1tht › Citations

Structure of a myristoyl-ACP-specific thioesterase from Vibrio harveyi.

Lawson DM, Derewenda U, Serre L, Ferri S, Szittner R, Wei Y, Meighen EA, Derewenda ZS
Biochemistry 33 9382-8 (1994)
Cited: 56 times
EuropePMC logo PMID: 8068614

Abstract

The crystal structure of a myristoyl acyl carrier protein specific thioesterase (C14ACP-TE) from a bioluminescent bacterium, Vibrio harveyi, was solved by multiple isomorphous replacement methods and refined to an R factor of 22% at 2.1-A resolution. This is the first elucidation of a three-dimensional structure of a thioesterase. The overall tertiary architecture of the enzyme resembles closely the consensus fold of the rapidly expanding superfamily of alpha/beta hydrolases, although there is no detectable homology with any of its members at the amino acid sequence level. Particularly striking similarity exists between the C14ACP-TE structure and that of haloalkane dehalogenase from Xanthobacter autotrophicus. Contrary to the conclusions of earlier studies [Ferri, S. R., & Meighen, E. A. (1991) J. Biol. Chem. 266, 12852-12857] which implicated Ser77 in catalysis, the crystal structure of C14ACP-TE reveals a lipase-like catalytic triad made up of Ser114, His241, and Asp211. Surprisingly, the gamma-turn with Ser114 in a strained secondary conformation (phi = 53 degrees, psi = -127 degrees), characteristic of the so-called nucleophilic elbow, does not conform to the frequently invoked lipase/esterase consensus sequence (Gly-X-Ser-X-Gly), as the positions of both glycines are occupied by larger amino acids. Site-directed mutagenesis and radioactive labeling support the catalytic function of Ser114. Crystallographic analysis of the Ser77-->Gly mutant at 2.5-A resolution revealed no structural changes; in both cases the loop containing the residue in position 77 is disordered.(ABSTRACT TRUNCATED AT 250 WORDS)

Reviews - 1tht mentioned but not cited (2)

  1. Thioesterases: a new perspective based on their primary and tertiary structures. Cantu DC, Chen Y, Reilly PJ. Protein Sci 19 1281-1295 (2010)
  2. Molecular Mechanisms of Bacterial Bioluminescence. Brodl E, Winkler A, Macheroux P. Comput Struct Biotechnol J 16 551-564 (2018)

Articles - 1tht mentioned but not cited (4)

  1. Role of key salt bridges in thermostability of G. thermodenitrificans EstGtA2: distinctive patterns within the new bacterial lipolytic enzyme subfamily XIII.2 [corrected]. Charbonneau DM, Beauregard M. PLoS One 8 e76675 (2013)
  2. Thioesterase enzyme families: Functions, structures, and mechanisms. Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Protein Sci 31 652-676 (2022)
  3. Cryo-EM structure of the fatty acid reductase LuxC-LuxE complex provides insights into bacterial bioluminescence. Tian Q, Wu J, Xu H, Hu Z, Huo Y, Wang L. J Biol Chem 298 102006 (2022)
  4. Protein Model and Function Analysis in Quorum-Sensing Pathway of Vibrio qinghaiensis sp.-Q67. Wang ZJ, Chen F, Xu YQ, Huang P, Liu SS. Biology (Basel) 10 638 (2021)


Reviews citing this publication (5)

  1. Bacterial biocatalysts: molecular biology, three-dimensional structures, and biotechnological applications of lipases. Jaeger KE, Dijkstra BW, Reetz MT. Annu Rev Microbiol 53 315-351 (1999)
  2. Polyester synthases: natural catalysts for plastics. Rehm BH. Biochem J 376 15-33 (2003)
  3. The ubiquitous carrier protein--a window to metabolite biosynthesis. Mercer AC, Burkart MD. Nat Prod Rep 24 750-773 (2007)
  4. Sinapoyltransferases in the light of molecular evolution. Stehle F, Brandt W, Stubbs MT, Milkowski C, Strack D. Phytochemistry 70 1652-1662 (2009)
  5. Biosynthesis of fatty acids and related metabolites. Rawlings BJ. Nat Prod Rep 15 275-308 (1998)

Articles citing this publication (45)

