Stuible HP, Kombrink E: Identification of the substrate specificity-conferring amino acid residues of 4-coumarate:coenzyme A ligase allows the rational design of mutant enzymes with new catalytic properties. J Biol Chem 2001, 276(29):26893–26897. 10.1074/jbc.M100355200
Article
CAS
PubMed
Google Scholar
Trivedi OA, Arora P, Sridharan V, Tickoo R, Mohanty D, Gokhale RS: Enzymic activation and transfer of fatty acids as acyl-adenylates in mycobacteria. Nature 2004, 428(6981):441–445. 10.1038/nature02384
Article
CAS
PubMed
Google Scholar
Arora P, Goyal A, Natarajan VT, Rajakumara E, Verma P, Gupta R, Yousuf M, Trivedi OA, Mohanty D, Tyagi A, et al.: Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis. Nat Chem Biol 2009, 5(3):166–173. 10.1038/nchembio.143
Article
CAS
PubMed
PubMed Central
Google Scholar
Korchak HM, Kane LH, Rossi MW, Corkey BE: Long chain acyl coenzyme A and signaling in neutrophils. An inhibitor of acyl coenzyme A synthetase, triacsin C, inhibits superoxide anion generation and degranulation by human neutrophils. J Biol Chem 1994, 269(48):30281–30287.
CAS
PubMed
Google Scholar
Murakami K, Ide T, Nakazawa T, Okazaki T, Mochizuki T, Kadowaki T: Fatty-acyl-CoA thioesters inhibit recruitment of steroid receptor co-activator 1 to alpha and gamma isoforms of peroxisome-proliferator-activated receptors by competing with agonists. Biochem J 2001, 353(Pt2):231–238. 10.1042/0264-6021:3530231
Article
CAS
PubMed
PubMed Central
Google Scholar
Gordon JI, Duronio RJ, Rudnick DA, Adams SP, Gokel GW: Protein N-myristoylation. J Biol Chem 1991, 266(14):8647–8650.
CAS
PubMed
Google Scholar
Li ZN, Hongo S, Sugawara K, Sugahara K, Tsuchiya E, Matsuzaki Y, Nakamura K: The sites for fatty acylation, phosphorylation and intermolecular disulphide bond formation of influenza C virus CM2 protein. J Gen Virol 2001, 82(Pt 5):1085–1093.
Article
CAS
PubMed
Google Scholar
Rubenstein JL, Fine RE, Luskey BD, Rothman JE: Purification of coated vesicles by agarose gel electrophoresis. J Cell Biol 1981, 89(2):357–361. 10.1083/jcb.89.2.357
Article
CAS
PubMed
Google Scholar
DiRusso CC, Metzger AK, Heimert TL: Regulation of transcription of genes required for fatty acid transport and unsaturated fatty acid biosynthesis in Escherichia coli by FadR. Mol Microbiol 1993, 7(2):311–322. 10.1111/j.1365-2958.1993.tb01122.x
Article
CAS
PubMed
Google Scholar
DiRusso CC, Heimert TL, Metzger AK: Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A. J Biol Chem 1992, 267(12):8685–8691.
