Nonribosomal peptide synthetases: Structures and dynamics

Current Opinion in Structural Biology

Volumn 20, Issue 2, 2010, Pages 234-240

  Strieker, Matthias ^a   Tanović, Alan ^a   Marahiel, Mohamed A ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PEPTIDYL CARRIER PROTEIN; SURFACTIN; THIOL ESTER HYDROLASE;

ADENYLATION; BIOCATALYST; CHEMICAL REACTION KINETICS; COVALENT BOND; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; NONRIBOSOMAL PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN SECRETION; PROTEIN STRUCTURE; REVIEW; STEREOSPECIFICITY;

ANIMALS; CATALYTIC DOMAIN; HUMANS; MODELS, BIOLOGICAL; PEPTIDE BIOSYNTHESIS, NUCLEIC ACID-INDEPENDENT; PEPTIDE SYNTHASES; PEPTIDES; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY;

EID: 77951294519     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.01.009     Document Type: Review

References (46)

1. Walsh C.T. The chemical versatility of natural-product assembly lines. Acc Chem Res 2008, 41:4-10.
2. Finking R., Marahiel M.A. Biosynthesis of nonribosomal peptides 1. Annu Rev Microbiol 2004, 58:453-488.
3. Caboche S., Pupin M., Leclere V., Fontaine A., Jacques P., Kucherov G. NORINE: a database of nonribosomal peptides. Nucleic Acids Res 2008, 36:D326-331.
4. Fischbach M.A., Walsh C.T. Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 2006, 106:3468-3496.
5. Kopp F., Marahiel M.A. Macrocyclization strategies in polyketide and nonribosomal peptide biosynthesis. Nat Prod Rep 2007, 24:735-749.
6. Challis G.L., Naismith J.H. Structural aspects of non-ribosomal peptide biosynthesis. Curr Opin Struct Biol 2004, 14:748-756.
7. Lambalot R.H., Gehring A.M., Flugel R.S., Zuber P., LaCelle M., Marahiel M.A., Reid R., Khosla C., Walsh C.T. A new enzyme superfamily-the phosphopantetheinyl transferases. Chem Biol 1996, 3:923-936.
8. Reuter K., Mofid M.R., Marahiel M.A., Ficner R. Crystal structure of the surfactin synthetase-activating enzyme sfp: a prototype of the 4′-phosphopantetheinyl transferase superfamily. EMBO J 1999, 18:6823-6831.
9. Koglin A., Mofid M.R., Lohr F., Schafer B., Rogov V.V., Blum M.M., Mittag T., Marahiel M.A., Bernhard F., Dotsch V. Conformational switches modulate protein interactions in peptide antibiotic synthetases. Science 2006, 312:273-276.
10. Vallari D.S., Jackowski S., Rock C.O. Regulation of pantothenate kinase by coenzyme A and its thioesters. J Biol Chem 1987, 262:2468-2471.
11. Schwarzer D., Mootz H.D., Linne U., Marahiel M.A. Regeneration of misprimed nonribosomal peptide synthetases by type II thioesterases. Proc Natl Acad Sci U S A 2002, 99:14083-14088.
12. Koglin A., Lohr F., Bernhard F., Rogov V.V., Frueh D.P., Strieter E.R., Mofid M.R., Guntert P., Wagner G., Walsh C.T., et al. Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 2008, 454:907-911.
13. Stachelhaus T., Mootz H.D., Marahiel M.A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 1999, 6:493-505.
14. Conti E., Stachelhaus T., Marahiel M.A., Brick P. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J 1997, 16:4174-4183.
15. Rausch C., Weber T., Kohlbacher O., Wohlleben W., Huson D.H. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res 2005, 33:5799-5808.
16. Weber T., Rausch C., Lopez P., Hoof I., Gaykova V., Huson D.H., Wohlleben W. CLUSEAN: a computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters. J Biotechnol 2009, 140:13-17.
17. Jenke-Kodama H., Dittmann E. Bioinformatic perspectives on NRPS/PKS megasynthases: advances and challenges. Nat Prod Rep 2009, 26:874-883.
18. Li M.H., Ung P.M., Zajkowski J., Garneau-Tsodikova S., Sherman D.H. Automated genome mining for natural products. BMC Bioinformatics 2009, 10:185.
19. Gulick A.M. Conformational dynamics in the acyl-CoA synthetases, adenylation domains of non-ribosomal peptide synthetases, and firefly luciferase. ACS Chem Biol 2009, 4:811-827.
20. Yonus H., Neumann P., Zimmermann S., May J.J., Marahiel M.A., Stubbs M.T. Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains. J Biol Chem 2008, 283:32484-32491.
21. Conti E., Franks N.P., Brick P. Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 1996, 4:287-298.
22. May J.J., Kessler N., Marahiel M.A., Stubbs M.T. Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Proc Natl Acad Sci U S A 2002, 99:12120-12125.