  1. Peptide cyclization catalysed by the thioesterase domain of tyrocidine synthetase. Trauger JW, Kohli RM, Mootz HD, Marahiel MA, Walsh CT. Nature 407 215-218 (2000)
  2. Palmitoyl-acyl carrier protein (ACP) thioesterase and the evolutionary origin of plant acyl-ACP thioesterases. Jones A, Davies HM, Voelker TA. Plant Cell 7 359-371 (1995)
  3. Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Bruner SD, Weber T, Kohli RM, Schwarzer D, Marahiel MA, Walsh CT, Stubbs MT. Structure 10 301-310 (2002)
  4. Anatomy of lipase binding sites: the scissile fatty acid binding site. Pleiss J, Fischer M, Schmid RD. Chem Phys Lipids 93 67-80 (1998)
  5. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Tsai SC, Miercke LJ, Krucinski J, Gokhale R, Chen JC, Foster PG, Cane DE, Khosla C, Stroud RM. Proc Natl Acad Sci U S A 98 14808-14813 (2001)
  6. Identification of Claisen cyclase domain in fungal polyketide synthase WA, a naphthopyrone synthase of Aspergillus nidulans. Fujii I, Watanabe A, Sankawa U, Ebizuka Y. Chem Biol 8 189-197 (2001)
  7. N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. Maurer-Stroh S, Eisenhaber B, Eisenhaber F. J Mol Biol 317 523-540 (2002)
  8. The crystal structure of a triacylglycerol lipase from Pseudomonas cepacia reveals a highly open conformation in the absence of a bound inhibitor. Kim KK, Song HK, Shin DH, Hwang KY, Suh SW. Structure 5 173-185 (1997)
  9. Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization. Shaw-Reid CA, Kelleher NL, Losey HC, Gehring AM, Berg C, Walsh CT. Chem Biol 6 385-400 (1999)
  10. The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis. Bellizzi JJ, Widom J, Kemp C, Lu JY, Das AK, Hofmann SL, Clardy J. Proc Natl Acad Sci U S A 97 4573-4578 (2000)
  11. Mechanism and specificity of the terminal thioesterase domain from the erythromycin polyketide synthase. Gokhale RS, Hunziker D, Cane DE, Khosla C. Chem Biol 6 117-125 (1999)
  12. A novel variant of the catalytic triad in the Streptomyces scabies esterase. Wei Y, Schottel JL, Derewenda U, Swenson L, Patkar S, Derewenda ZS. Nat Struct Biol 2 218-223 (1995)
  13. How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes. Rauwerdink A, Kazlauskas RJ. ACS Catal 5 6153-6176 (2015)
  14. Molecular cloning and expression of palmitoyl-protein thioesterase 2 (PPT2), a homolog of lysosomal palmitoyl-protein thioesterase with a distinct substrate specificity. Soyombo AA, Hofmann SL. J Biol Chem 272 27456-27463 (1997)
  15. Crystal structure of the human acyl protein thioesterase I from a single X-ray data set to 1.5 A. Devedjiev Y, Dauter Z, Kuznetsov SR, Jones TL, Derewenda ZS. Structure 8 1137-1146 (2000)
  16. Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity. Kim KK, Song HK, Shin DH, Hwang KY, Choe S, Yoo OJ, Suh SW. Structure 5 1571-1584 (1997)
  17. Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering. Yuan L, Voelker TA, Hawkins DJ. Proc Natl Acad Sci U S A 92 10639-10643 (1995)
  18. Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9 A resolution. Wei Y, Swenson L, Castro C, Derewenda U, Minor W, Arai H, Aoki J, Inoue K, Servin-Gonzalez L, Derewenda ZS. Structure 6 511-519 (1998)
  19. Structural and mechanistic insights into polyketide macrolactonization from polyketide-based affinity labels. Giraldes JW, Akey DL, Kittendorf JD, Sherman DH, Smith JL, Fecik RA. Nat Chem Biol 2 531-536 (2006)
  20. Biosynthesis of lipoteichoic acid in Lactobacillus rhamnosus: role of DltD in D-alanylation. Debabov DV, Kiriukhin MY, Neuhaus FC. J Bacteriol 182 2855-2864 (2000)
  21. Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis. Wagner UG, Hasslacher M, Griengl H, Schwab H, Kratky C. Structure 4 811-822 (1996)
  22. Evidence that a novel thioesterase is responsible for polyketide chain release during biosynthesis of the polyether ionophore monensin. Harvey BM, Hong H, Jones MA, Hughes-Thomas ZA, Goss RM, Heathcote ML, Bolanos-Garcia VM, Kroutil W, Staunton J, Leadlay PF, Spencer JB. Chembiochem 7 1435-1442 (2006)
  23. Methyl phenylalkanoates as substrates to probe the active sites of esterases. Kroon PA, Faulds CB, Brézillon C, Williamson G. Eur J Biochem 248 245-251 (1997)