CAS
PubMed
Google Scholar
Marahiel MA, Stachelhaus T, Mootz HD: Modular Peptide Synthetases Involved in Nonribosomal Peptide Synthesis. Chem Rev 1997, 97(7):2651–2674. 10.1021/cr960029e
Article
CAS
PubMed
Google Scholar
Hahlbrock K, Scheel D: Physiology and molecular biology of phenylpropanoid metabolism. Annu Rev Plant Physiol Plant Mol Biol 1989, 40: 347–369. 10.1146/annurev.pp.40.060189.002023
Article
CAS
Google Scholar
Ferreras JA, Ryu JS, Di Lello F, Tan DS, Quadri LE: Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis. Nat Chem Biol 2005, 1(1):29–32. 10.1038/nchembio706
Article
CAS
PubMed
Google Scholar
Contag CH, Spilman SD, Contag PR, Oshiro M, Eames B, Dennery P, Stevenson DK, Benaron DA: Visualizing gene expression in living mammals using a bioluminescent reporter. Photochem Photobiol 1997, 66(4):523–531. 10.1111/j.1751-1097.1997.tb03184.x
Article
CAS
PubMed
Google Scholar
Kricka LJ: Chemiluminescence and bioluminescence. Anal Chem 1995, 67(12):499R-502R. 10.1021/ac00108a035
Article
CAS
PubMed
Google Scholar
Kricka LJ: Application of bioluminescence and chemiluminescence in biomedical sciences. Methods Enzymol 2000, 305: 333–345. full_text
Article
CAS
PubMed
Google Scholar
Fulda M, Heinz E, Wolter FP: The fadD gene of Escherichia coli K12 is located close to rnd at 39.6 min of the chromosomal map and is a new member of the AMP-binding protein family. Mol Gen Genet 1994, 242(3):241–249. 10.1007/BF00280412
Article
CAS
PubMed
Google Scholar
Conti E, Stachelhaus T, Marahiel MA, Brick P: Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. Embo J 1997, 16(14):4174–4183. 10.1093/emboj/16.14.4174
Article
CAS
PubMed
PubMed Central
Google Scholar
May JJ, Kessler N, Marahiel MA, Stubbs MT: Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Proc Natl Acad Sci USA 2002, 99(19):12120–12125. 10.1073/pnas.182156699
Article
CAS
PubMed
PubMed Central
Google Scholar
Conti E, Franks NP, Brick P: Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes. Structure 1996, 4(3):287–298. 10.1016/S0969-2126(96)00033-0
Article
CAS
PubMed
Google Scholar
Franks NP, Jenkins A, Conti E, Lieb WR, Brick P: Structural basis for the inhibition of firefly luciferase by a general anesthetic. Biophys J 1998, 75(5):2205–2211. 10.1016/S0006-3495(98)77664-7
Article
CAS
PubMed
PubMed Central
Google Scholar
Gulick AM, Starai VJ, Horswill AR, Homick KM, Escalante-Semerena JC: The 1.75 A crystal structure of acetyl-CoA synthetase bound to adenosine-5'-propylphosphate and coenzyme A. Biochemistry 2003, 42(10):2866–2873. 10.1021/bi0271603
Article
CAS
PubMed
Google Scholar
Jogl G, Tong L: Crystal structure of yeast acetyl-coenzyme A synthetase in complex with AMP. Biochemistry 2004, 43(6):1425–1431. 10.1021/bi035911a
Article
CAS
PubMed
Google Scholar
Hisanaga Y, Ago H, Nakagawa N, Hamada K, Ida K, Yamamoto M, Hori T, Arii Y, Sugahara M, Kuramitsu S: Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J Biol Chem 2004, 279(30):31717–31726. 10.1074/jbc.M400100200
Article
CAS
PubMed
Google Scholar
Gulick AM, Lu X, Dunaway-Mariano D: Crystal structure of 4-chlorobenzoate:CoA ligase/synthetase in the unliganded and aryl substrate-bound states. Biochemistry 2004, 43(27):8670–8679. 10.1021/bi049384m
Article
CAS
PubMed
Google Scholar
Reger AS, Wu R, Dunaway-Mariano D, Gulick AM: Structural characterization of a 140 degrees domain movement in the two-step reaction catalyzed by 4-chlorobenzoate:CoA ligase. Biochemistry 2008, 47(31):8016–8025. 10.1021/bi800696y
Article
CAS
PubMed
PubMed Central
Google Scholar
Nakatsu T, Ichiyama S, Hiratake J, Saldanha A, Kobashi N, Sakata K, Kato H: Structural basis for the spectral difference in luciferase bioluminescence. Nature 2006, 440(7082):372–376. 10.1038/nature04542
Article
CAS
PubMed
Google Scholar
Tanovic A, Samel SA, Essen LO, Marahiel MA: Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 2008, 321(5889):659–663. 10.1126/science.1159850
Article
CAS
PubMed
Google Scholar
