Divergence of substrate specificity and function in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB

Biochemistry

Volumn 53, Issue 29, 2014, Pages 4775-4787

  Latham, John A ^a   Chen, Danqi ^a   Allen, Karen N ^b   Dunaway Mariano, Debra ^a  

^a UNIVERSITY OF NEW MEXICO   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGICAL SYSTEMS; BIOSYNTHESIS; ESCHERICHIA COLI;

BIOINFORMATIC ANALYSIS; BIOLOGICAL FUNCTIONS; BIOSYNTHETIC PATHWAY; ELECTRON ACCEPTOR; PHYSIOLOGICAL SUBSTRATE; SEQUENCE IDENTITY; SUBSTRATE ACTIVITY SCREENING; SUBSTRATE SPECIFICITY;

SUBSTRATES;

ACYL COENZYME A; BACTERIAL PROTEIN; COENZYME A; ENTEROCHELIN; MENAQUINONE; THIOL ESTER HYDROLASE; UNCLASSIFIED DRUG; YBDB PROTEIN; YDII PROTEIN; 1,4-DIHYDROXY-2-NAPHTHOYL-COENZYME A THIOESTERASE, E COLI; ENTH PROTEIN, E COLI; ESCHERICHIA COLI PROTEIN; FARNOQUINONE;

AMINO ACID SEQUENCE; ANAEROBIC GROWTH; ARTICLE; BACTERIAL GROWTH; BIOINFORMATICS; BIOLOGICAL FUNCTIONS; CATALYST; CONTROLLED STUDY; ENZYME SPECIFICITY; ESCHERICHIA COLI; EVOLUTION; METABOLITE; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN HYDROLYSIS; PROTEIN SYNTHESIS; WILD TYPE; BIOCATALYSIS; BIOLOGY; CHEMISTRY; ENZYMOLOGY; GENE INACTIVATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HYDROLYSIS; KINETICS; METABOLISM; PH; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN FOLDING; SITE DIRECTED MUTAGENESIS;

BIOCATALYSIS; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE KNOCKOUT TECHNIQUES; HYDROGEN-ION CONCENTRATION; HYDROLYSIS; KINETICS; MUTAGENESIS, SITE-DIRECTED; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN FOLDING; SUBSTRATE SPECIFICITY; THIOLESTER HYDROLASES; VITAMIN K 2;

EID: 84905020126     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi500333m     Document Type: Article

References (36)

