H. The proline-activating activity of the multienzyme gramicidin S synthetase 2 can be recovered on a 115-kDa tryptic fragment. Eur. J. Biochem. 187:1990b;627-633.
41. Smith D. J., Earl A. J., Turner G. The multifunctional peptide synthetase performing the first step of penicillin biosynthesis in P. chrysogenum is a 421073 dalton protein similar to Bacillus brevis peptide antibiotic synthetases. EMBO J. 9:1990;2743-2750.
42. Smith S. The animal fatty acid synthase: one gene, one polypeptide, seven enzymes. FASEB J. 8:1994;1248-1259.
43. Stachelhaus T., Marahiel M. A. Modular structure of peptide synthetases revealed by dissection of the multifunctional enzyme GrsA. J. Biol. Chem. 279:1995;6163-6169.
44. Stachelhaus T., Schneider A., Marahiel M. A. Rational design of peptide antibiotics by targeted replacement of bacterial and fungal domains. Science. 269:1995;69-72.
45. Stachelhaus T., Hüser A., Marahiel M. A. Biochemical characterization of peptidyl carrier protein (PCP), the thiolation domain of multifunctional peptide synthetases. Chem. Biol. 3:1996;913-921.
46. Stachelhaus T., Mootz H. D., Bergendahl V., Marahiel M. A. Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain. J. Biol. Chem. 273:1998;22773-22781.
47. Stein T., Vater J. Amino acid activation and polymerization at modular multienzymes in nonribosomal peptide biosynthesis. Amino Acids. 10:1996;201-227.
48. von Döhren H., Keller U., Vater J., Zocher R. Multifunctional peptide synthetases. Chem. Rev. 97:1997;2675-2705.
49. Webb M., Taylor I. A., Firman K., Kneale G. G. Probing the domain structure of the type IC DNA methyltransferase M. EcoR124I by limited proteolysis. J. Mol. Biol. 250:1995;181-190.
50. Witkowski A., Rangan V. S., Randhawa Z. I., Amy C. M., Smith S. Structural organization of the multifunctional animal fatty-acid synthase. Eur. J. Biochem. 198:1991;571-579.