Du L, He Y, Luo Y: Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus. Biochemistry 2008, 47(44):11473–11480. 10.1021/bi801363b
Article
CAS
PubMed
Google Scholar
Bains J, Boulanger MJ: Biochemical and structural characterization of the paralogous benzoate CoA ligases from Burkholderia xenovorans LB400: defining the entry point into the novel benzoate oxidation (box) pathway. J Mol Biol 2007, 373(4):965–977. 10.1016/j.jmb.2007.08.008
Article
CAS
PubMed
Google Scholar
Challis GL, Ravel J, Townsend CA: Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 2000, 7(3):211–224. 10.1016/S1074-5521(00)00091-0
Article
CAS
PubMed
Google Scholar
Stachelhaus T, Mootz HD, Marahiel MA: The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 1999, 6(8):493–505. 10.1016/S1074-5521(99)80082-9
Article
CAS
PubMed
Google Scholar
von Dohren H, Dieckmann R, Pavela-Vrancic M: The nonribosomal code. Chem Biol 1999, 6(10):R273–279. 10.1016/S1074-5521(00)80014-9
Article
CAS
PubMed
Google Scholar
Ansari MZ, Yadav G, Gokhale RS, Mohanty D: NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 2004, (32 Web Server):W405–413. 10.1093/nar/gkh359
Stuible H, Buttner D, Ehlting J, Hahlbrock K, Kombrink E: Mutational analysis of 4-coumarate:CoA ligase identifies functionally important amino acids and verifies its close relationship to other adenylate-forming enzymes. FEBS Lett 2000, 467(1):117–122. 10.1016/S0014-5793(00)01133-9
Article
CAS
PubMed
Google Scholar
Ehlting J, Shin JJ, Douglas CJ: Identification of 4-coumarate:coenzyme A ligase (4CL) substrate recognition domains. Plant J 2001, 27(5):455–465. 10.1046/j.1365-313X.2001.01122.x
Article
CAS
PubMed
Google Scholar
Schneider K, Hovel K, Witzel K, Hamberger B, Schomburg D, Kombrink E, Stuible HP: The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc Natl Acad Sci USA 2003, 100(14):8601–8606. 10.1073/pnas.1430550100
Article
CAS
PubMed
PubMed Central
Google Scholar
Lindermayr C, Fliegmann J, Ebel J: Deletion of a single amino acid residue from different 4-coumarate:CoA ligases from soybean results in the generation of new substrate specificities. J Biol Chem 2003, 278(5):2781–2786. 10.1074/jbc.M202632200
Article
CAS
PubMed
Google Scholar
Branchini BR, Magyar RA, Murtiashaw MH, Anderson SM, Zimmer M: Site-directed mutagenesis of histidine 245 in firefly luciferase: a proposed model of the active site. Biochemistry 1998, 37(44):15311–15319. 10.1021/bi981150d
Article
CAS
PubMed
Google Scholar
Branchini BR, Southworth TL, Murtiashaw MH, Boije H, Fleet SE: A mutagenesis study of the putative luciferin binding site residues of firefly luciferase. Biochemistry 2003, 42(35):10429–10436. 10.1021/bi030099x
Article
CAS
PubMed
Google Scholar
Sandalova TP, Ugarova NN: Model of the active site of firefly luciferase. Biochemistry (Mosc) 1999, 64(8):962–967.
CAS
Google Scholar
Oba Y, Ojika M, Inouye S: Characterization of CG6178 gene product with high sequence similarity to firefly luciferase in Drosophila melanogaster. Gene 2004, 329: 137–145. 10.1016/j.gene.2003.12.026
Article
CAS
PubMed
Google Scholar
Oba Y, Sato M, Ojika M, Inouye S: Enzymatic and genetic characterization of firefly luciferase and Drosophila CG6178 as a fatty acyl-CoA synthetase. Biosci Biotechnol Biochem 2005, 69(4):819–828. 10.1271/bbb.69.819
Article
CAS
PubMed
Google Scholar
Schneider K, Kienow L, Schmelzer E, Colby T, Bartsch M, Miersch O, Wasternack C, Kombrink E, Stuible HP: A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid. J Biol Chem 2005, 280(14):13962–13972. 10.1074/jbc.M413578200
Article
CAS
PubMed
Google Scholar
de Azevedo Souza C, Kim SS, Koch S, Kienow L, Schneider K, McKim SM, Haughn GW, Kombrink E, Douglas CJ: A novel fatty Acyl-CoA Synthetase is required for pollen development and sporopollenin biosynthesis in Arabidopsis. Plant Cell 2009, 21(2):507–525. 10.1105/tpc.108.062513
Article
PubMed
PubMed Central
Google Scholar
Souza Cde A, Barbazuk B, Ralph SG, Bohlmann J, Hamberger B, Douglas CJ: Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella. New Phytol 2008, 179(4):987–1003.