23. Stevens B.W., Lilien R.H., Georgiev I., Donald B.R., Anderson A.C. Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity. Biochemistry 2006, 45:15495-15504.
24. Samel S.A., Schoenafinger G., Knappe T.A., Marahiel M.A., Essen L.O. Structural and functional insights into a peptide bond-forming bidomain from a nonribosomal peptide synthetase. Structure 2007, 15:781-792.
25. Mootz H.D., Marahiel M.A. The tyrocidine biosynthesis operon of Bacillus brevis: complete nucleotide sequence and biochemical characterization of functional internal adenylation domains. J Bacteriol 1997, 179:6843-6850.
26. Keating T.A., Marshall C.G., Walsh C.T., Keating A.E. The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains. Nat Struct Biol 2002, 9:522-526.
27. Leslie A.G. Refined crystal structure of type III chloramphenicol acetyltransferase at 1.75A resolution. J Mol Biol 1990, 213:167-186.
28. Frueh D.P., Arthanari H., Koglin A., Vosburg D.A., Bennett A.E., Walsh C.T., Wagner G. Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature 2008, 454:903-906.
29. Rusnak F., Sakaitani M., Drueckhammer D., Reichert J., Walsh C.T. Biosynthesis of the Escherichia coli siderophore enterobactin: sequence of the entF gene, expression and purification of EntF, and analysis of covalent phosphopantetheine. Biochemistry 1991, 30:2916-2927.
30. Baltz R.H. Biosynthesis and genetic engineering of lipopeptide antibiotics related to daptomycin. Curr Top Med Chem 2008, 8:618-638.
31. Baltz R.H. Molecular engineering approaches to peptide, polyketide and other antibiotics. Nat Biotechnol 2006, 24:1533-1540.
32. Tanovic A., Samel S.A., Essen L.O., Marahiel M.A. Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 2008, 321:659-663.
33. Marahiel M.A., Essen L.O. Chapter 13. Nonribosomal peptide synthetases mechanistic and structural aspects of essential domains. Methods Enzymol 2009, 458:337-351.
34. Koglin A., Walsh C.T. Structural insights into nonribosomal peptide enzymatic assembly lines. Nat Prod Rep 2009, 26:987-1000.
35. Maier T., Leibundgut M., Ban N. The crystal structure of a mammalian fatty acid synthase. Science 2008, 321:1315-1322.
36. Jenni S., Leibundgut M., Boehringer D., Frick C., Mikolasek B., Ban N. Structure of fungal fatty acid synthase and implications for iterative substrate shuttling. Science 2007, 316:254-261.
37. Tang Y., Kim C.Y., Mathews I.I., Cane D.E., Khosla C. The 2.7-Angstrom crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc Natl Acad Sci U S A 2006, 103:11124-11129.
38. Crawford J.M., Korman T.P., Labonte J.W., Vagstad A.L., Hill E.A., Kamari-Bidkorpeh O., Tsai S.C., Townsend C.A. Structural basis for biosynthetic programming of fungal aromatic polyketide cyclization. Nature 2009, 461:1139-1143.
39. Doekel S., Gal M., Gu J.Q., Chu M., Baltz R.H., Brian P. Non-ribosomal peptide synthetase module fusions to produce derivatives of daptomycin in Streptomyces roseosporus. Microbiology 2008, 154:2872-2880.
40. Liu Y., Bruner S.D. Rational manipulation of carrier-domain geometry in nonribosomal peptide synthetases. Chembiochem 2007, 8:617-621.
41. Strieker M., Nolan E.M., Walsh C.T., Marahiel M.A. Stereospecific synthesis of threo- and erythro-beta-hydroxyglutamic acid during kutzneride biosynthesis. J Am Chem Soc 2009, 131:13523-13530.
42. Hur G.H., Meier J.L., Baskin J., Codelli J.A., Bertozzi C.R., Marahiel M.A., Burkart M.D. Crosslinking studies of protein-protein interactions in nonribosomal peptide biosynthesis. Chem Biol 2009, 16:372-381.
43. Kainosho M., Torizawa T., Iwashita Y., Terauchi T., Mei Ono A., Guntert P. Optimal isotope labelling for NMR protein structure determinations. Nature 2006, 440:52-57.
44. Neylon C. Small angle neutron and X-ray scattering in structural biology: recent examples from the literature. Eur Biophys J 2008, 37:531-541.
45. Weber T., Baumgartner R., Renner C., Marahiel M.A., Holak T.A. Solution structure of PCP, a prototype for the peptidyl carrier domains of modular peptide synthetases. Structure 2000, 8:407-418.
46. Bruner S.D., Weber T., Kohli R.M., Schwarzer D., Marahiel M.A., Walsh C.T., Stubbs M.T. Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Structure 2002, 10:301-310.