A Method for Prediction of the Locations of Linker Regions Within Large Multifunctional Proteins, and Application to a Type I Polyketide Synthase

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2002 Oct 17

PMID 12381311

Citations 51

Authors

Daniel W Udwary

Matthew Merski

Craig A Townsend

Affiliations

Soon will be listed here.

Abstract

Multifunctional proteins often appear to result from fusion of smaller proteins and in such cases typically can be separated into their ancestral components simply by cleaving the linker regions that separate the domains. Though possibly guided by sequence alignment, structural evidence, or light proteolysis, determination of the locations of linker regions remains empirical. We have developed an algorithm, named UMA, to predict the locations of linker regions in multifunctional proteins by quantification of the conservation of several properties within protein families, and the results agree well with structurally characterized proteins. This technique has been applied to a family of fungal type I iterative polyketide synthases (PKS), allowing prediction of the locations of all of the standard PKS domains, as well as two previously unidentified domains. Using these predictions, we report the cloning of the first fragment from the PKS norsolorinic acid synthase, responsible for biosynthesis of the first isolatable intermediate in aflatoxin production. The expression, light proteolysis and catalytic abilities of this acyl carrier protein-thioesterase didomain are discussed.

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References

Drennan C, Huang S, Drummond J, Matthews R, Ludwig M . How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. Science. 1994; 266(5191):1669-74. DOI: 10.1126/science.7992050. View

Cleland W . Statistical analysis of enzyme kinetic data. Methods Enzymol. 1979; 63:103-38. DOI: 10.1016/0076-6879(79)63008-2. View

Linne U, Marahiel M . Control of directionality in nonribosomal peptide synthesis: role of the condensation domain in preventing misinitiation and timing of epimerization. Biochemistry. 2000; 39(34):10439-47. DOI: 10.1021/bi000768w. View

Marahiel M, Stachelhaus T, Mootz H . Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis. Chem Rev. 2002; 97(7):2651-2674. DOI: 10.1021/cr960029e. View

Tsai S, Miercke L, Krucinski J, Gokhale R, Chen J, Foster P . Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc Natl Acad Sci U S A. 2001; 98(26):14808-13. PMC: 64940. DOI: 10.1073/pnas.011399198. View

Ollis D, Brick P, Hamlin R, Xuong N, Steitz T . Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature. 1985; 313(6005):762-6. DOI: 10.1038/313762a0. View

Mueller E, BUCK C, Palenchar P, Barnhart L, Paulson J . Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res. 1998; 26(11):2606-10. PMC: 147624. DOI: 10.1093/nar/26.11.2606. View

Rost B . Twilight zone of protein sequence alignments. Protein Eng. 1999; 12(2):85-94. DOI: 10.1093/protein/12.2.85. View

Wong H, Mattick J, WAKIL S . The architecture of the animal fatty acid synthetase. III. Isolation and characterization of beta-ketoacyl reductase. J Biol Chem. 1983; 258(24):15305-11. View

10.

Langfelder K, Jahn B, Gehringer H, Schmidt A, Wanner G, Brakhage A . Identification of a polyketide synthase gene (pksP) of Aspergillus fumigatus involved in conidial pigment biosynthesis and virulence. Med Microbiol Immunol. 1998; 187(2):79-89. DOI: 10.1007/s004300050077. View

11.

Rangan V, Joshi A, Smith S . Mapping the functional topology of the animal fatty acid synthase by mutant complementation in vitro. Biochemistry. 2001; 40(36):10792-9. DOI: 10.1021/bi015535z. View

12.

KYTE J, Doolittle R . A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982; 157(1):105-32. DOI: 10.1016/0022-2836(82)90515-0. View

13.

Chirala S, Huang W, Jayakumar A, Sakai K, WAKIL S . Animal fatty acid synthase: functional mapping and cloning and expression of the domain I constituent activities. Proc Natl Acad Sci U S A. 1997; 94(11):5588-93. PMC: 20822. DOI: 10.1073/pnas.94.11.5588. View

14.

Brown D, Yu J, Kelkar H, Fernandes M, Nesbitt T, Keller N . Twenty-five coregulated transcripts define a sterigmatocystin gene cluster in Aspergillus nidulans. Proc Natl Acad Sci U S A. 1996; 93(4):1418-22. PMC: 39953. DOI: 10.1073/pnas.93.4.1418. View

15.

Tsai H, Chang Y, Washburn R, Wheeler M, Kwon-Chung K . The developmentally regulated alb1 gene of Aspergillus fumigatus: its role in modulation of conidial morphology and virulence. J Bacteriol. 1998; 180(12):3031-8. PMC: 107801. DOI: 10.1128/JB.180.12.3031-3038.1998. View

16.

Webb E, Claas K, Downs D . Characterization of thiI, a new gene involved in thiazole biosynthesis in Salmonella typhimurium. J Bacteriol. 1997; 179(13):4399-402. PMC: 179266. DOI: 10.1128/jb.179.13.4399-4402.1997. View

17.

Walsh C . Combinatorial biosynthesis of antibiotics: challenges and opportunities. Chembiochem. 2002; 3(2-3):125-34. DOI: 10.1002/1439-7633(20020301)3:2/3<124::AID-CBIC124>3.0.CO;2-J. View

18.

Crump M, Crosby J, Dempsey C, Parkinson J, Murray M, Hopwood D . Solution structure of the actinorhodin polyketide synthase acyl carrier protein from Streptomyces coelicolor A3(2). Biochemistry. 1997; 36(20):6000-8. DOI: 10.1021/bi970006+. View

19.

Tsukamoto Y, WAKIL S . Isolation and mapping of the beta-hydroxyacyl dehydratase activity of chicken liver fatty acid synthase. J Biol Chem. 1988; 263(31):16225-9. View

20.

Morgenstern B, Frech K, Dress A, Werner T . DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics. 1998; 14(3):290-4. DOI: 10.1093/bioinformatics/14.3.290. View