1. Guo, Z.-F., Sun, Y., Zheng, S., and Guo, Z. (2009) Preferential hydrolysis of aberrant intermediates by the type II thioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues Biochemistry 48, 1712-1722
2. Wu, R., Latham, J. A., Chen, D., Farelli, J. D., Zhao, H., Matthews, K., Allen, K. N., and Dunaway-Mariano, D. (2014) Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB Biochemistry 10.1021/bi500334v
3. Zhuang, Z, Song, F, Takami, H, and Dunaway-Mariano, D. (2004) The BH1999 protein of Bacillus halodurans C-125 is gentisyl-coenzyme A thioesterase J. Bacteriol. 186, 393-399
4. Widhalm, J. R., van Oostende, C., Furt, F., and Basset, G. J. (2009) A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1 Proc. Natl. Acad. Sci. U.S.A. 106, 5599-5603
5. Scholten, J. D., Chang, K. H., Babbitt, P. C., Charest, H., Sylvestre, M., and Dunaway-Mariano, D. (1991) Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic Science 253, 182-185
6. Leduc, D., Battesti, A., and Bouveret, E. (2007) The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB J. Bacteriol. 189, 7112-7126
7. Song, F., Zhuang, Z., Finci, L., Dunaway-Mariano, D., Kniewel, R., Buglino, J. A., Solorzano, V., Wu, J., and Lima, C. D. (2006) Structure, function, and mechanism of the phenylacetate pathway hot dog-fold thioesterase PaaI J. Biol. Chem. 281, 11028-11038
8. Weeks, A. M and Chang, M. C. (2012) Catalytic control of enzymatic fluorine specificity Proc. Natl. Acad. Sci. U.S.A. 109, 19667-19672
9. Hunt, M..C, Siponen, M. I., and Alexson, S. E. (2012) The emerging role of acyl-CoA thioesterases and acyltransferases in regulating peroxisomal lipid metabolism Biochim. Biophys. Acta 1822, 1397-1410
10. Cohen, D. E. (2013) New Players on the Metabolic Stage: How Do You Like Them Acots? Adipocyte 2, 3-6
11. Dillon, S. C. and Bateman, A. (2004) The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases BMC Bioinf. 5, 109
12. Ollis, D. L., Cheah, E., Cyglerl, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schragl, J., Sussman, J. L., and Goldmans, A. (1992) The α/β hydrolase fold Protein Eng. 5, 197-211
13. Benning, M. M., Wesenberg, G., Liu, R., Taylor, K. L., Dunaway-Mariano, D., and Holden, H. M. (1998) The three-dimensional structure of 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3 J. Biol. Chem. 273, 33572-33579
14. Cao, J., Xu, H., Zhao, H., Gong, W., and Dunaway-Mariano, D. (2009) The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis Biochemistry 48, 1293-1304
15. Smotrys, J. E. and Linder, M. E. (2004) Palmitoylation of intracellular signaling proteins: regulation and function Annu. Rev. Biochem. 73, 559-587
16. Khersonsky, O. and Tawfik, D. S. (2010) Enzyme promiscuity: a mechanistic and evolutionary perspective Annu. Rev. Biochem. 79, 471-505
17. Chen, D., Wu, R., Bryan, T. L., and Dunaway-Mariano, D. (2009) In vitro kinetic analysis of substrate specificity in enterobactin biosynthetic lower pathway enzymes provides insight into the biochemical function of the hot dog-fold thioesterase EntH Biochemistry 48, 511-513
18. Chen, M., Ma, X., Chen, X., Jiang, M., Song, H., and Guo, Z. (2013) Identification of a hotdog fold thioesterase involved in the biosynthesis of menaquinone in Escherichia coli J. Bacteriol. 195, 2768-2775
19. Wang, M., Song, F, Wu, R., Allen, K. N., Mariano, P. S., and Dunaway-Mariano, D. (2013) Co-evolution of HAD phosphatase and hotdog-fold thioesterase domain function in the menaquinone-pathway fusion proteins BF1314 and PG1653 FEBS Lett. 587, 2851-2859
20. Latham, J. A. (2012) Structure to function: case studies of hotdog-fold superfamily thioesterases from Escherichia coli. PhD Thesis, University of New Mexico, pp 2-96.
21. Luo, L., Taylor, K. L, Xiang, H., Wei, Y., Zhang, W., and Dunaway-Mariano., D. (2001) Role of active site binding interactions in 4-chlorobenzoyl-coenzyme A dehalogenase catalysis Biochemistry 40, 15684-15692
22. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. a, Tomita, M., Wanner, B. L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection Mol. Syst. Biol. 10.1038/msb4100049
23. Cronan, J. E. and Klages, A. L. (1981) Chemical synthesis of acyl thioesters of acyl carrier protein with native structure Biochemistry Proc. Natl. Acad. Sci. U.S.A. 78, 5440-5444
24. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding Anal. Biochem. 72, 248-254
25. Papadopoulos, J. S. and Agarwala, R. (2007) COBALT: constraint-based alignment tool for multiple protein sequences Bioinformatics 23, 1073-1079
26. Gouet, P., Robert, X., and Courcelle, E. (2003) ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins Nucleic Acids Res. 31, 3320-3323
27. 13C-NMR spectral studies of dehalogenase complexes of benzoyl-CoA adducts Biochemistry 34, 13881-13888
28. De Lay, N. R. and Cronan, J. E. (2007) In vivo functional analyses of the type II acyl carrier proteins of fatty acid biosynthesis J. Biol. Chem. 282, 20319-20328
29. Gehring, A. M., Mori, I., and Walsh, C. T. (1998) Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF Biochemistry 37, 2648-2659
30. Guest, J. R. (1979) Anaerobic growth of Escherichia coli K12 with fumarate as terminal electron acceptor: Genetic studies with menaquinone and fluoroacetate-resistant mutants J. Gen. Microbiol. 115, 259-271
31. Sangurdekar, D. P., Srienc, F., and Khodursky, A. B. (2006) A classification based framework for quantitative description of large-scale microarray data Genome Biol. 7, R32
32. Sandy, M. and Butler, A. (2011) Chrysobactin siderophores produced by Dickeya chrysanthemi EC16 J. Nat. Prod. 74, 1207-1212
33. Outten, F. W., Djaman, O., and Storz, G. (2004) A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli Mol. Microbiol. 52, 861-872
34. Taylor, J. S. and Raes, J. (2004) Duplication and divergence: The evolution of new genes and old ideas Annu. Rev. Genetics 38, 615-643
35. Zhang, J. (2003) Evolution by gene duplication: An update Trends Ecol. Evol. 18, 282-298
36. Brickman, T. J., Ozenberger, B. A., and McIntosh, M. A. (1990) Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli J. Mol. Biol. 212, 669-682