  24. Streptogramin B biosynthesis in Streptomyces pristinaespiralis and Streptomyces virginiae: molecular characterization of the last structural peptide synthetase gene. de Crécy-Lagard V, Saurin W, Thibaut D, Gil P, Naudin L, Crouzet J, Blanc V. Antimicrob Agents Chemother 41 1904-1909 (1997)
  25. The thioesterase domain from a nonribosomal peptide synthetase as a cyclization catalyst for integrin binding peptides. Kohli RM, Takagi J, Walsh CT. Proc Natl Acad Sci U S A 99 1247-1252 (2002)
  26. The atomic-resolution structure of a novel bacterial esterase. Bourne PC, Isupov MN, Littlechild JA. Structure 8 143-151 (2000)
  27. Expression, purification, and characterization of the Mycobacterium tuberculosis acyl carrier protein, AcpM. Schaeffer ML, Agnihotri G, Kallender H, Brennan PJ, Lonsdale JT. Biochim Biophys Acta 1532 67-78 (2001)
  28. Different active-site loop orientation in serine hydrolases versus acyltransferases. Jiang Y, Morley KL, Schrag JD, Kazlauskas RJ. Chembiochem 12 768-776 (2011)
  29. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Zhang L, Godzik A, Skolnick J, Fetrow JS. Fold Des 3 535-548 (1998)
  30. Crystal structure of bovine duodenase, a serine protease, with dual trypsin and chymotrypsin-like specificities. Pletnev VZ, Zamolodchikova TS, Pangborn WA, Duax WL. Proteins 41 8-16 (2000)
  31. Spinach holo-acyl carrier protein: overproduction and phosphopantetheinylation in Escherichia coli BL21(DE3), in vitro acylation, and enzymatic desaturation of histidine-tagged isoform I. Broadwater JA, Fox BG. Protein Expr Purif 15 314-326 (1999)
  32. Functional analysis of putative beta-ketoacyl:acyl carrier protein synthase and acyltransferase active site motifs in a type II polyketide synthase of Streptomyces glaucescens. Meurer G, Hutchinson CR. J Bacteriol 177 477-481 (1995)
  33. The structural basis of the Tle4-Tli4 complex reveals the self-protection mechanism of H2-T6SS in Pseudomonas aeruginosa. Lu D, Zheng Y, Liao N, Wei L, Xu B, Liu X, Liu J. Acta Crystallogr D Biol Crystallogr 70 3233-3243 (2014)
  34. Chemical and posttranslational modification of Escherichia coli acyl carrier protein for preparation of dansyl-acyl carrier proteins. Haas JA, Frederick MA, Fox BG. Protein Expr Purif 20 274-284 (2000)
  35. Hydroxynitrile lyase from Hevea brasiliensis: molecular characterization and mechanism of enzyme catalysis. Hasslacher M, Kratky C, Griengl H, Schwab H, Kohlwein SD. Proteins 27 438-449 (1997)
  36. Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution. Janda I, Devedjiev Y, Cooper D, Chruszcz M, Derewenda U, Gabrys A, Minor W, Joachimiak A, Derewenda ZS. Acta Crystallogr D Biol Crystallogr 60 1101-1107 (2004)
  37. New Insights Into Sunflower (Helianthus annuus L.) FatA and FatB Thioesterases, Their Regulation, Structure and Distribution. Aznar-Moreno JA, Sánchez R, Gidda SK, Martínez-Force E, Moreno-Pérez AJ, Venegas Calerón M, Garcés R, Mullen RT, Salas JJ. Front Plant Sci 9 1496 (2018)
  38. Enzymes for peptide cyclization. Bordusa F. Chembiochem 2 405-409 (2001)
  39. Crystallization and preliminary diffraction studies of thioesterase II from rat mammary gland. Buchbinder JL, Witkowski A, Smith S, Fletterick RJ. Proteins 22 73-75 (1995)
  40. Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies. Zornetzer GA, White RD, Markley JL, Fox BG. Protein Expr Purif 46 446-455 (2006)
  41. Hyperactivity and interactions of a chimeric myristoryl-ACP thioesterase from the lux system of luminescent bacteria. Li J, Szittner R, Meighen EA. Biochim Biophys Acta 1481 237-246 (2000)
  42. Substrate spectrum of tyrocidine thioesterase probed with randomized peptide N-acetylcysteamine thioesters. Xie G, Uttamchandani M, Chen GY, Bu X, Lin SS, Wong KM, Yan W, Yao SQ, Guo Z. Bioorg Med Chem Lett 12 989-992 (2002)
  43. Mutation of the nucleophilic elbow of the Lux-specific thioesterase from Vibrio harveyi. Li J, Ahvazi B, Szittner R, Meighen E. Biochem Biophys Res Commun 275 704-708 (2000)
  44. Substrate selectivity of bacterial monoacylglycerol lipase based on crystal structure. Tsurumura T, Tsuge H. J Struct Funct Genomics 15 83-89 (2014)
  45. Kinetics of hydrolysis and mutational analysis of N,N-diethyl-m-toluamide hydrolase from Pseudomonas putida DTB. Rivera-Cancel G, Sanders JM, Hay AG. FEBS J 279 1044-1053 (2012)


Quick links