Identification of novel protein domains required for the expression of an active dehydratase fragment from a polyunsaturated fatty acid synthase

Protein Science

Volumn 22, Issue 7, 2013, Pages 954-963

  Oyola Robles, Delise ^a   Gay, Darren C ^b   Trujillo, Uldaeliz ^a   Sanchez Pares, John M ^a   Bermudez, Mei Ling ^a   Rivera Daz, Monica ^a   Carballeira, Nestor M ^c   Baerga Ortiz, Abel ^a  

^a UNIVERSITY OF PUERTO RICO SCHOOL OF MEDICINE   (Puerto Rico)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c UNIVERSITY OF PUERTO RICO RIO PIEDRAS   (Puerto Rico)

Author keywords

Dehydratase; Polyketide synthase; Polyunsaturated fatty acids; Udwary Merski Algorithm

Indexed keywords

3 HYDROXYBUTYRYL COENZYME A; COENZYME A; CROTOCONYL COENZYME A; HISTIDINE; HYDROLYASE; POLYUNSATURATED FATTY ACID SYNTHASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS;

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; FATTY ACID SYNTHASES; FATTY ACIDS, UNSATURATED; HYDRO-LYASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 84881290740     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2278     Document Type: Article

References (29)

1. Metz JG, Roessler P, Facciotti D, Levering C, Dittrich F, Lassner M, Valentine R, Lardizabal K, Domergue F, Yamada A, Yazawa K, Knauf V, Browse J (2001) Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes. Science 293:290.
2. Allen EE, Bartlett DH (2002) Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology 148:1903-1913.
3. Orikasa Y, Nishida T, Hase A, Watanabe K, Morita N, Okuyama H (2006) A phosphopantetheinyl transferase gene essential for biosynthesis of n23 polyunsaturated fatty acids from Moritella marina strain MP-1. FEBS Lett 580:4423-4429.
4. Okuyama H, Orikasa Y, Nishida T, Watanabe K, Morita N (2007) Bacterial genes responsible for the biosynthesis of eicosapentaenoic and docosahexaenoic acids and their heterologous expression. Appl Environ Microbiol 73:665-670.
5. Jiang H, Zirkle R, Metz JG, Braun L, Richter L, Van Lanen SG, Shen B (2008) The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis. J Am Chem Soc 130:6336-6337.
6. Bumpus SB, Magarvey NA, Kelleher NL, Walsh CT, Calderone CT (2008) Polyunsaturated fatty-acid-like trans-enoyl reductases utilized in polyketide biosynthesis. J Am Chem Soc 130:11614-11616.
7. Trujillo U, Vazquez-Rosa E, Oyola-Robles D, Stagg LJ, Vassallo DA, Vega IE, Arold ST, Baerga-Ortiz A (2013) Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration. PLoS ONE 8: e57859.
8. Rodriguez-Guilbe M, Oyola-Robles D, Schreiter ER, Baerga-Ortiz A (2013) Structure, activity and substrate selectivity of the Orf6 thioesterase from Photobacterium profundum. J Biol Chem 288:10841-10848.
9. Kass LR, Brock DJH, Bloch K (1967) b-hydroxydecanoyl thioester dehydrase. J Biol Chem 242:4418-4431.
10. Brock DJH, Kass LR, Bloch K (1967) b-hydroxydecanoyl thioester dehydrase. J Biol Chem 242:4432-4440.
11. Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL (1996) Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure 4:253-264.
12. Pasta S, Witkowski A, Joshi AK, Smith S (2007) Catalytic residues are shared between two pseudosubunits of the dehydratase domain of the animal fatty acid synthase. Chem Biol 14:1377-1385.
13. Keatinge-Clay A (2008) Crystal structure of the erythromycin polyketide synthase dehydratase. J Mol Biol 384:941-953.
14. Yadav G, Gokhale RS, Mohanty D (2003) SEARCHPKS: a program for detection and analysis of polyketide synthase domains. Nucleic Acids Res 31: 3654-3658.
15. Yadav G, Gokhale RS, Mohanty D (2003) Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J Mol Biol 328:335-363.
16. Udwary DW, Merski M, Townsend CA (2002) A method for prediction of the locations of linker regions within large multifunctional proteins, and application to a Type I polyketide synthase. J Mol Biol 323:585-598.
17. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH (2009) CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37: D205-D210.
18. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39: D225-D229.
19. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protocols 4:363-371.
20. Valenzano CR, You Y, Garg A, Keatinge-Clay A, Khosla C, Cane DE (2010) Stereospecificity of the dehydratase domain of the erythromycin polyketide synthase. J Am Chem Soc 132:14697-14699.
21. Shulse CN, Allen EE (2011) Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environ Microbiol 13: 684-695.
22. Crawford JM, Vagstad AL, Ehrlich KC, Udwary DW, Townsend CA (2008) Acyl carrier proteinphosphopantetheinyltransferase partnerships in fungal fatty acid synthases. ChemBioChem 9:1559-1563.
23. Schroeckh V, Scherlach K, Nutzmann H, Shelest E, Schmidt-Heck W, Schuemann J, Martin K, Hertweck C, Brakhage AA (2009) Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. Proc Nat Acad Sci USA 106: 14558-14563.
24. Akey DL, Razelun JR, Tehranisa J, Sherman DH, Gerwick WH, Smith JL (2010) Crystal structures of dehydratase domains from the curacin polyketide biosynthetic pathway. Structure 18:94-105.
25. Maier T, Leibundgut M, Ban N (2008) The crystal structure of a mammalian fatty acid synthase. Science 321:1315-1322.
26. Witkowski A, Joshi AK, Smith S (2004) Characterization of the B-carbon processing reactions of the mammalian cytosolic fatty acid synthase: role of the central core. Biochemistry 43:10458-10466.
27. Neises B, Steglich W (1978) Simple method for the esterification of carboxylic acids. Angew Chem Intl Ed 17:522-524.
28. Zheng J, Gay DC, Demeler B, White MA, Keatinge-Clay AT (2012) Divergence of multimodular polyketide synthases revealed by a didomain structure. Nat Chem Biol 8:615-621.
29. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.