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389
Article
CAS
PubMed
PubMed Central
Google Scholar
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank: update. Nucleic Acids Res 2004, (32 Database):D23–26. 10.1093/nar/gkh045
Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14(9):755–763. 10.1093/bioinformatics/14.9.755
Article
CAS
PubMed
Google Scholar
Lichtarge O, Bourne HR, Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257(2):342–358. 10.1006/jmbi.1996.0167
Article
CAS
PubMed
Google Scholar
Oba Y, Ojika M, Inouye S: Firefly luciferase is a bifunctional enzyme: ATP-dependent monooxygenase and a long chain fatty acyl-CoA synthetase. FEBS Lett 2003, 540(1–3):251–254. 10.1016/S0014-5793(03)00272-2
Article
CAS
PubMed
Google Scholar
Ingram-Smith C, Woods BI, Smith KS: Characterization of the acyl substrate binding pocket of acetyl-CoA synthetase. Biochemistry 2006, 45(38):11482–11490. 10.1021/bi061023e
Article
CAS
PubMed
Google Scholar
Branchini BR, Murtiashaw MH, Magyar RA, Anderson SM: The role of lysine 529, a conserved residue of the acyl-adenylate-forming enzyme superfamily, in firefly luciferase. Biochemistry 2000, 39(18):5433–5440. 10.1021/bi9928804
Article
CAS
PubMed
Google Scholar
Branchini BR, Magyar RA, Murtiashaw MH, Anderson SM, Helgerson LC, Zimmer M: Site-directed mutagenesis of firefly luciferase active site amino acids: a proposed model for bioluminescence color. Biochemistry 1999, 38(40):13223–13230. 10.1021/bi991181o
Article
CAS
PubMed
Google Scholar
An JH, Lee GY, Jung JW, Lee W, Kim YS: Identification of residues essential for a two-step reaction by malonyl-CoA synthetase from Rhizobium trifolii. Biochem J 1999, 344(Pt 1):159–166. 10.1042/0264-6021:3440159
Article
CAS
PubMed
PubMed Central
Google Scholar
Jung JW, An JH, Na KB, Kim YS, Lee W: The active site and substrates binding mode of malonyl-CoA synthetase determined by transferred nuclear Overhauser effect spectroscopy, site-directed mutagenesis, and comparative modeling studies. Protein Sci 2000, 9(7):1294–1303. 10.1110/ps.9.7.1294
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones DT: GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999, 287(4):797–815. 10.1006/jmbi.1999.2583
Article
CAS
PubMed
Google Scholar
Sali A, Blundell TL: Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993, 234(3):779–815. 10.1006/jmbi.1993.1626
Article
CAS
PubMed
Google Scholar
Choudhury D: Functional Implications of Macromolecular Recognition: Assembly of Adhesive Pili and enzyme substrate interactions. Ph.D. Thesis. Uppsala: Swedish University of Agricultural Sciences, Uppsala; 2001.
Google Scholar
Ehlting J, Buttner D, Wang Q, Douglas CJ, Somssich IE, Kombrink E: Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms. Plant J 1999, 19(1):9–20. 10.1046/j.1365-313X.1999.00491.x
Article
CAS
PubMed
Google Scholar
Branchini BR, Magyar RA, Murtiashaw MH, Portier NC: The role of active site residue arginine 218 in firefly luciferase bioluminescence. Biochemistry 2001, 40(8):2410–2418. 10.1021/bi002246m
Article
CAS
PubMed
Google Scholar
Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16(6):276–277. 10.1016/S0168-9525(00)02024-2
Article
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403–410.
Article
CAS
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673–4680. 10.1093/nar/22.22.4673
Article
CAS
PubMed
PubMed Central
Google Scholar
Garrett M, Morris DSG, Halliday RobertS, Huey Ruth, Hart WilliamE, Belew RichardK, Olson ArthurJ: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry 1998, 19(14):1639–1662. Publisher Full Text 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
Article
Google Scholar